text:
008,
  author = {Mikolai Fajer and Donald Hamelberg and J. Andrew McCammon},
  title = {Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied
	to Thermodynamic Integration.},
  journal = {J Chem Theory Comput},
  year = {2008},
  volume = {4},
  pages = {1565--1569},
  number = {10},
  month = {Oct},
  abstract = {Accelerated molecular dynamics (AMD) is an efficient strategy for
	accelerating the sampling of molecular dynamics simulations, and
	observable quantities such as free energies derived on the biased
	AMD potential can be reweighted to yield results consistent with
	the original, unmodified potential. In conventional AMD the reweighting
	procedure has an inherent statistical problem in systems with large
	acceleration, where the points with the largest biases will dominate
	the reweighted result and reduce the effective number of data points.
	We propose a replica exchange of various degrees of acceleration
	(REXAMD) to retain good statistics while achieving enhanced sampling.
	The REXAMD method is validated and benchmarked on two simple gas-phase
	model systems, and two different strategies for computing reweighted
	averages over a simulation are compared.},
  doi = {10.1021/ct800250m},
  institution = {Department of Chemistry and Biochemistry, University of California
	at San Diego, La Jolla, California 92093-0365, Center for Theoretical
	Biological Physics, University of California at San Diego, La Jolla,
	California 92039-0365, Department of Chemistry, Georgia State University,
	Atlanta, Georgia 30302-4098, Department of Pharmacology, University
	of California at San Diego, La Jolla, California 92093-0365, and
	Howard Hughes Medical Institute, University of California at San
	Diego, La Jolla, California 92093-0365.},
  owner = {emilio},
  pmid = {19461870},
  timestamp = {2010.09.13},
  url = {http://dx.doi.org/10.1021/ct800250m}
}

@ARTICLE{Fajer2009,
  author = {Mikolai Fajer and Robert V Swift and J. Andrew McCammon},
  title = {Using multistate free energy techniques to improve the efficiency
	of replica exchange accelerated molecular dynamics.},
  journal = {J Comput Chem},
  year = {2009},
  volume = {30},
  pages = {1719--1725},
  number = {11},
  month = {Aug},
  abstract = {Replica exchange accelerated molecular dynamics (REXAMD) is a method
	that enhances conformational sampling while retaining at least one
	replica on the original potential, thus avoiding the statistical
	problems of exponential reweighting. In this article, we study three
	methods that can combine the data from the accelerated replicas to
	enhance the estimate of properties on the original potential: weighted
	histogram analysis method (WHAM), pairwise multistate Bennett acceptance
	ratio (PBAR), and multistate Bennett acceptance ratio (MBAR). We
	show that the method that makes the most efficient use of equilibrium
	data from REXAMD simulations is the MBAR method. This observation
	holds for both alchemical free energy and structural observable prediction.
	The combination of REXAMD and MBAR should allow for more efficient
	scaling of the REXAMD method to larger biopolymer systems.},
  doi = {10.1002/jcc.21285},
  institution = {Department of Chemistry and Biochemistry, University of California
	at San Diego, La Jolla, California 92093-0365, USA. mfajer@gmail.com},
  keywords = {Butanes; Computer Simulation; Models, Chemical; Molecular Conformation;
	Thermodynamics},
  owner = {emilio},
  pmid = {19421994},
  timestamp = {2010.09.13},
  url = {http://dx.doi.org/10.1002/jcc.21285}
}

