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@ARTICLE{Aqvist:Hansson:1996,
  author = {{\AA}qvist, J. and Hansson, T.},
  title = {On the validity of electrostatic linear response in polar solvents},
  journal = {J. Phys. Chem.},
  year = {1996},
  volume = {100},
  pages = {9512--9521},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Aqvist:Medina:Samuelsson:1994,
  author = {{\AA}qvist, J. and Medina, C. and Samuelsson, J.-E.},
  title = {A new method for predicting binding affinity in computer-aided drug
	design},
  journal = {Prot. Engineering},
  year = {1994},
  volume = {7},
  pages = {385--391},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Abel2010,
  author = {Robert Abel and Lingle Wang and Richard A Friesner and B. J. Berne},
  title = {A displaced-solvent functional analysis of model hydrophobic enclosures.},
  journal = {J Chem Theory Comput},
  year = {2010},
  volume = {6},
  pages = {2924--2934},
  number = {9},
  month = {Aug},
  abstract = {Calculation of protein-ligand binding affinities continues to be a
	hotbed of research. Although many techniques for computing protein-ligand
	binding affinities have been introduced--ranging from computationally
	very expensive approaches, such as free energy perturbation (FEP)
	theory; to more approximate techniques, such as empirically derived
	scoring functions, which, although computationally efficient, lack
	a clear theoretical basis--there remains pressing need for more robust
	approaches. A recently introduced technique, the displaced-solvent
	functional (DSF) method, was developed to bridge the gap between
	the high accuracy of FEP and the computational efficiency of empirically
	derived scoring functions. In order to develop a set of reference
	data to test the DSF theory for calculating absolute protein-ligand
	binding affinities, we have pursued FEP theory calculations of the
	binding free energies of a methane ligand with 13 different model
	hydrophobic enclosures of varying hydrophobicity. The binding free
	energies of the methane ligand with the various hydrophobic enclosures
	were then recomputed by DSF theory and compared with the FEP reference
	data. We find that the DSF theory, which relies on no empirically
	tuned parameters, shows excellent quantitative agreement with the
	FEP. We also explored the ability of buried solvent accessible surface
	area and buried molecular surface area models to describe the relevant
	physics, and find the buried molecular surface area model to offer
	superior performance over this dataset.},
  doi = {10.1021/ct100215c},
  institution = {Schrodinger, L.L.C., New York, New York, USA.},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {21135914},
  timestamp = {2012.06.21},
  url = {http://dx.doi.org/10.1021/ct100215c}
}

@ARTICLE{Abel2008,
  author = {Robert Abel and Tom Young and Ramy Farid and Bruce J Berne and Richard
	A Friesner},
  title = {Role of the active-site solvent in the thermodynamics of factor Xa
	ligand binding.},
  journal = {J. Am. Chem. Soc.},
  year = {2008},
  volume = {130},
  pages = {2817--2831},
  number = {9},
  month = {Mar},
  abstract = {Understanding the underlying physics of the binding of small-molecule
	ligands to protein active sites is a key objective of computational
	chemistry and biology. It is widely believed that displacement of
	water molecules from the active site by the ligand is a principal
	(if not the dominant) source of binding free energy. Although continuum
	theories of hydration are routinely used to describe the contributions
	of the solvent to the binding affinity of the complex, it is still
	an unsettled question as to whether or not these continuum solvation
	theories describe the underlying molecular physics with sufficient
	accuracy to reliably rank the binding affinities of a set of ligands
	for a given protein. Here we develop a novel, computationally efficient
	descriptor of the contribution of the solvent to the binding free
	energy of a small molecule and its associated receptor that captures
	the effects of the ligand displacing the solvent from the protein
	active site with atomic detail. This descriptor quantitatively predicts
	(R(2) = 0.81) the binding free energy differences between congeneric
	ligand pairs for the test system factor Xa, elucidates physical properties
	of the active-site solvent that appear to be missing in most continuum
	theories of hydration, and identifies several features of the hydration
	of the factor Xa active site relevant to the structure-activity relationship
	of its inhibitors.},
  doi = {10.1021/ja0771033},
  institution = {Department of Chemistry, Columbia University, 3000 Broadway, New
	York, New York 10027, USA.},
  keywords = {Binding Sites; Computer Simulation; Crystallography, X-Ray; Factor
	Xa; Ligands; Models, Biological; Models, Molecular; Solvents; Thermodynamics;
	Water},
  owner = {emilio},
  pmid = {18266362},
  timestamp = {2010.05.20},
  url = {http://dx.doi.org/10.1021/ja0771033}
}

@ARTICLE{Affentranger:Tavernelli:Iorio:2006,
  author = {Affentranger, R. and Tavernelli, I. and Iorio, {E. E. D.}},
  title = {A Novel Hamiltonian Replica Exchange MD Protocol to Enhance Protein
	Conformational Space Sampling},
  journal = {J. Chem. Theory Comput.},
  year = {2006},
  volume = {2},
  pages = {217-228},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Ahmed2001,
  author = {S. Ahmed and N. Majeux and A. Caflisch},
  title = {Hydrophobicity and functionality maps of farnesyltransferase.},
  journal = {J Mol Graph Model},
  year = {2001},
  volume = {19},
  pages = {307--17, 380-7},
  number = {3-4},
  abstract = {Farnesyltransferase (FTase) catalyzes the attachment of a 15-carbon
	isoprenoid moiety, farnesyl, through a thioether linkage to a cysteine
	near the C-terminus of oncogenic Ras proteins. These transform animal
	cells to a malignant phenotype when farnesylated. Hence, FTase is
	an interesting target for the development of antitumor agents. In
	this work we first investigate the active site of FTase by mapping
	its hydrophobic patches. Then the program SEED is used to dock functional
	groups into the active site by an exhaustive search and efficient
	evaluation of the binding energy with solvation. The electrostatic
	energy is SEED is based on the continuum dielectric approximation
	and consists of screened intermolecular energy and protein and fragment
	desolvation terms. The results are found to be consistent with the
	sequence variability of the tetrapeptide substrate. The distribution
	of functional groups (functionality maps) on the substrate binding
	site allows for identification of modifications of the tetrapeptide
	sequence that are consistent with potent peptidic inhibitors. Furthermore,
	the best minima of benzene match corresponding moieties of an inhibitor
	in clinical trials. The functionality maps are also used to design
	a library of disubstituted indoles that might prevent the binding
	of the protein substrates.},
  institution = {Department of Biochemistry, University of Zürich, Zürich, Switzerland.},
  keywords = {Alkyl and Aryl Transferases; Animals; Catalytic Domain; Combinatorial
	Chemistry Techniques; Computer Simulation; Enzyme Inhibitors; Farnesyltranstransferase;
	Hydrophobicity; Indoles; Ligands; Models, Molecular; Protein Conformation;
	Software; Substrate Specificity; Thermodynamics},
  owner = {emilio},
  pii = {S1093-3263(00)00075-9},
  pmid = {11449569},
  timestamp = {2010.04.22}
}

@BOOK{Allen:Tildesley,
  title = {Computer Simulation of Liquids},
  publisher = {Oxford University Press},
  year = {1993},
  author = {Allen, M. P. and Tildesley, D. J.},
  address = {New York},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Almlof:Aqvist:Smalas:Brandsal:2006,
  author = {Alml\"{o}f, M. and {\AA}qvist, J. and Sm{\aa}las, {A. O.} and Brandsdal,
	{B. O.}},
  title = {Probing the effect of point mutations at protein-protein interfaces
	with free energy calculations},
  journal = {Biophys. J.},
  year = {2006},
  volume = {90},
  pages = {433-442},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Almlof:Brandsal:Aqvist:2004,
  author = {Alml\"{o}f, M. and Brandsdal, {B. O.} and {\AA}qvist, J.},
  title = {Binding Affinity Prediction with Different Force Fields: Examination
	of the Linear Interaction Energy Model},
  journal = {J. Comput. Chem.},
  year = {2004},
  volume = {25},
  pages = {1242--1254},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Alper:Levy:93,
  author = {Alper, H. and Levy, R. M.},
  journal = {J. Chem. Phys.},
  year = {1993},
  volume = {99},
  pages = {9847-9852},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Alper:Levy:90,
  author = {Alper, H. and Levy, R. M.},
  title = {Field Strength Dependence of Dielectric Saturation in Liquid Water},
  journal = {J. Phys. Chem.},
  year = {1990},
  volume = {94},
  pages = {8401-8403},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Alper:Levy:89,
  author = {Alper, H. E. and Levy, R. M.},
  journal = {J. Chem. Phys.},
  year = {1989},
  volume = {91},
  pages = {1242-1251},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Amaro2008a,
  author = {Rommie E Amaro and Riccardo Baron and J. Andrew McCammon},
  title = {An improved relaxed complex scheme for receptor flexibility in computer-aided
	drug design.},
  journal = {J Comput Aided Mol Des},
  year = {2008},
  volume = {22},
  pages = {693--705},
  number = {9},
  month = {Sep},
  abstract = {The interactions among associating (macro)molecules are dynamic, which
	adds to the complexity of molecular recognition. While ligand flexibility
	is well accounted for in computational drug design, the effective
	inclusion of receptor flexibility remains an important challenge.
	The relaxed complex scheme (RCS) is a promising computational methodology
	that combines the advantages of docking algorithms with dynamic structural
	information provided by molecular dynamics (MD) simulations, therefore
	explicitly accounting for the flexibility of both the receptor and
	the docked ligands. Here, we briefly review the RCS and discuss new
	extensions and improvements of this methodology in the context of
	ligand binding to two example targets: kinetoplastid RNA editing
	ligase 1 and the W191G cavity mutant of cytochrome c peroxidase.
	The RCS improvements include its extension to virtual screening,
	more rigorous characterization of local and global binding effects,
	and methods to improve its computational efficiency by reducing the
	receptor ensemble to a representative set of configurations. The
	choice of receptor ensemble, its influence on the predictive power
	of RCS, and the current limitations for an accurate treatment of
	the solvent contributions are also briefly discussed. Finally, we
	outline potential methodological improvements that we anticipate
	will assist future development.},
  comment = {Receptr reorganization},
  doi = {10.1007/s10822-007-9159-2},
  institution = {Department of Chemistry and Biochemistry, University of California
	at San Diego, La Jolla, CA, 92093-0365, USA. ramaro@mccammon.ucsd.edu},
  keywords = {Carbon-Oxygen Ligases; Computer Simulation; Computer-Aided Design;
	Cytochrome-c Peroxidase; Drug Design; Enzyme Inhibitors; Ligands;
	Models, Molecular; Pharmaceutical Preparations; Phylogeny; Pliability;
	Protein Conformation; RNA Editing},
  owner = {emilio},
  pmid = {18196463},
  timestamp = {2010.09.09},
  url = {http://dx.doi.org/10.1007/s10822-007-9159-2}
}

@ARTICLE{Amaro2009,
  author = {Rommie E Amaro and Xiaolin Cheng and Ivaylo Ivanov and Dong Xu and
	J. Andrew McCammon},
  title = {Characterizing loop dynamics and ligand recognition in human- and
	avian-type influenza neuraminidases via generalized born molecular
	dynamics and end-point free energy calculations.},
  journal = {J Am Chem Soc},
  year = {2009},
  volume = {131},
  pages = {4702--4709},
  number = {13},
  month = {Apr},
  abstract = {The comparative dynamics and inhibitor binding free energies of group-1
	and group-2 pathogenic influenza A subtype neuraminidase (NA) enzymes
	are of fundamental biological interest and relevant to structure-based
	drug design studies for antiviral compounds. In this work, we present
	seven generalized Born molecular dynamics simulations of avian (N1)-
	and human (N9)-type NAs in order to probe the comparative flexibility
	of the two subtypes, both with and without the inhibitor oseltamivir
	bound. The enhanced sampling obtained through the implicit solvent
	treatment suggests several provocative insights into the dynamics
	of the two subtypes, including that the group-2 enzymes may exhibit
	similar motion in the 430-binding site regions but different 150-loop
	motion. End-point free energy calculations elucidate the contributions
	to inhibitor binding free energies and suggest that entropic considerations
	cannot be neglected when comparing across the subtypes. We anticipate
	the findings presented here will have broad implications for the
	development of novel antiviral compounds against both seasonal and
	pandemic influenza strains.},
  comment = {Receptor reorganization},
  doi = {10.1021/ja8085643},
  institution = { Biochemistry, Center for Theoretical Biological Physics, University
	of California, San Diego, La Jolla, California 92093-0365, USA. ramaro@mccammon.ucsd.edu},
  keywords = {Catalytic Domain; Computer Simulation; Humans; Influenza A Virus,
	H5N1 Subtype; Ligands; Models, Molecular; Neuraminidase; Protein
	Binding; Protein Conformation; Protein Multimerization; Thermodynamics;
	Viral Proteins},
  owner = {emilio},
  pmid = {19296611},
  timestamp = {2010.09.09},
  url = {http://dx.doi.org/10.1021/ja8085643}
}

@ARTICLE{Amaro2007a,
  author = {Rommie E Amaro and David D L Minh and Lily S Cheng and William M
	Lindstrom and Arthur J Olson and Jung-Hsin Lin and Wilfred W Li and
	J. Andrew McCammon},
  title = {Remarkable loop flexibility in avian influenza N1 and its implications
	for antiviral drug design.},
  journal = {J Am Chem Soc},
  year = {2007},
  volume = {129},
  pages = {7764--7765},
  number = {25},
  month = {Jun},
  comment = {Receptor reorganization},
  doi = {10.1021/ja0723535},
  institution = { Biochemistry, NSF Center for Theoretical Biological Physics, University
	of California San Diego, La Jolla, California 92093-0365, USA. ramaro@mccammon.ucsd.edu},
  keywords = {Amino Acid Sequence; Antiviral Agents; Influenza A Virus, H5N1 Subtype;
	Models, Molecular; Neuraminidase; Protein Conformation},
  owner = {emilio},
  pmid = {17539643},
  timestamp = {2010.09.09},
  url = {http://dx.doi.org/10.1021/ja0723535}
}

@ARTICLE{Amaro2008,
  author = {Rommie E Amaro and Achim Schnaufer and Heidrun Interthal and Wim
	Hol and Kenneth D Stuart and J. Andrew McCammon},
  title = {Discovery of drug-like inhibitors of an essential RNA-editing ligase
	in Trypanosoma brucei.},
  journal = {Proc Natl Acad Sci U S A},
  year = {2008},
  volume = {105},
  pages = {17278--17283},
  number = {45},
  month = {Nov},
  abstract = {Trypanosomatid RNA editing is a unique process and essential for these
	organisms. It therefore represents a drug target for a group of protozoa
	that includes the causative agents for African sleeping sickness
	and other devastating tropical and subtropical diseases. Here, we
	present drug-like inhibitors of a key enzyme in the editing machinery,
	RNA-editing ligase 1 (REL1). These inhibitors were identified through
	a strategy employing molecular dynamics to account for protein flexibility.
	A virtual screen of the REL1 crystal structure against the National
	Cancer Institute Diversity Set was performed by using AutoDock4.
	The top 30 compounds, predicted to interact with REL1's ATP-binding
	pocket, were further refined by using the relaxed complex scheme
	(RCS), which redocks the compounds to receptor structures extracted
	from an explicitly solvated molecular dynamics trajectory. The resulting
	reordering of the ligands and filtering based on drug-like properties
	resulted in an initial recommended set of 8 ligands, 2 of which exhibited
	micromolar activity against REL1. A subsequent hierarchical similarity
	search with the most active compound over the full National Cancer
	Institute database and RCS rescoring resulted in an additional set
	of 6 ligands, 2 of which were confirmed as REL1 inhibitors with IC(50)
	values of approximately 1 microM. Tests of the 3 most promising compounds
	against the most closely related bacteriophage T4 RNA ligase 2, as
	well as against human DNA ligase IIIbeta, indicated a considerable
	degree of selectivity for RNA ligases. These compounds are promising
	scaffolds for future drug design and discovery efforts against these
	important pathogens.},
  comment = {Receptor reorganization},
  doi = {10.1073/pnas.0805820105},
  institution = {Department of Chemistry and Biochemistry and Center for Theoretical
	Biological Physics, University of California at San Diego, La Jolla,
	CA 92093-0365, USA. ramaro@mccammon.ucsd.edu},
  keywords = {Animals; Carbon-Oxygen Ligases; Computational Biology; DNA Ligases;
	Drug Discovery; Enzyme Inhibitors; Humans; Inhibitory Concentration
	50; Ligands; Mitochondrial Proteins; Molecular Structure; RNA Editing;
	RNA Ligase (ATP); Trypanosoma brucei brucei; Viral Proteins},
  owner = {emilio},
  pii = {0805820105},
  pmid = {18981420},
  timestamp = {2010.09.09},
  url = {http://dx.doi.org/10.1073/pnas.0805820105}
}

@ARTICLE{Amaro2007,
  author = {Rommie E Amaro and Robert V Swift and J. Andrew McCammon},
  title = {Functional and structural insights revealed by molecular dynamics
	simulations of an essential RNA editing ligase in Trypanosoma brucei.},
  journal = {PLoS Negl Trop Dis},
  year = {2007},
  volume = {1},
  pages = {e68},
  number = {2},
  abstract = {RNA editing ligase 1 (TbREL1) is required for the survival of both
	the insect and bloodstream forms of Trypanosoma brucei, the parasite
	responsible for the devastating tropical disease African sleeping
	sickness. The type of RNA editing that TbREL1 is involved in is unique
	to the trypanosomes, and no close human homolog is known to exist.
	In addition, the high-resolution crystal structure revealed several
	unique features of the active site, making this enzyme a promising
	target for structure-based drug design. In this work, two 20 ns atomistic
	molecular dynamics (MD) simulations are employed to investigate the
	dynamics of TbREL1, both with and without the ATP substrate present.
	The flexibility of the active site, dynamics of conserved residues
	and crystallized water molecules, and the interactions between TbREL1
	and the ATP substrate are investigated and discussed in the context
	of TbREL1's function. Differences in local and global motion upon
	ATP binding suggest that two peripheral loops, unique to the trypanosomes,
	may be involved in interdomain signaling events. Notably, a significant
	structural rearrangement of the enzyme's active site occurs during
	the apo simulations, opening an additional cavity adjacent to the
	ATP binding site that could be exploited in the development of effective
	inhibitors directed against this protozoan parasite. Finally, ensemble
	averaged electrostatics calculations over the MD simulations reveal
	a novel putative RNA binding site, a discovery that has previously
	eluded scientists. Ultimately, we use the insights gained through
	the MD simulations to make several predictions and recommendations,
	which we anticipate will help direct future experimental studies
	and structure-based drug discovery efforts against this vital enzyme.},
  comment = {Receptor reorganization},
  doi = {10.1371/journal.pntd.0000068},
  institution = {Department of Chemistry and Biochemistry, University of California
	San Diego, La Jolla, California, USA. ramaro@mccammon.ucsd.edu},
  keywords = {Amino Acid Sequence; Animals; Binding Sites; Catalytic Domain; Molecular
	Dynamics Simulation; Molecular Sequence Data; Phosphorus-Oxygen Lyases;
	Protein Structure, Secondary; Protein Structure, Tertiary; Protozoan
	Proteins; Sequence Homology, Amino Acid; Water},
  owner = {emilio},
  pmid = {18060084},
  timestamp = {2010.09.09},
  url = {http://dx.doi.org/10.1371/journal.pntd.0000068}
}

@ARTICLE{Amidon:Yalkowsky:Anil:Valvani:75,
  author = {G. L. Amidon and S. H. Yalkowsky and S. T. Anil and S. C. Valvani},
  journal = {J. Phys. Chme.},
  year = {1975},
  volume = {72},
  pages = {2239},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Andersen:83,
  author = {Andersen, H. C.},
  journal = {J. Comput. Phys.},
  year = {1983},
  volume = {52},
  pages = {24},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Andrea:Swope:Andersen:83,
  author = {Andrea, T. and Swope, A. and Andersen, H. C.},
  journal = {J. Chem. Phys.},
  year = {1983},
  volume = {79},
  pages = {4576-4584},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Andrec2005,
  author = {Michael Andrec and Anthony K Felts and Emilio Gallicchio and Ronald
	M Levy},
  title = {Protein folding pathways from replica exchange simulations and a
	kinetic network model.},
  journal = {Proc Natl Acad Sci U S A},
  year = {2005},
  volume = {102},
  pages = {6801--6806},
  number = {19},
  month = {May},
  abstract = {We present an approach to the study of protein folding that uses the
	combined power of replica exchange simulations and a network model
	for the kinetics. We carry out replica exchange simulations to generate
	a large ( approximately 10(6)) set of states with an all-atom effective
	potential function and construct a kinetic model for folding, using
	an ansatz that allows kinetic transitions between states based on
	structural similarity. We use this network to perform random walks
	in the state space and examine the overall network structure. Results
	are presented for the C-terminal peptide from the B1 domain of protein
	G. The kinetics is two-state after small temperature perturbations.
	However, the coil-to-hairpin folding is dominated by pathways that
	visit metastable helical conformations. We propose possible mechanisms
	for the alpha-helix/beta-hairpin interconversion.},
  doi = {10.1073/pnas.0408970102},
  institution = {Department of Chemistry and Chemical Biology and BIOMAPS Institute
	for Quantitative Biology, Rutgers, The State University of New Jersey,
	Piscataway, NJ 08854, USA.},
  keywords = {Biophysics; Computer Simulation; Hydrogen Bonding; Kinetics; Models,
	Chemical; Models, Molecular; Molecular Structure; Monte Carlo Method;
	Peptides; Protein Conformation; Protein Folding; Protein Structure,
	Secondary; Protein Structure, Tertiary; Temperature; Thermodynamics;
	Time Factors},
  owner = {emilio},
  pii = {0408970102},
  pmid = {15800044},
  timestamp = {2010.07.14},
  url = {http://dx.doi.org/10.1073/pnas.0408970102}
}

@ARTICLE{Andrec:Felts:Gallicchio:Levy:2005,
  author = {Andrec, M. and Felts, A. K. and Gallicchio, E. and Levy, R. M.},
  title = {Protein Folding Pathways from Replica Exchange Simulations and a
	Kinetic Network Model},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {2005},
  volume = {102},
  pages = {6801-6806},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Andries2004,
  author = {Koen Andries and Hilde Azijn and Theo Thielemans and Donald Ludovici
	and Michael Kukla and Jan Heeres and Paul Janssen and Bart De Corte
	and Johan Vingerhoets and Rudi Pauwels and Marie-Pierre de Béthune},
  title = {TMC125, a novel next-generation nonnucleoside reverse transcriptase
	inhibitor active against nonnucleoside reverse transcriptase inhibitor-resistant
	human immunodeficiency virus type 1.},
  journal = {Antimicrob Agents Chemother},
  year = {2004},
  volume = {48},
  pages = {4680--4686},
  number = {12},
  month = {Dec},
  abstract = {Nonnucleoside reverse transcriptase inhibitors (NNRTIs) are potent
	inhibitors of human immunodeficiency virus type 1 (HIV-1); however,
	currently marketed NNRTIs rapidly select resistant virus, and cross-resistance
	within the class is extensive. A parallel screening strategy was
	applied to test candidates from a series of diarylpyrimidines against
	wild-type and resistant HIV strains carrying clinically relevant
	mutations. Serum protein binding and metabolic stability were addressed
	early in the selection process. The emerging clinical candidate,
	TMC125, was highly active against wild-type HIV-1 (50\% effective
	concentration [EC50] = 1.4 to 4.8 nM) and showed some activity against
	HIV-2 (EC50 = 3.5 microM). TMC125 also inhibited a series of HIV-1
	group M subtypes and circulating recombinant forms and a group O
	virus. Incubation of TMC125 with human liver microsomal fractions
	suggested good metabolic stability (15\% decrease in drug concentration
	and 7\% decrease in antiviral activity after 120 min). Although TMC125
	is highly protein bound, its antiviral effect was not reduced by
	the presence of 45 mg of human serum albumin/ml, 1 mg of alpha1-acid
	glycoprotein/ml, or 50\% human serum. In an initial screen for activity
	against a panel of 25 viruses carrying single and double reverse
	transcriptase amino acid substitutions associated with NNRTI resistance,
	the EC50 of TMC125 was <5 nM for 19 viruses, including the double
	mutants K101E+K103N and K103N+Y181C. TMC125 also retained activity
	(EC50 < 100 nM) against 97\% of 1,081 recent clinically derived recombinant
	viruses resistant to at least one of the currently marketed NNRTIs.
	TMC125 is a potent next generation NNRTI, with the potential for
	use in individuals infected with NNRTI-resistant virus.},
  doi = {10.1128/AAC.48.12.4680-4686.2004},
  institution = { Development, Beerse, Belgium.},
  keywords = {Cell Line; Drug Design; Drug Evaluation, Preclinical; Drug Resistance,
	Viral; Genotype; HIV-1, drug effects/genetics; Humans; Microbial
	Sensitivity Tests; Microsomes, Liver, metabolism; Mutagenesis, Site-Directed;
	Pyridazines, pharmacokinetics/pharmacology; Reverse Transcriptase
	Inhibitors, pharmacokinetics/pharmacology},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pii = {48/12/4680},
  pmid = {15561844},
  timestamp = {2012.02.28},
  url = {http://dx.doi.org/10.1128/AAC.48.12.4680-4686.2004}
}