@ARTICLE{Fan:Mark:Zhu:Honig:2005,
  author = {Fan, H. and Mark, {A. E.} Zhu, J. and Honig, B.},
  title = {Comparative study of generalized Born models: Protein dynamics},
  journal = {Proc. Natl. Acad. Sci.},
  year = {2005},
  volume = {102},
  pages = {6760--6764},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Feig:Brooks:Review:2004,
  author = {Feig, M. and Brooks, {C. L. III}},
  title = {Recent advances in the development and application of implicit solvent
	models in biomolecule simulations},
  journal = {Curr. Op. Struct. Biol.},
  year = {2004},
  volume = {14},
  pages = {217-224},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Feig:Karanicolas:Brooks:2004,
  author = {Feig, M. and Karanicolas, J. and Brooks III, {C. L.}},
  title = {MMTSB Tool Set: enhanced sampling and multiscale modeling methods
	for applications in structural biology},
  journal = {Journal of Molecular Graphics and Modelling},
  year = {2004},
  volume = {22},
  pages = {377--395},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Feig:Brooks:2004,
  author = {Feig, M. and Onufriev, A. and Lee, {M. S.} and Im, W. and Case, {D.
	A.} and Brooks III, {C. L.}},
  title = {Performance comparison of generalized born and Poisson methods in
	the calculation of electrostatic solvation energies for protein structures},
  journal = {J. Comput. Chem.},
  year = {2004},
  volume = {25},
  pages = {265--284},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Felts:Gallicchio:Levy:2008,
  author = {Anthony K Felts and Emilio Gallicchio and Dmitriy Chekmarev and Kristina
	A Paris and Richard A Friesner and Ronald M Levy},
  title = {Prediction of Protein Loop Conformations using the AGBNP Implicit
	Solvent Model and Torsion Angle Sampling.},
  journal = {J. Chem. Theory Comput.},
  year = {2008},
  volume = {4},
  pages = {855--868},
  number = {5},
  abstract = {The OPLS-AA all-atom force field and the Analytical Generalized Born
	plus Non-Polar (AGBNP) implicit solvent model, in conjunction with
	torsion angle conformational search protocols based on the Protein
	Local Optimization Program (PLOP), are shown to be effective in predicting
	the native conformations of 57 9-residue and 35 13-residue loops
	of a diverse series of proteins with low sequence identity. The novel
	nonpolar solvation free energy estimator implemented in AGBNP augmented
	by correction terms aimed at reducing the occurrence of ion pairing
	are important to achieve the best prediction accuracy. Extended versions
	of the previously developed PLOP-based conformational search schemes
	based on calculations in the crystal environment are reported that
	are suitable for application to loop homology modeling without the
	crystal environment. Our results suggest that in general the loop
	backbone conformation is not strongly influenced by crystal packing.
	The application of the temperature Replica Exchange Molecular Dynamics
	(T-REMD) sampling method for a few examples where PLOP sampling is
	insufficient are also reported. The results reported indicate that
	the OPLS-AA/AGBNP effective potential is suitable for high-resolution
	modeling of proteins in the final stages of homology modeling and/or
	protein crystallographic refinement.},
  doi = {10.1021/ct800051k},
  institution = {Department of Chemistry and Chemical Biology and BioMaPS Institute
	for Quantitative Biology, Rutgers University, Piscataway, New Jersey
	08854.},
  owner = {emilio},
  pmid = {18787648},
  timestamp = {2010.06.14},
  url = {http://dx.doi.org/10.1021/ct800051k}
}

@ARTICLE{Felts:Gallicchio:Wallqvist:Levy:2002,
  author = {Felts, A. K. and Gallicchio, E. and Wallqvist, A. and Levy, R. M.},
  title = {Distinguishing Native Conformations of Proteins from Decoys with
	an Effective Free Energy Estimator based on the OPLS All-Atom Force
	Field and the Surface Generalized Born Solvent Model},
  journal = {Proteins: Structure, Function and Genetics},
  year = {2002},
  volume = {48},
  pages = {404-422},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Felts:Harano:Gallicchio:Levy:2004,
  author = {Felts, A. K. and Harano, Y. and Gallicchio, E. and Levy, R. M.},
  title = {Free energy surfaces of beta-hairpin and alpha-helical peptides generated
	by replica exchange molecular dynamics with the AGBNP implicit solvent
	model},
  journal = {Proteins: Struct., Funct., Bioinf.},
  year = {2004},
  volume = {56},
  pages = {310--321},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Felts2011,
  author = {Anthony K Felts and Krystal Labarge and Joseph D Bauman and Dishaben
	V Patel and Daniel M Himmel and Eddy Arnold and Michael A Parniak
	and Ronald M Levy},
  title = {Identification of alternative binding sites for inhibitors of HIV-1
	ribonuclease H through comparative analysis of virtual enrichment
	studies.},
  journal = {J Chem Inf Model},
  year = {2011},
  volume = {51},
  pages = {1986--1998},
  number = {8},
  month = {Aug},
  __markedentry = {[emilio]},
  abstract = {The ribonuclease H (RNase H) domain on the p66 monomer of HIV-1 reverse
	transcriptase enzyme has become a target for inhibition. The active
	site is one potential binding site, but other RNase H sites can accommodate
	inhibitors. Using a combination of experimental and computational
	studies, potential new binding sites and binding modes have been
	identified. Libraries of compounds were screened with an experimental
	assay to identify actives without knowledge of the binding site.
	The compounds were computationally docked at putative binding sites.
	Based on positive enrichment of natural-product actives relative
	to the database of compounds, we propose that many inhibitors bind
	to an alternative, potentially allosteric, site centered on Q507
	of p66. For a series of hydrazone compounds, a small amount of positive
	enrichment was obtained when active compounds were bound by induced-fit
	docking at the interface between the DNA:RNA substrate and the RNase
	H domain near residue Q500.},
  doi = {10.1021/ci200194w},
  institution = {BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway,
	New Jersey 08854, USA. felts@lutece.rutgers.edu},
  keywords = {Allosteric Site, drug effects; Binding Sites; Catalytic Domain, drug
	effects; Computer Simulation; Glutamine, chemistry/genetics/metabolism;
	HIV Infections, drug therapy/virology; HIV Reverse Transcriptase,
	analysis/chemistry/metabolism; HIV-1, chemistry/enzymology; Humans;
	Hydrazines, chemistry/metabolism/pharmacology; Hydrazones, chemistry/metabolism/pharmacology;
	Models, Molecular; Protein Binding; Protein Structure, Tertiary;
	ROC Curve; Reverse Transcriptase Inhibitors, chemistry/metabolism/pharmacology;
	Ribonuclease H, analysis/chemistry/metabolism; Small Molecule Libraries},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {21714567},
  timestamp = {2012.07.13},
  url = {http://dx.doi.org/10.1021/ci200194w}
}

@INBOOK{Felts:Andrec:Gallicchio:Levy:2008,
  title = {Water and Biomolecules - Physical Chemistry of Life Phenomena},
  publisher = {Springer Science},
  year = {2008},
  author = {Felts, {A. K.} and Andrec, M. and Gallicchio, E. and Levy, {R. M.}},
  abstract = {Protein Folding and Binding: Effective Potentials, Replica Exchange
	Simulations, and Network Models},
  owner = {emilio},
  timestamp = {2010.07.15}
}