@ARTICLE{Antosiewicz:96,
  author = {Antosiewicz, J. and McCammon, J. A. and Gilson, M. K.},
  journal = {Biochemistry},
  year = {1996},
  volume = {35},
  pages = {7819-7833},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Apostoloakis:Ferrara:Calfish:99,
  author = {Apostolakis, J. and Ferrara, P. and Calfish, A.},
  title = {Calculation of conformational transitions and barriers in solvated
	systems: application to the alanine dipeptide in water},
  journal = {J. Chem. Phys.},
  year = {1999},
  volume = {110},
  pages = {2099-2108},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Aqvist:94,
  author = {Aqvist, J. and Medina, C. and Samuelsson, J. E.},
  journal = {Protein Eng.},
  year = {1994},
  volume = {7},
  pages = {385-391},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Ashbaugh:Kaler:Paulaitis:99,
  author = {Ashbaugh, H. S. and Kaler, E. W. and Paulaitis, M. E.},
  title = {A Universal Surface Area Correlation for Molecular Hydrophobic Phenomena},
  journal = {J. Am. Chem. Soc.},
  year = {1999},
  volume = {121},
  pages = {9243-9244},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Ashbaugh:Kaler:Paulaitis:98,
  author = {Ashbaugh, H. S. and Kaler, E. W. and Paulaitis, M. E.},
  title = {Hydration and Conformational Equilibria of Simple Hydrophobic and
	Amphiphilic Solutes},
  journal = {Biophys. J.},
  year = {1998},
  volume = {75},
  pages = {755-768},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Ashbaugh:Paulaitis:96,
  author = {Ashbaugh, H. S. and Paulaitis, M. E.},
  title = {Entropy of Hydrophobic Hydration: Extension to Hydrophobic Chains},
  journal = {J. Phys. Chem},
  year = {1996},
  volume = {100},
  pages = {1900-1913},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Bader:Chandler:92,
  author = {Bader, J. S. and Chandler, D.},
  journal = {J. Phys. Chem.},
  year = {1992},
  volume = {96},
  pages = {6423-6429},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Baker:2005,
  author = {Baker, {N. A.}},
  title = {Improving implicit solvent simulations: a Poisson-centric view.},
  journal = {Curr. Opin. Struct. Biol.},
  year = {2005},
  volume = {15},
  pages = {137-143},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Baldwin:86,
  author = {Baldwin, R. L.},
  title = {Temperature Dependence of the Hydrophobic Interaction in Protein
	Folding},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {1986},
  volume = {83},
  pages = {8069-8072},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Banks:Gallicchio:Levy:2005,
  author = {Banks, {J. L.} and Beard, {J. S.} and Cao, Y. and Cho, {A. E.} and
	Damm, W. and Farid, R. and Felts, {A. K.} and Halgren, {T. A.} and
	Mainz, {D. T.} and Maple, {J. R.} and Murphy, R. and Philipp, {D.
	M.} and Repasky, {M. P.} and Zhang, {L. Y.} and Berne, {B. J.} and
	Friesner, {R. A.} and Gallicchio, E. and Levy, {R. M.} },
  title = {Integrated Modeling Program, Applied Chemical Theory {(IMPACT)}},
  journal = {J. Comp. Chem.},
  year = {2005},
  volume = {26},
  pages = {1752--1780},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Barbieri2007,
  author = {Barbieri, Christopher M. and Kaul, Malvika and Pilch, Daniel S.},
  title = {Use of 2-aminopurine as a fluorescent tool for characterizing antibiotic
	recognition of the bacterial rRNA A-site},
  journal = {Tetrahedron},
  year = {2007},
  volume = {63},
  pages = {3567--3574},
  number = {17},
  month = apr,
  abstract = {Spectroscopic and calorimetric techniques have been employed to characterize
	the impact on an Escherichia coli rRNA A-site model oligonucleotide
	of incorporating the fluorescent base analog 2-aminopurine into the
	1492- or the 1493-position, as well as the energetics and dynamics
	associated with recognition of this A-site model oligomer by aminoglycoside
	antibiotics. The results of these studies indicate that incorporation
	of 2AP into either the 1492- or the 1493-position does not perturb
	the structure or stability of the host RNA or its aminoglycoside
	binding affinity. In addition, the results also highlight drug-induced
	reduction in the mobilities of the bases at both the 1492- and 1493-positions
	as a potentially key determinant of bactericidal potency.},
  booktitle = {Fluorescent Nucleoside Analogs: Synthesis, Properties and Applications},
  issn = {0040-4020},
  owner = {emilio},
  timestamp = {2011.02.08},
  url = {http://www.sciencedirect.com/science/article/B6THR-4MYVG55-F/2/797dd1ca6464ac57ee1f2f9956f11119}
}

@ARTICLE{Barillari2007,
  author = {Barillari, Caterina and Taylor, Justine and Viner, Russell and Essex,
	Jonathan W.},
  title = {Classification of Water Molecules in Protein Binding Sites},
  journal = {J. Am. Chem. Soc.},
  year = {2007},
  volume = {129},
  pages = {2577--2587},
  number = {9},
  month = mar,
  abstract = {Water molecules play a crucial role in mediating the interaction between
	a ligand and a macromolecular receptor. An understanding of the nature
	and role of each water molecule in the active site of a protein could
	greatly increase the efficiency of rational drug design approaches: if
	the propensity of a water molecule for displacement can be determined,
	then synthetic effort may be most profitably applied to the design
	of specific ligands with the displacement of this water molecule
	in mind. In this paper, a thermodynamic analysis of water molecules
	in the binding sites of six proteins, each complexed with a number
	of inhibitors, is presented. Two classes of water molecules were
	identified:  those conserved and not displaced by any of the ligands,
	and those that are displaced by some ligands. The absolute binding
	free energies of 54 water molecules were calculated using the double
	decoupling method, with replica exchange thermodynamic integration
	in Monte Carlo simulations. It was found that conserved water molecules
	are on average more tightly bound than displaced water molecules.
	In addition, Bayesian statistics is used to calculate the probability
	that a particular water molecule may be displaced by an appropriately
	designed ligand, given the calculated binding free energy of the
	water molecule. This approach therefore allows the numerical assessment
	of whether or not a given water molecule should be targeted for displacement
	as part of a rational drug design strategy.},
  comment = {doi: 10.1021/ja066980q},
  issn = {0002-7863},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2010.09.17},
  url = {http://dx.doi.org/10.1021/ja066980q}
}

@ARTICLE{Barker:Watts:73,
  author = {Barker, J. A. and Watts, R. O.},
  journal = {Mol. Phys.},
  year = {1973},
  volume = {26},
  pages = {789-796},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Baron2008a,
  author = {Riccardo Baron and J. Andrew McCammon},
  title = {({T}hermo)dynamic role of receptor flexibility, entropy, and motional
	correlation in protein-ligand binding.},
  journal = {ChemPhysChem},
  year = {2008},
  volume = {9},
  pages = {983--988},
  number = {7},
  month = {May},
  abstract = {The binding of 2-amino-5-methylthiazole to the W191G cavity mutant
	of cytochrome c peroxidase is an ideal test case to investigate the
	entropic contribution to the binding free energy due to changes in
	receptor flexibility. The dynamic and thermodynamic role of receptor
	flexibility are studied by 50 ns-long explicit-solvent molecular
	dynamics simulations of three separate receptor ensembles: W191G
	binding a K(+) ion, W191G-2a5mt complex with a closed 190-195 gating
	loop, and apo with an open loop. We employ a method recently proposed
	to estimate accurate absolute single-molecule configurational entropies
	and their differences for systems undergoing conformational transitions.
	We find that receptor flexibility plays a generally underestimated
	role in protein-ligand binding (thermo)dynamics and that changes
	of receptor motional correlation determine such large entropy contributions.},
  doi = {10.1002/cphc.200700857},
  institution = { Biochemistry and Center for Theoretical and Biological Physics,
	University of California at San Diego, La Jolla, CA 92093-0365, USA.},
  keywords = {Computational Biology; Computer Simulation; Crystallography, X-Ray;
	Cytochrome-c Peroxidase; Entropy; Escherichia coli; Ligands; Models,
	Chemical; Models, Molecular; Protein Binding; Protein Conformation;
	Thermodynamics; Thiazoles},
  owner = {emilio},
  pmid = {18418822},
  timestamp = {2010.09.23},
  url = {http://dx.doi.org/10.1002/cphc.200700857}
}

@ARTICLE{Baron2010,
  author = {Riccardo Baron and Piotr Setny and J. Andrew McCammon},
  title = {Water in cavity-ligand recognition.},
  journal = {J Am Chem Soc},
  year = {2010},
  volume = {132},
  pages = {12091--12097},
  number = {34},
  month = {Sep},
  abstract = {We use explicit solvent molecular dynamics simulations to estimate
	free energy, enthalpy, and entropy changes along the cavity-ligand
	association coordinate for a set of seven model systems with varying
	physicochemical properties. Owing to the simplicity of the considered
	systems we can directly investigate the role of water thermodynamics
	in molecular recognition. A broad range of thermodynamic signatures
	is found in which water (rather than cavity or ligand) enthalpic
	or entropic contributions appear to drive cavity-ligand binding or
	rejection. The unprecedented, nanoscale picture of hydration thermodynamics
	can help the interpretation and design of protein-ligand binding
	experiments. Our study opens appealing perspectives to tackle the
	challenge of solvent entropy estimation in complex systems and for
	improving molecular simulation models.},
  doi = {10.1021/ja1050082},
  institution = {Department of Chemistry and Biochemistry, Center for Theoretical
	Biological Physics, Howard Hughes Medical Institute, University of
	California, San Diego, California 92093, USA. rbaron@mccammon.ucsd.edu},
  owner = {emilio},
  pmid = {20695475},
  timestamp = {2010.09.23},
  url = {http://dx.doi.org/10.1021/ja1050082}
}

@ARTICLE{Bartels1997,
  author = {Bartels, C. and Karplus, M.},
  title = {Multidimensional adaptive umbrella sampling: Application to main
	chain and side chain peptide conformations},
  journal = {J. Com. Chem.},
  year = {1997},
  volume = {18},
  pages = {1450-1462},
  owner = {emilio},
  timestamp = {2011.11.06}
}

@ARTICLE{Bashford:Case:2000,
  author = {Bashford, D. and Case, D. A.},
  title = {Generalized Born Models of Macromolecular Solvation Effects},
  journal = {Annu. Rev. Phys. Chem.},
  year = {2000},
  volume = {51},
  pages = {129-152},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Bashford:Gerwert:92,
  author = {Bashford, D. and Gerwert, K.},
  journal = {J. Mol. Biol.},
  year = {1992},
  volume = {224},
  pages = {473-486},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Bashford:Karplus:90,
  author = {Bashford, D. and Karplus, M.},
  journal = {Biochemistry},
  year = {1990},
  volume = {29},
  pages = {10219-10225},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Bassolino1988,
  author = {D. Bassolino and F. Hirata and D. Kitchen and D. Kominos and A. Pardi
	and R. M. Levy},
  title = {Determination of Protein Structures in Solution using NMR Data and
	IMPACT},
  journal = {Intl. J. of Supercomputer Applications},
  year = {1988},
  volume = {2},
  pages = {41-61},
  owner = {emilio},
  timestamp = {2011.03.15}
}

@ARTICLE{Baum2009,
  author = {Baum, Bernhard and Muley, Laveena and Heine, Andreas and Smolinski,
	Michael and Hangauer, David and Klebe, Gerhard},
  title = {Think Twice: Understanding the High Potency of Bis(phenyl)methane
	Inhibitors of Thrombin},
  journal = {Journal of Molecular Biology},
  year = {2009},
  volume = {391},
  pages = {552--564},
  number = {3},
  month = aug,
  abstract = {Successful design of potent and selective protein inhibitors, in terms
	of structure-based drug design, strongly relies on the correct understanding
	of the molecular features determining the ligand binding to the target
	protein. We present a case study of serine protease inhibitors with
	a bis(phenyl)methane moiety binding into the S3 pocket. These inhibitors
	bind with remarkable potency to the active site of thrombin, the
	blood coagulation factor IIa. A combination of X-ray crystallography
	and isothermal titration calorimetry provides conclusive insights
	into the driving forces responsible for the surprisingly high potency
	of these inhibitors. Analysis of six well-resolved crystal structures
	(resolution 1.58-2.25��) along with the thermodynamic data allows
	an explanation of the tight binding of the bis(phenyl)methane inhibitors.
	Interestingly, the two phenyl rings contribute to binding affinity
	for very different reasons -- a fact that can only be elucidated
	by a structure-based approach. The first phenyl moiety occupies the
	hydrophobic S3 pocket, resulting in a mainly entropic advantage of
	binding. This observation is based on the displacement of structural
	water molecules from the S3 pocket that are observed in complexes
	with inhibitors that do not bind in the S3 pocket. The same classic
	hydrophobic effect cannot explain the enhanced binding affinity resulting
	from the attachment of the second, more solvent-exposed phenyl ring.
	For the bis(phenyl)methane inhibitors, an observed adaptive rotation
	of a glutamate residue adjacent to the S3 binding pocket attracted
	our attention. The rotation of this glutamate into salt-bridging
	distance with a lysine moiety correlates with an enhanced enthalpic
	contribution to binding for these highly potent thrombin binders.
	This explanation for the magnitude of the attractive force is confirmed
	by data retrieved by a Relibase search of several thrombin-inhibitor
	complexes deposited in the Protein Data Bank exhibiting similar molecular
	features. Special attention was attributed to putative changes in
	the protonation states of the interaction partners. For this purpose,
	two analogous inhibitors differing mainly in their potential to change
	the protonation state of a hydrogen-bond donor functionality were
	compared. Buffer dependencies of the binding enthalpy associated
	with complex formation could be traced by isothermal titration calorimetry,
	which revealed, along with analysis of the crystal structures (resolution
	1.60 and 1.75��), that a virtually compensating proton interchange
	between enzyme, inhibitor and buffer is responsible for the observed
	buffer-independent thermodynamic signatures.},
  issn = {0022-2836},
  keywords = {structure-based drug design, thrombin, thermodynamic driving forces,
	protonation states},
  owner = {emilio},
  timestamp = {2011.07.14},
  url = {http://www.sciencedirect.com/science/article/pii/S0022283609007207}
}

@ARTICLE{Beck2007b,
  author = {David A C Beck and George W N White and Valerie Daggett},
  title = {Exploring the energy landscape of protein folding using replica-exchange
	and conventional molecular dynamics simulations.},
  journal = {J Struct Biol},
  year = {2007},
  volume = {157},
  pages = {514--523},
  number = {3},
  month = {Mar},
  abstract = {Two independent replica-exchange molecular dynamics (REMD) simulations
	with an explicit water model were performed of the Trp-cage mini-protein.
	In the first REMD simulation, the replicas started from the native
	conformation, while in the second they started from a nonnative conformation.
	Initially, the first simulation yielded results qualitatively similar
	to those of two previously published REMD simulations: the protein
	appeared to be over-stabilized, with the predicted melting temperature
	50-150K higher than the experimental value of 315K. However, as the
	first REMD simulation progressed, the protein unfolded at all temperatures.
	In our second REMD simulation, which starts from a nonnative conformation,
	there was no evidence of significant folding. Transitions from the
	unfolded to the folded state did not occur on the timescale of these
	simulations, despite the expected improvement in sampling of REMD
	over conventional molecular dynamics (MD) simulations. The combined
	1.42 micros of simulation time was insufficient for REMD simulations
	with different starting structures to converge. Conventional MD simulations
	at a range of temperatures were also performed. In contrast to REMD,
	the conventional MD simulations provide an estimate of Tm in good
	agreement with experiment. Furthermore, the conventional MD is a
	fraction of the cost of REMD and continuous, realistic pathways of
	the unfolding process at atomic resolution are obtained.},
  doi = {10.1016/j.jsb.2006.10.002},
  institution = {Biomolecular Structure and Design Program, University of Washington,
	Seattle, WA 98195, USA.},
  keywords = {Protein Folding; Proteins; Temperature; Thermodynamics; Tryptophan;
	Water},
  owner = {emilio},
  pii = {S1047-8477(06)00314-5},
  pmid = {17113307},
  timestamp = {2010.10.27},
  url = {http://dx.doi.org/10.1016/j.jsb.2006.10.002}
}

@BOOK{PDTbook:2006,
  title = {The Potential Distribution Theorem and Models of Molecular Solutions},
  publisher = {Cambridge University Press, New York},
  year = {2006},
  author = {Tom L. Beck and Michael E. Paulaitis and Lawrence R. Pratt},
  owner = {emilio},
  timestamp = {2010.04.30}
}

@ARTICLE{Beglov:Roux:94,
  author = {Beglov, D. and Roux, B.},
  title = {Finite Representation of an Infinite Bulk System: Solvent Boundary
	Potential for Computer Simulations},
  journal = {J. Chem. Phys.},
  year = {1994},
  volume = {100},
  pages = {9050-9062},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Belle:Wodak:93,
  author = {van Belle, D. and Wodak, S. J.},
  journal = {J. Am. Chem. Soc.},
  year = {1993},
  volume = {115},
  pages = {647},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@BOOK{Ben-Naim:74,
  title = {Water and Aqueous Solutions},
  publisher = {Plenum},
  year = {1974},
  author = {Ben Naim, A.},
  address = {New York},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@BOOK{Ben-Naim:80,
  title = {Hydrophobic Interactions},
  publisher = {Plenum Press},
  year = {1980},
  author = {Ben-naim, A.},
  address = {New York},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Ben-Naim:78,
  author = {Ben-Naim, A.},
  title = {A simple model for demonstrating the relation between solubility,
	hydrophobic interaction, and structural changes in the solvent},
  journal = {J. Phys. Chem.},
  year = {1978},
  volume = {82},
  pages = {874-85},
  number = {8},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Ben-Naim:75,
  author = {Ben-Naim, A.},
  title = {Hydrophpbic Interaction and Structural Changes in the Solvent},
  journal = {Biopolymers},
  year = {1975},
  volume = {14},
  pages = {1337-1355},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{B-N:Marcus:84,
  author = {Ben-Naim, A. and Marcus, Y.},
  journal = {J. Chem. Phys.},
  year = {1984},
  volume = {81},
  pages = {2016},
  number = {4},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Bennett1976,
  author = {Bennett, Charles H.},
  title = {Efficient estimation of free energy differences from Monte Carlo
	data},
  journal = {Journal of Computational Physics},
  year = {1976},
  volume = {22},
  pages = {245--268},
  number = {2},
  month = oct,
  abstract = {Near-optimal strategies are developed for estimating the free energy
	difference between two canonical ensembles, given a Metropolis-type
	Monte Carlo program for sampling each one. The estimation strategy
	depends on the extent of overlap between the two ensembles, on the
	smoothness of the density-of-states as a function of the difference
	potential, and on the relative Monte Carlo sampling costs, per statistically
	independent data point. The best estimate of the free energy difference
	is usually obtained by dividing the available computer time approximately
	equally between the two ensembles; its efficiency (variance x computer
	time)-1 is never less, and may be several orders of magnitude greater,
	than that obtained by sampling only one ensemble, as is done in perturbation
	theory.},
  issn = {0021-9991},
  owner = {emilio},
  timestamp = {2011.02.07},
  url = {http://www.sciencedirect.com/science/article/B6WHY-4DD1NKM-FW/2/08eb4944391d063102a3a200e95f5728}
}

@ARTICLE{Berendsen:Postma:vanGunsteren:84,
  author = {Berendsen, H. J. C. and Postma, J. P. and van Gunsteren, W. F. and
	Di Nola, A. and Haak, J. R.},
  journal = {J. Chem. Phys.},
  year = {1984},
  volume = {81},
  pages = {3684},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Berezhkovskii2009,
  author = {Alexander Berezhkovskii and Gerhard Hummer and Attila Szabo},
  title = {Reactive flux and folding pathways in network models of coarse-grained
	protein dynamics.},
  journal = {J Chem Phys},
  year = {2009},
  volume = {130},
  pages = {205102},
  number = {20},
  month = {May},
  abstract = {The reactive flux between folded and unfolded states of a two-state
	protein, whose coarse-grained dynamics is described by a master equation,
	is expressed in terms of the commitment or splitting probabilities
	of the microstates in the bottleneck region. This allows one to determine
	how much each transition through a dividing surface contributes to
	the reactive flux. By repeating the analysis for a series of dividing
	surfaces or, alternatively, by partitioning the reactive flux into
	contributions of unidirectional pathways that connect reactants and
	products, insight can be gained into the mechanism of protein folding.
	Our results for the flux in a network with complex connectivity,
	obtained using the discrete counterpart of Kramers' theory of activated
	rate processes, show that the number of reactive transitions is typically
	much smaller than the total number of transitions that cross a dividing
	surface at equilibrium.},
  doi = {10.1063/1.3139063},
  institution = {Mathematical and Statistical Computing Laboratory, Division of Computational
	Bioscience, Center for Information Technology, National Institutes
	of Health, Bethesda, Maryland 20892, USA. berezh@helix.nih.gov},
  keywords = {Humans; Models, Chemical; Monte Carlo Method; Physical Processes;
	Protein Conformation; Protein Folding; Proteins; Proteomics; Surface
	Properties; Temperature; Thermodynamics; Time Factors},
  owner = {emilio},
  pmid = {19485483},
  timestamp = {2010.07.14},
  url = {http://dx.doi.org/10.1063/1.3139063}
}

@ARTICLE{Berne:96,
  author = {Berne, B. J.},
  title = {Inferring the hydrophobic interaction from the properties of neat
	water},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {1996},
  volume = {93},
  pages = {8800-8803},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Beutler:Beguelin:vanGunsteren:95,
  author = {Beutler, T. C. and B\'{e}guelin and van Gunsteren, W. F.},
  title = {Free Energy of Cavity Formation in Solvent: Computational, Methodological,
	and Physical Aspects},
  journal = {J. Chem. Phys.},
  year = {1995},
  volume = {102},
  pages = {3787},
  number = {9},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Beveridge:89,
  author = {Beveridge, D. L. and Di Capua, F. M.},
  journal = {Annu. Rev. Biophys. Chem.},
  year = {1989},
  volume = {18},
  pages = {431},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Bhat2006a,
  author = {Sathesh Bhat and Enrico O Purisima},
  title = {Molecular surface generation using a variable-radius solvent probe.},
  journal = {Proteins},
  year = {2006},
  volume = {62},
  pages = {244--261},
  number = {1},
  month = {Jan},
  abstract = {Protein-ligand binding occurs through interactions at the molecular
	surface. Hence, a proper description of this surface is essential
	to our understanding of the process of molecular recognition. Recent
	studies have noted the inadequacy of using a fixed 1.4 A solvent
	probe radius to generate the molecular surface. This assumes that
	water molecules approach all surface atoms at an equal distance irrespective
	of polarity, which is not the case. To adequately model the protein-water
	boundary requires that the solvent probe radius change according
	to the polarity of its contacting atoms, smaller near polar atoms
	and larger near apolar atoms. To our knowledge, no method currently
	exists to generate the molecular surface of a protein in this manner.
	Using a modification of the marching tetrahedra algorithm, we present
	a method to generate molecular surfaces using a variable radius solvent
	probe. The resulting surface lacks many of the unrealistic small
	crevices in nonpolar regions that are found when utilizing an invariant
	1.4 A solvent probe, while maintaining the fine detail of the surface
	at polar regions. On application of the method on a test set of 20
	protein structures taken from the Protein Data Bank (PDB), we also
	find far fewer empty unsolvated cavities that are present when using
	only a 1.4 A solvent probe, while the majority of solvated and polar
	cavities is retained. This suggests that the majority of empty cavities
	previously observed in protein structures might simply be artifacts
	of the surfacing method. We also find that the variable probe surface
	can have significant effects on electrostatic calculations by generating
	a better tuned description of the protein-water boundary. We also
	examined the binding interfaces of a diverse set of 55 protein-protein
	complexes. We find that using a variable probe results in an increase
	in perceived shape complementarity at these sites compared to using
	a 1.4 A solvent probe. The molecular volume and surface area are
	geometric values that determine various important properties for
	macromolecules, and the altered description afforded by a variable
	solvent probe molecular surface can have significant implications
	in protein recognition, energetics, folding, and stability calculations.},
  doi = {10.1002/prot.20682},
  institution = {Department of Biochemistry, McGill University, Montreal, Quebec,
	Canada.},
  keywords = {Entropy; Models, Molecular; Protein Conformation; Proteins; Solvents;
	Surface Properties; Thermodynamics},
  owner = {emilio},
  pmid = {16287115},
  timestamp = {2010.05.20},
  url = {http://dx.doi.org/10.1002/prot.20682}
}

@BOOK{BillingsleyBook,
  title = {Probability and Measure},
  publisher = {Wiley, New York},
  year = {1995},
  author = {P. Billingsley},
  comment = {From Zhiqiang},
  owner = {emilio},
  timestamp = {2011.11.06}
}