@ARTICLE{Fernandez:Crovetto:89,
  author = {Fernandez-Prini, R. and Crovetto, R.},
  journal = {J. Phys. Chem. Ref. Data},
  year = {1989},
  volume = {18},
  pages = {1231},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Ferrari2004,
  author = {Anna Maria Ferrari and Binqing Q Wei and Luca Costantino and Brian
	K Shoichet},
  title = {Soft docking and multiple receptor conformations in virtual screening.},
  journal = {J Med Chem},
  year = {2004},
  volume = {47},
  pages = {5076--5084},
  number = {21},
  month = {Oct},
  abstract = {Protein conformational change is an important consideration in ligand-docking
	screens, but it is difficult to predict. A simple way to account
	for protein flexibility is to soften the criterion for steric fit
	between ligand and receptor. A more comprehensive but more expensive
	method would be to sample multiple receptor conformations explicitly.
	Here, these two approaches are compared. A "soft" scoring function
	was created by attenuating the repulsive term in the Lennard-Jones
	potential, allowing for a closer approach between ligand and protein.
	The standard, "hard" Lennard-Jones potential was used for docking
	to multiple receptor conformations. The Available Chemicals Directory
	(ACD) was screened against two cavity sites in the T4 lysozyme. These
	sites undergo small but significant conformational changes on ligand
	binding, making them good systems for soft docking. The ACD was also
	screened against the drug target aldose reductase, which can undergo
	large conformational changes on ligand binding. We evaluated the
	ability of the scoring functions to identify known ligands from among
	the over 200 000 decoy molecules in the database. The soft potential
	was always better at identifying known ligands than the hard scoring
	function when only a single receptor conformation was used. Conversely,
	the soft function was worse at identifying known leads than the hard
	function when multiple receptor conformations were used. This was
	true even for the cavity sites and was especially true for aldose
	reductase. To test the multiple-conformation method predictively,
	we screened the ACD for molecules that preferentially docked to the
	expanded conformation of aldose reductase, known to bind larger ligands.
	Six novel molecules that ranked among the top 0.66\% of hits from
	the multiple-conformation calculation, but ranked relatively poorly
	in the soft docking calculation, were tested experimentally for enzyme
	inhibition. Four of these six inhibited the enzyme, the best with
	an IC(50) of 8 microM. Although ligands can get better scores in
	soft docking, the same is also true for decoys. The improved ranking
	of such decoys can come at the expense of true ligands.},
  doi = {10.1021/jm049756p},
  institution = {Department of Pharmaceutical Chemistry, University of California-San
	Francisco, Genentech Hall, 600 16th Street, San Francisico, CA 94143-2240,
	USA.},
  keywords = {Aldehyde Reductase; Bacteriophage T4; Binding Sites; Ligands; Models,
	Molecular; Muramidase; Protein Binding; Protein Conformation; Quantitative
	Structure-Activity Relationship},
  owner = {emilio},
  pmid = {15456251},
  timestamp = {2010.10.27},
  url = {http://dx.doi.org/10.1021/jm049756p}
}

@ARTICLE{Ferrari2003,
  author = {Stefania Ferrari and Paola M Costi and Rebecca C Wade},
  title = {Inhibitor specificity via protein dynamics: insights from the design
	of antibacterial agents targeted against thymidylate synthase.},
  journal = {Chem Biol},
  year = {2003},
  volume = {10},
  pages = {1183--1193},
  number = {12},
  month = {Dec},
  abstract = {Structure-based drug design of species-specific inhibitors generally
	exploits structural differences in proteins from different organisms.
	Here, we demonstrate how achieving specificity can be aided by targeting
	differences in the dynamics of proteins. Thymidylate synthase (TS)
	is a good target for anticancer agents and a potential target for
	antibacterial agents. Most inhibitors are folate-analogs that bind
	at the folate binding site and are not species specific. In contrast,
	alpha156 is not a folate-analog and is specific for bacterial TS;
	it has been shown crystallographically to bind in a nonconserved
	binding site. Docking calculations and crystal structure-based estimation
	of the essential dynamics of TSs from five different species show
	that differences in the dynamics of TSs make the active site more
	accessible to alpha156 in the prokaryotic than in the eukaryotic
	TSs and thereby enhance the specificity of alpha156.},
  institution = {Dipartimento di Scienze Farmaceutiche, Università di Modena e Reggio
	Emilia, Via Campi 183, 41100 Modena, Italy. ferrari.stefania@unimore.it},
  keywords = {Anti-Bacterial Agents; Binding Sites; Drug Design; Enzyme Inhibitors;
	Models, Molecular; Pliability; Protein Conformation; Protein Structure,
	Tertiary; Software; Substrate Specificity; Thymidylate Synthase},
  owner = {emilio},
  pii = {S1074552103002655},
  pmid = {14700626},
  timestamp = {2010.09.07}
}

@ARTICLE{Ferrenberg:Swendsen:89,
  author = {Ferrenberg, A. M. and Swendsen, R. H.},
  title = {Optimized Monte Carlo Data Analysis},
  journal = {Phys. Rev. Lett.},
  year = {1989},
  volume = {63},
  pages = {1195-1198},
  owner = {emilio},
  timestamp = {2011.02.08}
}

@ARTICLE{Ferrenberg:Swendsen:89a,
  author = {Ferrenberg, A. M. and Swendsen, R. H.},
  title = {Optimized Monte Carlo Data Analysis},
  journal = {Computers in Physics},
  year = {1989},
  volume = {Sep/Oct},
  pages = {101-104},
  owner = {emilio},
  timestamp = {2011.02.08}
}

@ARTICLE{Figueirido:97a,
  author = {Figueirido, F. and Del Buono, G. and Levy, R. M.},
  journal = {J. Phys. Chem. B},
  year = {1997},
  volume = {101},
  pages = {5622-5623},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Figueirido:96,
  author = {Figueirido, F. and Del Buono, G. and Levy, R. M.},
  journal = {J. Phys. Chem.},
  year = {1996},
  volume = {100},
  pages = {6389-6392},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Figueirido:95,
  author = {Figueirido, F. and Del Buono, G. and Levy, R. M.},
  journal = {J. Chem. Phys.},
  year = {1995},
  volume = {103},
  pages = {6133-6142},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Figueirido:94,
  author = {Figueirido, F. and Del Buono, G. and Levy, R. M.},
  title = {Molecular Mechanics and Electrostatic Effects},
  journal = {Biophys. Chem.},
  year = {1994},
  volume = {51},
  pages = {235-241},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Figueirido:97b,
  author = {Figueirido, F. and Levy, R. M. and Zhou, R. and Berne, B. J.},
  title = {Large scale simulation of macromolecules in solution: combining the
	periodic fast multiple method with multiple time step integrators},
  journal = {J. Chem. Phys.},
  year = {1997},
  volume = {106},
  pages = {9835-9849},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@BOOK{AlexeiV.Finkelstein2002,
  title = {Protein Physics},
  publisher = {Academic Press, San Diego CA},
  year = {2002},
  author = {Alexei V. Finkelstein and Oleg Ptitsyn},
  owner = {mauro},
  timestamp = {2011.08.04}
}

@ARTICLE{Fleischman:Brooks:87,
  author = {Fleischman, S. H. and Brooks, C. L.},
  journal = {J. Chem. Phys.},
  year = {1987},
  volume = {87},
  pages = {3029},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Florian:Goodman:Warshel:2002,
  author = {Flori\'{a}n, J. and Goodman, {M. F.} and Warshel, A.},
  title = {Theoretical Investigation of the Binding Free Energies and key substrate-recognition
	components of the replication fidelity of human {DNA} polymerase
	$\beta$},
  journal = {J. Phys. Chem. B},
  year = {2002},
  volume = {106},
  pages = {5739--5753},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Floris:Tomasi:89,
  author = {F. Floris and J. Tomasi},
  journal = {J. Comput. Chem.},
  year = {1989},
  volume = {10},
  pages = {616},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Fogolari:Esposito:Viglino:Molinari:2001,
  author = {Fogolari, F. and Esposito, G. and Viglino, P. and Molinari, H.},
  title = {Molecular Mechanics and Dynamics of Biomolecules Using a Solvent
	Continuum Model},
  journal = {J. Comp. Chem.},
  year = {2001},
  volume = {22},
  pages = {1830-1842},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Foloppe2006,
  author = {N. Foloppe and R. Hubbard},
  title = {Towards predictive ligand design with free-energy based computational
	methods?},
  journal = {Curr Med Chem},
  year = {2006},
  volume = {13},
  pages = {3583--3608},
  number = {29},
  abstract = {The accurate prediction of ligand-biopolymer binding affinities is
	of general interest to medicinal chemistry, as well as to the broader
	field of molecular recognition. The ability to predict computationally
	the thermodynamics of these molecular recognition processes has been
	relatively weak until recently, however, continued developments on
	several fronts are extending the scope of applicability of these
	methods. The rapid growth in the number of protein-ligand structures
	has initially led to the development of a range of empirical scoring
	functions based on relatively simple descriptions of intermolecular
	interactions. These methods have had some success in ranking binding
	affinities when tuned to particular protein systems or in rather
	qualitative estimates of molecular fit in fast docking calculations.
	However, they are too unreliable for more detailed, quantitative,
	assessment and comparison of binding affinities. Physics-based free
	energy calculations are in principle more general and have the potential
	to be significantly more accurate. These approaches have seen steady
	development over many years and rely on carefully calibrated molecular
	energy functions (force-fields), simulations of the systems with
	explicit solvent, and the coming-of-age of continuum solvation models.
	In addition to the initially developped Free Energy Perturbation
	(FEP) and Thermodynamic Integration (TI) methods, new approaches
	include the Molecular Mechanics-Poisson-Boltzmann Surface Area (MM-PBSA)
	and the Linear Interaction Energy (LIE) approaches. This review concentrates
	on MM-PBSA and LIE, and their variants. The routine application of
	these calculations is becoming possible because of enhanced computational
	hardware and the development of a range of computational chemistry
	tools. This review addresses: i) the basic principles behind free
	energy calculations ii) recent methodological advances iii) comparisons
	of predicted and experimentally determined affinities iv) the uncertainties
	and limitations of both the computational and experimental data v)
	areas where progress can be made vi) the practicality of applying
	the methods at the different stages of the drug discovery and optimization
	process.},
  institution = {D) Ltd, Granta Park, Abington, Cambridge CB1 6GB, UK. n.foloppe@vernalis.com},
  keywords = {Animals; Drug Design; Humans; Ligands; Models, Molecular; Protein
	Binding; Proteins; Thermodynamics},
  owner = {emilio},
  pmid = {17168725},
  timestamp = {2010.09.23}
}