@ARTICLE{Bishop:97,
  author = {Bishop, T. C. and Skeel, R. D. and Schulten, K.},
  journal = {J. Comp. Chem.},
  year = {1997},
  volume = {18},
  pages = {1785-1791},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Bizzarri2011,
  author = {Marco Bizzarri and Simone Marsili and Piero Procacci},
  title = {Intraligand hydrophobic interactions rationalize drug affinities
	for peptidyl-prolyl cis-trans isomerase protein.},
  journal = {J. Phys. Chem. B},
  year = {2011},
  volume = {115},
  pages = {6193--6201},
  number = {19},
  month = {May},
  abstract = {The conformational landscape of three FK506-related drugs with disparate
	inhibition constants is determined in bulk solution using a replica
	exchange simulation method with solute torsional tempering. Energetic
	fitness of important drug conformations with respect to the FKBP12
	protein is evaluated by molecular mechanics. Results show that the
	experimental affinity toward peptidyl-prolyl cis-trans isomerase
	protein (FKBP12) of the analyzed ligands appears to be positively
	correlated to the observed population of specific chair structures
	of the drug piperidinic ring in bulk solution. This observation is
	rationalized on the basis that such structures, stabilized by stereospecific
	intramolecular hydrophobic interactions, allows the formation of
	a pair of protein-ligand hydrogen bonds upon binding.},
  doi = {10.1021/jp110585p},
  institution = {Dipartimento di Chimica, Università di Firenze, Via della Lastruccia
	3, I-50019 Sesto Fiorentino, Italy.},
  keywords = {Hydrogen Bonding; Hydrophobic and Hydrophilic Interactions; Molecular
	Dynamics Simulation; Protein Binding; Tacrolimus Binding Protein
	1A, chemistry/metabolism; Tacrolimus, analogs /&/ derivatives/chemistry},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {21500789},
  timestamp = {2011.11.22},
  url = {http://dx.doi.org/10.1021/jp110585p}
}

@ARTICLE{Bizzarri2011c,
  author = {Bizzarri, Marco and Tenori, Eleonora and Martina, Maria Raffaella
	and Marsili, Simone and Caminati, Gabriella and Menichetti, Stefano
	and Procacci, Piero},
  title = {New Perspective on How and Why Immunophilin FK506-Related Ligands
	Work},
  journal = {J. Phys. Chem. Lett.},
  year = {2011},
  volume = {2},
  pages = {2834--2839},
  number = {22},
  month = oct,
  booktitle = {The Journal of Physical Chemistry Letters},
  comment = {doi: 10.1021/jz201037u},
  issn = {1948-7185},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2011.11.23},
  url = {http://dx.doi.org/10.1021/jz201037u}
}

@ARTICLE{Blokzijl:Engberts:93,
  author = {Blokzijl, W. and Engberts, J. B. F. N.},
  title = {Hydrophobic Effects. Opinions and Facts.},
  journal = {Angew. Chem. Int. Ed. Engl.},
  year = {1993},
  volume = {32},
  pages = {1545-1579},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Board:92,
  author = {Board, J. A. and Causey, J. W. and Leathrum, J. F. and Windemuth,
	A. and Schulten, K.},
  journal = {Chem. Phys. Lett.},
  year = {1992},
  volume = {198},
  pages = {89-97},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Boehr2009,
  author = {David D Boehr and Ruth Nussinov and Peter E Wright},
  title = {The role of dynamic conformational ensembles in biomolecular recognition.},
  journal = {Nat Chem Biol},
  year = {2009},
  volume = {5},
  pages = {789--796},
  number = {11},
  month = {Nov},
  abstract = {Molecular recognition is central to all biological processes. For
	the past 50 years, Koshland's 'induced fit' hypothesis has been the
	textbook explanation for molecular recognition events. However, recent
	experimental evidence supports an alternative mechanism. 'Conformational
	selection' postulates that all protein conformations pre-exist, and
	the ligand selects the most favored conformation. Following binding
	the ensemble undergoes a population shift, redistributing the conformational
	states. Both conformational selection and induced fit appear to play
	roles. Following binding by a primary conformational selection event,
	optimization of side chain and backbone interactions is likely to
	proceed by an induced fit mechanism. Conformational selection has
	been observed for protein-ligand, protein-protein, protein-DNA, protein-RNA
	and RNA-ligand interactions. These data support a new molecular recognition
	paradigm for processes as diverse as signaling, catalysis, gene regulation
	and protein aggregation in disease, which has the potential to significantly
	impact our views and strategies in drug design, biomolecular engineering
	and molecular evolution.},
  doi = {10.1038/nchembio.232},
  institution = {Department of Chemistry, The Pennsylvania State University, University
	Park, Pennsylvania, USA. ddb12@psu.edu},
  keywords = {Binding Sites; DNA; Databases, Protein; Disease; Drug Design; Enzymes;
	Evolution, Molecular; Gene Expression Regulation; Genetic Engineering;
	Humans; Ligands; Models, Molecular; Molecular Conformation; Pattern
	Recognition, Visual; Protein Conformation; Proteins; RNA; Repressor
	Proteins; Thermodynamics},
  owner = {emilio},
  pii = {nchembio.232},
  pmid = {19841628},
  timestamp = {2011.01.18},
  url = {http://dx.doi.org/10.1038/nchembio.232}
}

@ARTICLE{Bogusz:98,
  author = {Bogusz, S. and Cheatham, T. E. and Brooks, B. R.},
  journal = {J. Chem. Phys.},
  year = {in press},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Bolhuis:Chandler:2000,
  author = {Bolhuis, P. G. and Chandler, D.},
  title = {Transition path sampling of cavitation between molecular scale solvophobic
	surfaces},
  journal = {J. Chem. Phys.},
  year = {2000},
  volume = {113},
  pages = {8154},
  number = {18},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Boresch:Karplus:2003,
  author = {Boresch, S and Tettinger, F and Leitgeb, M and Karplus, M},
  title = {Absolute binding free energies: A quantitative approach for their
	calculation},
  journal = {J. Phys. Chem. B},
  year = {{2003}},
  volume = {{107}},
  pages = {{9535-9551}},
  number = {{35}},
  abstract = {{The computation of absolute binding affinities by molecular dynamics
	(MD) based free energy simulations C, is analyzed, and an exact method
	to carry out such a computation is presented. The key to obtaining
	converged results is the introduction of suitable, auxiliary restraints
	to prevent the ligand from leaving the binding site when the native
	ligand-receptor interactions are turned off alchemically. We describe
	a versatile set of restraints that (i) can be used in MD simulations,
	that (ii) restricts both the position and the orientation of the
	ligand, and that (iii) is defined relative to the receptor rather
	than relative to a fixed point in space. The free energy cost. DeltaA(r),
	for this set of restraints can be evaluated analytically. Although
	the techniques were originally developed for the gas phase, the resulting
	expression is exact, since all contributions from solute-solvent
	interactions cancel from the final result. The value of DeltaA(r)
	depends only on the equilibrium values and force constants of the
	chosen harmonic restraint terms and, therefore, can be easily calculated.
	The standard state dependence of binding free energies is also investigated,
	and it is shown that the present approach takes this into account
	correctly. The analytical expression for DeltaA(r) is verified numerically
	by calculations on the complex formed by benzene with the L99A mutant
	of T4 lysozyme. The overall approach is illustrated by a complete
	binding free energy calculation for a complex based on a simplified
	model for tyrosine bound to tyrosyl-tRNA-synthetase. The results
	demonstrate the usefulness of the proposed set of restraints and
	confirm that the calculated binding free energy is independent of
	the details of the restraints. Comparisons are made with earlier
	formulations for the calculation of binding free energies, and certain
	limitations of that work are described. The relationship between
	DeltaA(r) and the loss of translational and rotational entropy during
	a binding process is analyzed.}},
  doi = {10.1021/jp0217839},
  issn = {{1520-6106}},
  owner = {emilio},
  timestamp = {2010.04.19},
  unique-id = {{ISI:000185034700054}}
}

@ARTICLE{Bossard1994,
  author = {Bossard, M. J. and Bergsma, D. J. and Brandt, M. and Livi, G. P.
	and Eng, W. K. and Johnson, R. K. and Levy, M. A.},
  title = {Catalytic and ligand binding properties of the FK506 binding protein
	FKBP12: effects of the single amino acid substitution of Tyr82 to
	Leu},
  journal = {Biochem. J.},
  year = {1994},
  volume = {297 ( Pt 2)},
  pages = {365--372},
  abstract = {The binding of FK506 and rapamycin to their cytosolic receptor FKBP12
	is an intermediate step in the paths leading to their potent immunosuppressive
	properties. One of the amino acids defining the hydrophobic binding
	cleft for the macrocycles is Tyr82, which is thought to form a hydrogen
	bond with the amide oxygens of the common pipecolyl structural element
	within the two macrolides. To understand better the influence of
	this amino acid residue in catalytic activity (cis-trans peptidyl
	prolyl isomerization) and ligand binding properties, a Tyr82 to Leu
	site-specific modification of FKBP12 was prepared, purified and characterized.
	Kinetic experiments have demonstrated that the Tyr82 to Leu modification
	has a greater effect on catalytic properties than on ligand binding
	affinities, a result which indicates that these inhibitors may not
	be binding as true transition-state analogues. In an additional test
	for cellular function, expression of both wild-type and mutant human
	FKBP12 in a strain of Saccharomyces cerevisiae rendered resistant
	to rapamycin by deletion of the gene encoding a cytosolic rapamycin
	binding protein (RPB1), the yeast homologue of FKBP12, restored wild-type
	drug sensitivity.},
  address = {Department of Medical Chemistry, SmithKline Beecham Pharmaceuticals,
	King of Prussia, PA 19406.},
  comment = {Jan 15

	Catalytic and ligand binding properties of the FK506 binding protein
	FKBP12: effects of the single amino acid substitution of Tyr82 to
	Leu

	7507662

	Bossard, M J Bergsma, D J Brandt, M Livi, G P Eng, W K Johnson, R
	K Levy, M A England The Biochemical journal Biochem J. 1994 Jan 15;297
	( Pt 2):365-72.

	eng},
  issn = {0264-6021 (Print) 0264-6021 (Linking)},
  keywords = {Base Sequence Carrier Proteins/*chemistry/metabolism DNA Primers/chemistry
	Heat-Shock Proteins/*chemistry/metabolism Humans Kinetics Ligands
	Molecular Sequence Data Mutagenesis, Site-Directed Polyenes/metabolism
	Protein Binding Saccharomyces cerevisiae/chemistry Sirolimus Spectrometry,
	Fluorescence Structure-Activity Relationship Substrate Specificity
	Tacrolimus/*metabolism Tacrolimus Binding Proteins},
  owner = {mauro},
  refid = {44},
  timestamp = {2011.07.22},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7507662}
}

@BOOK{Bottcher:73,
  title = {Theory fo Electric Polarization},
  publisher = {Elsevier},
  year = {1973},
  author = {Bottcher, C. J. F.},
  address = {Amsterdam},
  optedition = {2nd Edition},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@INPROCEEDINGS{Bowers:Shaw:2006,
  author = {Bowers, {K. J.} and Chow, E. and Xu, H. and Dror, {R. O.} and Eastwood,
	{M. P.} and Gregersen, {B. A.} and Klepeis, {J. L.} and Kolossv\'{a}ry,
	I. and Moraes, {M. A.} and Sacerdoti, {F. D.} and Salmon, {J. K.}
	and Shan, Y. and Shaw, {D. E.}},
  title = {Scalable Algorithms for Molecular Dynamics Simulations on Commodity
	Clusters},
  booktitle = {Proceedings of the ACM/IEEE Conference on Supercomputing (SC06)},
  year = {2006},
  address = {Tampa, Florida},
  month = {November 11-17},
  publisher = {IEEE},
  owner = {emilio},
  timestamp = {2010.11.02}
}

@ARTICLE{Bowers:Dror:Shaw:2006,
  author = {Bowers, {K. J.} and Dror, {R. O.} and Shaw, {D. E.}},
  title = {The midpoint method for parallelization of particle simulations},
  journal = {J. Chem. Phys.},
  year = {2006},
  volume = {124},
  pages = {184109--11},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Bowman2009,
  author = {Gregory R Bowman and Kyle A Beauchamp and George Boxer and Vijay
	S Pande},
  title = {Progress and challenges in the automated construction of Markov state
	models for full protein systems.},
  journal = {J Chem Phys},
  year = {2009},
  volume = {131},
  pages = {124101},
  number = {12},
  month = {Sep},
  abstract = {Markov state models (MSMs) are a powerful tool for modeling both the
	thermodynamics and kinetics of molecular systems. In addition, they
	provide a rigorous means to combine information from multiple sources
	into a single model and to direct future simulations/experiments
	to minimize uncertainties in the model. However, constructing MSMs
	is challenging because doing so requires decomposing the extremely
	high dimensional and rugged free energy landscape of a molecular
	system into long-lived states, also called metastable states. Thus,
	their application has generally required significant chemical intuition
	and hand-tuning. To address this limitation we have developed a toolkit
	for automating the construction of MSMs called MSMBUILDER (available
	at https://simtk.org/home/msmbuilder). In this work we demonstrate
	the application of MSMBUILDER to the villin headpiece (HP-35 NleNle),
	one of the smallest and fastest folding proteins. We show that the
	resulting MSM captures both the thermodynamics and kinetics of the
	original molecular dynamics of the system. As a first step toward
	experimental validation of our methodology we show that our model
	provides accurate structure prediction and that the longest timescale
	events correspond to folding.},
  doi = {10.1063/1.3216567},
  institution = {Biophysics Program, Stanford University, Stanford, California 94305,
	USA.},
  keywords = {Computer Simulation; Markov Chains; Models, Chemical; Models, Molecular;
	Models, Statistical; Protein Conformation; Proteins},
  owner = {emilio},
  pmid = {19791846},
  timestamp = {2010.11.03},
  url = {http://dx.doi.org/10.1063/1.3216567}
}

@ARTICLE{Boyce2009,
  author = {Sarah E Boyce and David L Mobley and Gabriel J Rocklin and Alan P
	Graves and Ken A Dill and Brian K Shoichet},
  title = {Predicting ligand binding affinity with alchemical free energy methods
	in a polar model binding site.},
  journal = {J. Mol. Biol.},
  year = {2009},
  volume = {394},
  pages = {747--763},
  number = {4},
  month = {Dec},
  abstract = {We present a combined experimental and modeling study of organic ligand
	molecules binding to a slightly polar engineered cavity site in T4
	lysozyme (L99A/M102Q). For modeling, we computed alchemical absolute
	binding free energies. These were blind tests performed prospectively
	on 13 diverse, previously untested candidate ligand molecules. We
	predicted that eight compounds would bind to the cavity and five
	would not; 11 of 13 predictions were correct at this level. The RMS
	error to the measurable absolute binding energies was 1.8 kcal/mol.
	In addition, we computed "relative" binding free energies for six
	phenol derivatives starting from two known ligands: phenol and catechol.
	The average RMS error in the relative free energy prediction was
	2.5 kcal/mol (phenol) and 1.1 kcal/mol (catechol). To understand
	these results at atomic resolution, we obtained x-ray co-complex
	structures for nine of the diverse ligands and for all six phenol
	analogs. The average RMSD of the predicted pose to the experiment
	was 2.0 A (diverse set), 1.8 A (phenol-derived predictions), and
	1.2 A (catechol-derived predictions). We found that predicting accurate
	affinities and rank-orderings required near-native starting orientations
	of the ligand in the binding site. Unanticipated binding modes, multiple
	ligand binding, and protein conformational change all proved challenging
	for the free energy methods. We believe that these results can help
	guide future improvements in physics-based absolute binding free
	energy methods.},
  doi = {10.1016/j.jmb.2009.09.049},
  institution = {Graduate Group in Chemistry and Chemical Biology, University of California-San
	Francisco, San Francisco, CA 94158-2518, USA.},
  keywords = {Binding Sites; Computer Simulation; Crystallography, X-Ray; Kinetics;
	Ligands; Models, Molecular; Organic Chemicals; Protein Binding; Protein
	Structure, Tertiary; Viral Proteins},
  owner = {emilio},
  pii = {S0022-2836(09)01176-0},
  pmid = {19782087},
  timestamp = {2010.04.20},
  url = {http://dx.doi.org/10.1016/j.jmb.2009.09.049}
}

@ARTICLE{Brady:Szabo:Sharp:96,
  author = {Brady, G. P. and Szabo, A. and Sharp, K. A.},
  title = {On the decomposition of free energies},
  journal = {J. Mol. Biol.},
  year = {1996},
  volume = {263},
  pages = {123-125},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Branco2008,
  author = {Ricardo J F Branco and Alexander Seifert and Michael Budde and Vlada
	B Urlacher and Maria J Ramos and Jürgen Pleiss},
  title = {Anchoring effects in a wide binding pocket: the molecular basis of
	regioselectivity in engineered cytochrome P450 monooxygenase from
	B. megaterium.},
  journal = {Proteins},
  year = {2008},
  volume = {73},
  pages = {597--607},
  number = {3},
  month = {Nov},
  abstract = {The molecular basis of regioselectivity of cytochrome P450 monooxygenases
	from Bacillus megaterium (CYP102A1) with its flexible and widely
	opened active site is still not well understood. In the present work
	(-)-alpha-pinene bound complexes with two triple mutants were modeled
	to elucidate the contribution of the three major factors that mediate
	selectivity: active site shape, protein flexibility, and chemical
	reactivity of the substrate. For the triple mutant A74G F87V L188Q
	(GVQ), one stable, productive conformation of the substrate (conformation
	I) was identified by multiple molecular dynamics simulations. The
	model predicts pinene epoxide as a major product (42\% pinene oxide,
	23\% verbenol) which is in agreement with the experimental product
	profile (70\% pinene oxide, 20\% verbenol). In contrast, for the
	triple mutant A74G F87G L188Q (GGQ) two stable productive substrate
	conformations were identified (conformations IIa and IIb), and verbenol
	was predicted as major product (81\% verbenol, 16\% myrtenol), which
	is in agreement with experimental results (77\% verbenol, 10\% myrtenol).
	The effect of chemical reactivity of the substrate was demonstrated
	by comparison of (-)-alpha-pinene to its regioisomer (-)-beta-pinene,
	where the product profile is shifted from 68\% pinocarveol and 32\%
	myrtanal in mutant GVQ, to 40\% pinocarveol and 60\% myrtanal in
	mutant GGQ. Our results strongly suggest a major role of residue
	87 in anchoring (-)-alpha-pinene during substrate binding which provides
	a simple and elegant rationalization of the dynamic structure of
	this enzyme-substrate complex.},
  doi = {10.1002/prot.22083},
  institution = {REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade
	do Porto, Rua do Campo Alegre, 687, P 4169-007 Porto, Portugal.},
  keywords = {Bacillus megaterium; Bicyclo Compounds; Catalytic Domain; Computer
	Simulation; Cytochrome P-450 Enzyme System; Hydrogen Bonding; Models,
	Molecular; Molecular Conformation; Monoterpenes; Mutant Proteins;
	Oxidation-Reduction; Protein Engineering; Stereoisomerism; Substrate
	Specificity; Thermodynamics},
  owner = {emilio},
  pmid = {18473391},
  timestamp = {2010.09.22},
  url = {http://dx.doi.org/10.1002/prot.22083}
}

@ARTICLE{Breneman:Wiberg:90,
  author = {Breneman, C. M. and Wiberg, K. B.},
  journal = {J. Comput. Chem.},
  year = {1990},
  volume = {5},
  pages = {129},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Brenner2007,
  author = {Sibylle Brenner and Sam Hay and Hazel M Girvan and Andrew W Munro
	and Nigel S Scrutton},
  title = {Conformational dynamics of the cytochrome P450 BM3/N-palmitoylglycine
	complex: the proposed "proximal-distal" transition probed by temperature-jump
	spectroscopy.},
  journal = {J Phys Chem B},
  year = {2007},
  volume = {111},
  pages = {7879--7886},
  number = {27},
  month = {Jul},
  abstract = {The ferric spin state equilibrium of the heme iron was analyzed in
	wild-type cytochrome P450 BM3 and its F87G mutant by using temperature
	(T)-jump relaxation spectroscopy in combination with static equilibrium
	experiments. No relaxation process was measurable in the substrate-free
	enzyme indicating a relaxation process with a rate constant>10,000
	s(-1). In contrast, a slow spin state transition process was observed
	in the N-palmitoylglycine (NPG)-bound enzyme species. This transition
	occurred with an observed rate constant (298 K) of approximately
	800 s(-1) in the wild-type, and approximately 2500 s(-1) in the F87G
	mutant, suggesting a significant contribution of the phenylalanine
	side chain to a reaction step rate limiting the actual spin state
	transition. These findings are discussed in terms of an equilibrium
	between different binding modes of the substrate, including a position
	7.5 A away from the heme iron ("distal") and the catalytically relevant
	"proximal" binding site, and are in accordance with results from
	X-ray crystallography, NMR studies, and molecular dynamics simulations.},
  doi = {10.1021/jp073036n},
  institution = {Manchester Interdisciplinary Biocentre and Faculty of Life Sciences,
	University of Manchester, 131 Princess Street, Manchester M1 7DN,
	United Kingdom.},
  keywords = {Algorithms; Bacterial Proteins; Binding Sites; Crystallography, X-Ray;
	Cytochrome P-450 Enzyme System; Glycine; Heme; Iron; Magnetic Resonance
	Spectroscopy; Mixed Function Oxygenases; NADPH-Ferrihemoprotein Reductase;
	Palmitic Acids; Phenylalanine; Protein Conformation; Spectrophotometry,
	Ultraviolet; Spectrum Analysis},
  owner = {emilio},
  pmid = {17571881},
  review = {Confirms our MD calculations},
  timestamp = {2010.06.07},
  url = {http://dx.doi.org/10.1021/jp073036n}
}

@ARTICLE{Breslauer:87,
  author = {Breslauer, K. J. and Remeta, D. P. and Chou, {W.-Y.} and Ferrante,
	R. and Curry, J. and Zaunczkowski, D. and Snyder, G. J. and Marky,
	L. A.},
  title = {Enthalpy-Entropy compensations in drug-DNA binding studies},
  journal = {Proc. Natl. Acad. Sci.},
  year = {1987},
  volume = {84},
  pages = {8922-8926},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Brooijmans2003,
  author = {Natasja Brooijmans and Irwin D Kuntz},
  title = {Molecular recognition and docking algorith},
  journal = {Annu. Rev. Biophys. Biomol. Struct.},
  year = {2003},
  volume = {32},
  pages = {335--373},
  abstract = {Molecular docking is an invaluable tool in modern drug discovery.
	This review focuses on methodological developments relevant to the
	field of molecular docking. The forces important in molecular recognition
	are reviewed and followed by a discussion of how different scoring
	functions account for these forces. More recent applications of computational
	chemistry tools involve library design and database screening. Last,
	we summarize several critical methodological issues that must be
	addressed in future developments.},
  doi = {10.1146/annurev.biophys.32.110601.142532},
  institution = {Chemistry and Chemical Biology Graduate Program University of California
	San Francisco, San Francisco, California 94143-2240, USA. nbrooij@itsa.ucsf.edu},
  keywords = {Algorithms; Binding Sites; Computer Simulation; Databases, Protein;
	Drug Design; Ligands; Macromolecular Substances; Models, Molecular;
	Motion; Peptide Library; Protein Binding; Protein Conformation; Proteins;
	Stress, Mechanical},
  owner = {emilio},
  pii = {110601.142532},
  pmid = {12574069},
  timestamp = {2010.04.20},
  url = {http://dx.doi.org/10.1146/annurev.biophys.32.110601.142532}
}

@ARTICLE{Brooks:87,
  author = {Brooks, C. L.},
  journal = {J. Chem. Phys.},
  year = {1987},
  volume = {86},
  pages = {5156-5162},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Brooks:86,
  author = {Brooks, C. L.},
  title = {Thermodynamics of Ionic Solvation: Monte Carlo Simulation of Aqueous
	Chloride and Bromide Ions},
  journal = {J. Phys. Chem.},
  year = {1986},
  volume = {90},
  pages = {6680-6684},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Brooks:85,
  author = {Brooks, C. L. and Pettitt, B. M. and Karplus, M.},
  journal = {J. Chem. Phys.},
  year = {1985},
  volume = {83},
  pages = {5897-5908},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Brown2009,
  author = {Scott P Brown and Steven W Muchmore},
  title = {Large-scale application of high-throughput molecular mechanics with
	Poisson-Boltzmann surface area for routine physics-based scoring
	of protein-ligand complexes.},
  journal = {J Med Chem},
  year = {2009},
  volume = {52},
  pages = {3159--3165},
  number = {10},
  month = {May},
  abstract = {We apply a high-throughput formulation of the molecular mechanics
	with Poisson-Boltzmann surface area (htMM-PBSA) to estimate relative
	binding potencies on a set of 308 small-molecule ligands in complex
	with the proteins urokinase, PTP-1B, and Chk-1. We observe statistically
	significant correlation to experimentally measured potencies and
	report correlation coefficients for the three proteins in the range
	0.72-0.83. The htMM-PBSA calculations illustrate the feasibility
	of procedural automation of physics-based scoring calculations to
	produce rank-ordered binding-potency estimates for protein-ligand
	complexes, with sufficient throughput for realization of practical
	implementation into scientist workflows in an industrial drug discovery
	research setting.},
  doi = {10.1021/jm801444x},
  institution = {Structural Biology, Abbott Laboratories, 100 Abbott Park Road, Abbott
	Park, Illinois 60064-3500, USA.},
  keywords = {Chemistry, Pharmaceutical; Drug Discovery; Humans; Ligands; Models,
	Theoretical; Poisson Distribution; Protein Binding; Protein Kinases;
	Protein Tyrosine Phosphatase, Non-Receptor Type 1; Proteins; Quantitative
	Structure-Activity Relationship; Urokinase-Type Plasminogen Activator},
  owner = {emilio},
  pmid = {19385614},
  timestamp = {2010.05.01},
  url = {http://dx.doi.org/10.1021/jm801444x}
}

@ARTICLE{Brown2007,
  author = {Scott P Brown and Steven W Muchmore},
  title = {Rapid estimation of relative protein-ligand binding affinities using
	a high-throughput version of MM-PBSA.},
  journal = {J. Chem. Inf. Model.},
  year = {2007},
  volume = {47},
  pages = {1493--1503},
  number = {4},
  abstract = {By employing a modified protocol of the Molecular Mechanics with Poisson-Boltzmann
	Surface Area (MM-PBSA) methodology we substantially decrease the
	required computation time for calculating relative estimates of protein-ligand
	binding affinities. The modified method uses a generalized Born implicit
	solvation model during molecular dynamics to enhance conformational
	sampling as well as a very efficient Poisson-Boltzmann solver and
	a computational design based on a distributed-computing paradigm.
	This construction allows for reduction of the computational cost
	of the calculations by roughly 2 orders of magnitude compared to
	the traditional formulation of MM-PBSA. With this high-throughput
	version of MM-PBSA we show that one can produce efficient physics-based
	estimates of relative binding free energies with reasonable correlation
	to experimental data and a total computation time that is sufficiently
	low such that an industrially relevant throughput can be realized
	given currently accessible computing resources. We demonstrate this
	approach by performing a comparison of different MM-PBSA implementations
	on a set of 18 ligands for the protein target urokinase.},
  doi = {10.1021/ci700041j},
  institution = {Abbott Laboratories, Global Pharmaceutical Research and Development,
	100 Abbott Park Road, Abbott Park, Illinois 60064-6115, USA. scott.brown@abbott.com},
  keywords = {Drug Design; Ligands; Models, Molecular; Protein Binding; Proteins},
  owner = {emilio},
  pmid = {17518461},
  timestamp = {2010.05.01},
  url = {http://dx.doi.org/10.1021/ci700041j}
}

@ARTICLE{Brown2006,
  author = {Scott P Brown and Steven W Muchmore},
  title = {High-throughput calculation of protein-ligand binding affinities:
	modification and adaptation of the MM-PBSA protocol to enterprise
	grid computing.},
  journal = {J Chem Inf Model},
  year = {2006},
  volume = {46},
  pages = {999--1005},
  number = {3},
  abstract = {We have developed a system for performing computations on an enterprise
	grid using a freely available package for grid computing that allows
	us to harvest unused CPU cycles off of employee desktop computers.
	By modifying the traditional formulation of Molecular Mechanics with
	Poisson-Boltzmann Surface Area (MM-PBSA) methodology, in combination
	with a coarse-grain parallelized implementation suitable for deployment
	onto our enterprise grid, we show that it is possible to produce
	rapid physics-based estimates of protein-ligand binding affinities
	that have good correlation to experimental data. This is demonstrated
	by examining the correlation of our calculated binding affinities
	to experimental data and also by comparison to the correlation obtained
	from the binding-affinity calculations using traditional MM-PBSA
	that are reported in the literature.},
  doi = {10.1021/ci050488t},
  institution = {Abbott Laboratories, Bldg AP10-LL, 100 Abbott Park Rd, Abbott Park,
	Illinois 60064-6115, USA. scott.brown@abbott.com},
  keywords = {Drug Design; Ligands; Poisson Distribution; Protein Binding; Proteins},
  owner = {emilio},
  pmid = {16711718},
  timestamp = {2010.05.01},
  url = {http://dx.doi.org/10.1021/ci050488t}
}

@ARTICLE{Brown2009a,
  author = {Scott P Brown and Steven W Muchmore and Philip J Hajduk},
  title = {Healthy skepticism: assessing realistic model performance.},
  journal = {Drug Discov Today},
  year = {2009},
  volume = {14},
  pages = {420--427},
  number = {7-8},
  month = {Apr},
  abstract = {Although the development of computational models to aid drug discovery
	has become an integral part of pharmaceutical research, the application
	of these models often fails to produce the expected impact on productivity.
	One reason for this may be that the expected performance of many
	models is simply not supported by the underlying data, because of
	often neglected effects of assay and prediction errors on the reliability
	of the predicted outcome. Another significant challenge to realizing
	the full potential of computational models is their integration into
	prospective medicinal chemistry campaigns. This article will analyze
	the impact of assay and prediction error on model quality, and explore
	scenarios where computational models can expect to have a significant
	influence on drug discovery research.},
  institution = {Structural Biology, Abbott Laboratories, 100 Abbott Park Road, Abbott
	Park, IL 60064, USA.},
  keywords = {Computer Simulation; Drug Discovery; Drug Evaluation, Preclinical;
	Models, Molecular},
  owner = {emilio},
  pmid = {19340931},
  timestamp = {2010.05.01}
}

@ARTICLE{Buchete2008,
  author = {Nicolae-Viorel Buchete and Gerhard Hummer},
  title = {Peptide folding kinetics from replica exchange molecular dynamics.},
  journal = {Phys Rev E Stat Nonlin Soft Matter Phys},
  year = {2008},
  volume = {77},
  pages = {030902},
  number = {3 Pt 1},
  month = {Mar},
  abstract = {We show how accurate kinetic information, such as the rates of protein
	folding and unfolding, can be extracted from replica-exchange molecular
	dynamics (REMD) simulations. From the brief and continuous trajectory
	segments between replica exchanges, we estimate short-time propagators
	in conformation space and use them to construct a master equation.
	For a helical peptide in explicit water, we determine the rates of
	transitions both locally between microscopic conformational states
	and globally for folding and unfolding. We show that accurate rates
	in the approximately 1(100 ns) to approximately 1(1 ns) range can
	be obtained from REMD with exchange times of 5 ps , in excellent
	agreement with results from long equilibrium molecular dynamics.},
  institution = {ional Institutes of Health, Building 5, Bethesda, Maryland 20892-0520,
	USA.},
  keywords = {Biophysics; Computer Simulation; Kinetics; Markov Chains; Models,
	Chemical; Models, Molecular; Models, Statistical; Molecular Conformation;
	Peptides; Protein Conformation; Protein Denaturation; Protein Folding;
	Thermodynamics; Time Factors},
  owner = {emilio},
  pmid = {18517321},
  timestamp = {2011.01.18}
}

@ARTICLE{Buckner:Jorgensen:89,
  author = {Buckner, J. K. and Jorgensen, W. L.},
  journal = {J. Am. Chem. Soc.},
  year = {1989},
  volume = {111},
  pages = {2507-2510},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Buelens2012,
  author = {Buelens, Floris P. and {Grubm\"{u}ller}, Helmut},
  title = {Linear-scaling soft-core scheme for alchemical free energy calculations},
  journal = {J. Comput. Chem.},
  year = {2012},
  volume = {33},
  pages = {25--33},
  number = {1},
  abstract = {Alchemical free energy calculations involving the removal or insertion
	of atoms into condensed phase systems generally make use of soft-core
	scaling of nonbonded interactions, designed to circumvent numerical
	instabilities that arise from weakly interacting “hard” atoms in
	close proximity. Current methods model soft-core atoms by introducing
	a nonlinear dependence between the shape of the interaction potential
	and the strength of the interaction. In this article, we propose
	a soft-core method that avoids introducing such a nonlinear dependence,
	through the application of a smooth flattening of the potential energy
	only in a region that is energetically accessible under normal conditions.
	We discuss the benefits that this entails and explore a selection
	of applications, including enhanced methods for the estimation of
	free energy differences and for the automated optimization of the
	placement of intermediate states in multistage alchemical calculations.
	© 2011 Wiley Periodicals, Inc. J Comput Chem, 2011},
  issn = {1096-987X},
  keywords = {free energy calculation, molecular dynamics, soft-core scaling, thermodynamics,
	algorithms},
  owner = {emilio},
  publisher = {Wiley Subscription Services, Inc., A Wiley Company},
  timestamp = {2011.11.06},
  url = {http://dx.doi.org/10.1002/jcc.21938}
}

@ARTICLE{Bussi2006,
  author = {Bussi, Giovanni and Gervasio, Francesco Luigi and Laio, Alessandro
	and Parrinello, Michele},
  title = {Free-Energy Landscape for $\beta$ Hairpin Folding from Combined Parallel
	Tempering and Metadynamics},
  journal = {Journal of the American Chemical Society},
  year = {2006},
  volume = {128},
  pages = {13435--13441},
  number = {41},
  month = oct,
  abstract = {We develope a new free-energy method, based on the combination of
	parallel tempering and metadynamics, and apply this method to the
	calculation of the free-energy landscape of the folding $\beta$ hairpin
	in explicit water. We show that the combined method greatly improves
	the performance of both parallel tempering and metadynamics. In particular,
	we are able to sample the high free-energy regions, which are not
	accessible with conventional parallel tempering. We use our results
	to calculate the difference in entropy and enthalpy between the folded
	and the unfolded state and to characterize the most populated configurations
	in the relevant free-energy basins.},
  comment = {doi: 10.1021/ja062463w},
  issn = {0002-7863},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2011.01.13},
  url = {http://dx.doi.org/10.1021/ja062463w}
}

@ARTICLE{Cabani:Gianni:Mollica:Lepori:81,
  author = {Cabani, S. and Gianni, P. and Mollica, V. and Lepori, L.},
  title = {Group contributions to the thermodynamic properties of non-ionic
	organic solutes in dilute aqueous solution},
  journal = {J. Solut. Chem.},
  year = {1981},
  volume = {10},
  pages = {563-595},
  number = {8},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Cann:Patey:97,
  author = {Cann, N. M. and Patey, G. N.},
  title = {An Investigation of the Influnce of Solute Size and Insertion Conditions
	on Solvation Thermodynamics},
  journal = {J. Chem. Phys.},
  year = {1997},
  volume = {106},
  pages = {8165},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Carlson:Jorgensen:93,
  author = {Carlson, H. A. and Nguyen, T. B. and Orozco, M. and Jorgensen, W.
	L.},
  title = {Accuracy of Free Energies of Hydration for Organic Molecules from
	6-31G$^*$-Derived Partial Charges},
  journal = {J. Comput. Chem.},
  year = {1993},
  volume = {14},
  pages = {1240},
  number = {10},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Carlson:Jorgensen:1995,
  author = {Carlson, {H. A.} and Jorgensen, {W. L.}},
  title = {An extended linear response method for determining free energies
	of hydration},
  journal = {J. Phys. Chem.},
  year = {1995},
  volume = {99},
  pages = {10667--10673},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Carlsson:Ander:Nervall:Aqvist:2006,
  author = {Carlsson, J. and And\'{e}r, M. and Nervall, M. and {\AA}qvist, J.},
  title = {Continuum Solvation Models in the Linear Interaction Energy Method},
  journal = {J. Phys. Chem. B},
  year = {2006},
  volume = {110},
  pages = {12034-12041},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Carter:Hynes:89,
  author = {Carter, E. A. and Hynes, J. T.},
  journal = {J. Phys. Chem.},
  year = {1989},
  volume = {93},
  pages = {2184-2187},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Case:Cheatham:2005,
  author = {Case, {D. A.} and Cheatham III, T. E. and Darden, T. and Gohlke,
	H. and Luo, R. and Merz Jr., K. M. and Onufriev, A. and Simmerling,
	C. and Wang, B. and Woods, R. J.},
  title = {The Amber biomolecular simulation programs},
  journal = {J. Comp. Chem.},
  year = {2005},
  volume = {26},
  pages = {1668--1688},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Chandler:93,
  author = {Chandler, D.},
  journal = {Phys. Rev. E},
  year = {1993},
  volume = {48},
  pages = {2898-2905},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Chandler:Weeks:Andersen:83,
  author = {Chandler, D. and Weeks, J. D. and Andersen, H. C.},
  title = {Van der Waals picture of liquids, solids, and phase transformations},
  journal = {Science},
  year = {1983},
  volume = {220},
  pages = {787-794},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Chang2005,
  author = {Chang, Chia-En and Chen, Wei and Gilson, Michael K.},
  title = {Evaluating the Accuracy of the Quasiharmonic Approximation},
  journal = {Journal of Chemical Theory and Computation},
  year = {2005},
  volume = {1},
  pages = {1017--1028},
  number = {5},
  month = sep,
  abstract = {The quasiharmonic approximation (QH) allows the configurational entropy
	of a molecule to be estimated on the basis of a molecular dynamics
	simulation, through construction of a Gaussian probability distribution
	of conformations with variances equal to those provided by the simulation.
	At its introduction in 1981, the QH method was successfully applied
	to simple molecular systems with only one highly occupied energy
	well, and fluctuations were analyzed in a system of internal bond-angle-torsion
	coordinates. However, more recent studies have applied the QH method
	to complex biomolecular systems and have relied upon Cartesian coordinates.
	The present study evaluates the accuracy of the QH method through
	comparisons with more detailed methods. The chief findings are that
	the QH method can markedly overestimate the configurational entropy
	for systems with multiple occupied energy wells and that such errors
	tend to be magnified by the use of Cartesian coordinates instead
	of bond-angle-torsion coordinates.},
  comment = {doi: 10.1021/ct0500904},
  issn = {1549-9618},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2011.02.05},
  url = {http://dx.doi.org/10.1021/ct0500904}
}

@ARTICLE{Chang2004,
  author = {Chia-En Chang and Michael K Gilson},
  title = {Free energy, entropy, and induced fit in host-guest recognition:
	calculations with the second-generation mining minima algorithm.},
  journal = {J. Am. Chem. Soc.},
  year = {2004},
  volume = {126},
  pages = {13156--13164},
  number = {40},
  month = {Oct},
  abstract = {This study applies a novel computational method to study molecular
	recognition for three sets of synthetic hosts: molecular clips, molecular
	tweezers, and a synthetic barbiturate receptor. The computed standard
	free energies of binding for the 12 binding reactions agree closely
	with experiment and provide insight into the roles of configurational
	entropy, preorganization, and induced fit in the systems studied.
	The computed changes in configurational entropy are comparable in
	magnitude to the changes in mean potential plus solvation energy,
	and they result primarily from changes in the average width of the
	energy wells upon binding. A strong correlation is observed between
	the changes in configurational energy and configurational entropy
	upon binding, resulting in near-linear compensation analogous to
	classical entropy-enthalpy compensation.},
  doi = {10.1021/ja047115d},
  institution = {Contribution from the Center for Advanced Research in Biotechnology,
	9600 Gudelsky Drive, Rockville, MD 20850, USA.},
  keywords = {Algorithms; Barbiturates; Entropy; Models, Chemical; Models, Molecular;
	Molecular Conformation; Receptors, GABA-A},
  owner = {emilio},
  pmid = {15469315},
  timestamp = {2010.04.21},
  url = {http://dx.doi.org/10.1021/ja047115d}
}

@ARTICLE{Chang2003,
  author = {Chia-En Chang and Michael K Gilson},
  title = {Tork: Conformational analysis method for molecules and complexes.},
  journal = {J Comput Chem},
  year = {2003},
  volume = {24},
  pages = {1987--1998},
  number = {16},
  month = {Dec},
  abstract = {A conformational search method for organic molecules and bimolecular
	complexes is presented. The method, termed Tork, uses normal-mode
	analysis in bond-angle-torsion coordinates and focuses on a key subset
	of torsional coordinates to identify natural molecular motions that
	lead the initial conformation to new energy minima. New conformations
	are generated via distortion along these modes and their pairwise
	combinations, followed by energy minimization. For complexes, special
	treatment is accorded to the six coordinates that specify the position
	and orientation of one molecule relative to the other. Tests described
	here show that Tork is highly efficient for cyclic, acyclic, and
	mixed single molecules, as well as for host-guest complexes.},
  doi = {10.1002/jcc.10325},
  institution = {Center for Advanced Research in Biotechnology, University of Maryland
	Biotechnology Institute, 9600 Gudelsky Drive, Rockville, Maryland
	20850, USA.},
  keywords = {Algorithms; Chemistry, Physical; Computer Simulation; Cycloparaffins;
	Ethers, Cyclic; Mathematical Computing; Menthol; Methods; Models,
	Chemical; Models, Molecular; Molecular Conformation; Octanes; Organic
	Chemicals; Physicochemical Phenomena; Piperidines; Thermodynamics},
  owner = {emilio},
  pmid = {14531053},
  timestamp = {2010.04.21},
  url = {http://dx.doi.org/10.1002/jcc.10325}
}

@ARTICLE{Chang2003a,
  author = {Chang, Chia-En and Potter, Michael J. and Gilson, Michael K.},
  title = {Calculation of Molecular Configuration Integrals},
  journal = {The Journal of Physical Chemistry B},
  year = {2003},
  volume = {107},
  pages = {1048--1055},
  number = {4},
  month = jan,
  abstract = {A method is presented for calculating the conformational free energy
	of a molecule in all degrees of freedom. The method uses the harmonic
	approximation with finite integration ranges, along with Mode Scanning,
	a fast correction for anharmonicity based upon internal bond-angle-torsion
	coordinates. Mode Scanning accounts for local anharmonicity without
	the need for expensive Monte Carlo integration. The method is efficient,
	and comparisons with analytic or highly detailed numerical calculations
	show excellent accuracy. Similar comparisons for the previously described
	Mode Integration method show that, although it is computationally
	demanding, it can be less accurate than the pure harmonic approximation.
	The inaccuracy of Mode Integration is traceable to its use of a Cartesian
	coordinate basis set; much more accurate results are obtained when
	the basis set consists of bond-angle-torsion coordinates.},
  comment = {doi: 10.1021/jp027149c},
  issn = {1520-6106},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2011.02.05},
  url = {http://dx.doi.org/10.1021/jp027149c}
}

@ARTICLE{Chang2007,
  author = {{Chia-en} A Chang and Wei Chen and Michael K Gilson},
  title = {Ligand configurational entropy and protein binding},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {2007},
  volume = {104},
  pages = {1534--1539},
  number = {5},
  month = {Jan},
  abstract = {The restriction of a small molecule's motion on binding to a protein
	causes a loss of configurational entropy, and thus a penalty in binding
	affinity. Some energy models used in computer-aided ligand design
	neglect this entropic penalty, whereas others account for it based
	on an expected drop in the number of accessible rotamers upon binding.
	However, the validity of the physical assumptions underlying the
	various approaches is largely unexamined. The present study addresses
	this issue by using Mining Minima calculations to analyze the association
	of amprenavir with HIV protease. The computed loss in ligand configurational
	entropy is large, contributing approximately 25 kcal/mol (4.184 kJ/kcal)
	to DeltaG degrees. Most of this loss results from narrower energy
	wells in the bound state, rather than a drop in the number of accessible
	rotamers. Coupling among rotation/translation and internal degrees
	of freedom complicates the decomposition of the entropy change into
	additive terms. The results highlight the potential to gain affinity
	by designing conformationally restricted ligands and have implications
	for the formulation of energy models for ligand scoring.},
  doi = {10.1073/pnas.0610494104},
  institution = {Department of Chemistry and Biochemistry, and Center for Theoretical
	Biological Physics, University of California at San Diego, La Jolla,
	CA 92093, USA.},
  keywords = {Algorithms; Anti-HIV Agents; Carbamates; Drug Design; Entropy; HIV
	Protease; Ligands; Models, Chemical; Models, Statistical; Molecular
	Conformation; Protein Binding; Protein Conformation; Proteins; Sulfonamides;
	Thermodynamics},
  owner = {emilio},
  pii = {0610494104},
  pmid = {17242351},
  timestamp = {2010.04.21},
  url = {http://dx.doi.org/10.1073/pnas.0610494104}
}

@ARTICLE{Charifson:97,
  author = {Charifson, P. S. and Shewchuk, L. M. and Rocque, W. and Hummel, C.
	W. and Jordan, S. R. and Mohr, C. and Pacofsky, G. J. and Peel, M.
	R. and Rodriguez, M. and Sternbach, D. D. and Consler, T. G.},
  title = {Peptide Ligands of pp60$^{\rm c-src}$ SH2 Domains: A thermodynamic
	and Structural Study},
  journal = {Biochemistry},
  year = {1997},
  volume = {36},
  pages = {6283-6293},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Che2008,
  author = {Jianwei Che and Joachim Dzubiella and Bo Li and J. Andrew McCammon},
  title = {Electrostatic free energy and its variations in implicit solvent
	models.},
  journal = {J Phys Chem B},
  year = {2008},
  volume = {112},
  pages = {3058--3069},
  number = {10},
  month = {Mar},
  abstract = {A mean-field approach to the electrostatics for solutes in electrolyte
	solution is revisited and rigorously justified. In this approach,
	an electrostatic free energy functional is constructed that depends
	solely on the local ionic concentrations. The unique set of such
	concentrations that minimize this free energy are given by the usual
	Boltzmann distributions through the electrostatic potential which
	is determined by the Poisson-Boltzmann equation. This approach is
	then applied to the variational implicit solvent description of the
	solvation of molecules [Dzubiella, Swanson, McCammon, Phys. Rev.
	Lett. 2006, 96, 087802; J. Chem. Phys. 2006, 124, 084905]. Care is
	taken for the singularities of the potential generated by the solute
	point charges. The variation of the electrostatic free energy with
	respect to the location change of solute-solvent interfaces, that
	is, dielectric boundaries, is derived. Such a variation gives rise
	to the normal component of the effective surface force per unit surface
	area that is shown to be attractive to the fixed point charges in
	the solutes. Two examples of applications are given to validate the
	analytical results. The first one is a one-dimensional model system
	resembling, for example, a charged solute or cavity in a one-dimensional
	channel. The second one, which is of its own interest, is the electrostatic
	free energy of a charged spherical solute immersed in an ionic solution.
	An analytical formula is derived for the Debye-Hückel approximation
	of the free energy, extending the classical Born's formula to one
	that includes ionic concentrations. Variations of the nonlinear Poisson-Boltzmann
	free energy are also obtained.},
  doi = {10.1021/jp7101012},
  institution = {The Genomics Institute of the Novartis Research Foundation, 10675
	John Jay Hopkins Drive, San Diego, CA 92121, USA.},
  keywords = {Models, Chemical; Solutions; Solvents, chemistry; Static Electricity},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {18275182},
  timestamp = {2011.02.03},
  url = {http://dx.doi.org/10.1021/jp7101012}
}

@ARTICLE{Cheatham1998,
  author = {T. E. Cheatham and J. Srinivasan and D. A. Case and P. A. Kollman},
  title = {Molecular dynamics and continuum solvent studies of the stability
	of polyG-polyC and polyA-polyT DNA duplexes in solution.},
  journal = {J Biomol Struct Dyn},
  year = {1998},
  volume = {16},
  pages = {265--280},
  number = {2},
  month = {Oct},
  abstract = {Molecular dynamics simulation in explicit solvent and continuum solvent
	models are applied to investigate the relative stability of A- and
	B-form helices for two DNA sequences, dA10-dT10 and dG10-dC10 in
	three structural forms. One structural form is based on an unrestrained
	molecular dynamics (MD) trajectory starting from a canonical B-DNA
	structure, the second is based on a MD trajectory starting in a canonical
	B-DNA structure with the sugars constrained to be C2'-endo and the
	third simulation started from a canonical A-DNA structure with the
	sugars constrained to C3'-endo puckers. For the energetic analysis,
	structures were taken as snapshots from nanosecond length molecular
	dynamics simulations computed in a consistent fashion in explicit
	solvent, applying the particle mesh Ewald method and the Cornell
	et al. force field. The electrostatic contributions to solvation
	free energies are computed using both a finite-difference Poisson-Boltzmann
	model and a pairwise Generalized Born model. The non-electrostatic
	contributions to the solvation free energies are estimated with a
	solvent accessible surface area dependent term. To estimate the gas
	phase component of the relative free energy between the various structures,
	the mean solute internal energies (determined with the Cornell et
	al. molecular mechanics potential including all pairwise interactions
	within the solute) and estimates of the solute entropy (using a harmonic
	approximation) were used. Consistent with experiment, the polyG-polyC
	(GC) structures are found to be much more A-phillic than the polyA-polyT
	(AT) structures, the latter being quite A-phobic. The dominant energy
	components responsible for this difference comes from the internal
	and van der Waal energies. A perhaps less appreciated difference
	between the GC and AT rich sequences is suggested by the calculated
	salt dependence which demonstrates a significantly enhanced ability
	to drive GC rich sequences towards an A-form structure compared to
	AT rich sequences. In addition to being A-phobic, the AT structure
	also has a noticably larger helical repeat than GC and other mixed
	sequence duplexes, consistent with experiment. Analysis of the average
	solvent density from the trajectories shows hydration patterns in
	qualitative agreement with experiment and previous theoretical treatments.},
  institution = {Laboratory of Biophysical Chemistry, National Heart, Lung and Blood
	Institute, National Institutes of Health, Bethesda, MD 20

repository: radical-papers/radical-references

repo_name: radical-papers/radical-references