@ARTICLE{Forsman:Jonsson:94,
  author = {Forsman, J. and {J\"{o}}nsson, B.},
  title = {Monte Carlo Simulations of Hydrophobic Interactions: A Test Particle
	Approach},
  journal = {J. Chem. Phys.},
  year = {1994},
  volume = {101},
  pages = {5116},
  number = {6},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Frank:Evans:45,
  author = {Frank, H. S. and Evans, M. W.},
  title = {Free Volume and Entropy in Condensed Systems. III. Entropy in Binary
	Liquid Mixtures; Partial Molal Entropy in Dilute Solutions; Structure
	and Thermodynamics in Aqueous Electrolytes},
  journal = {J. Chem. Phys.},
  year = {1945},
  volume = {13},
  pages = {507-532},
  number = {11},
  optannote = {First paper that talks about the iceberg model of the hydrophobic
	effect},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@PHDTHESIS{YuliaThesis2009,
  author = {Yulia Frenkel},
  title = {The roles of structural variability and amphiphilicity of {TMC278}/rilpivirine
	in mechanisms of {HIV} drug resistance avoidance and enhanced oral
	bioavailability},
  school = {Rutgers University},
  year = {2009},
  owner = {emilio},
  timestamp = {2012.02.28},
  url = {http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.000051347}
}

@ARTICLE{Frenkel2005,
  author = {Frenkel, Yulia Volovik and Clark, Arthur D. and Das, Kalyan and Wang,
	Yuh-Hwa and Lewi, Paul J. and Janssen, Paul A. J. and Arnold, Eddy},
  title = {Concentration and pH Dependent Aggregation of Hydrophobic Drug Molecules
	and Relevance to Oral Bioavailability},
  journal = {J. Med. Chem.},
  year = {2005},
  volume = {48},
  pages = {1974--1983},
  number = {6},
  month = feb,
  abstract = {We have examined selected physicochemical properties of compounds
	from the diaryltriazine/diarylpyrimidine (DATA/DAPY) classes of non-nucleoside
	reverse transcriptase inhibitors (NNRTIs) and explored possible correlations
	with their bioavailability. In simple aqueous solutions designed
	to mimic the gastrointestinal (GI) environment of a fasting individual,
	all NNRTIs demonstrated formation of aggregates as detected by dynamic
	light scattering and electron microscopy. Under various conditions
	mimicking physiological transitions in the GI environment, aggregate
	size distributions were shown to depend on compound concentration
	and pH. NNRTIs with good absorption were capable of forming aggregates
	with hydrodynamic radii of ≤100 nm at higher concentrations and over
	wide ranges of pH, while poorly absorbed inhibitors form aggregates
	with radii of ≥250 nm at concentrations above 0.01 mM, probably representing
	precipitate. We propose a model in which the uptake rate into systemic
	circulation depends on having hydrophobic drug aggregates of appropriate
	size available for absorption at different locations within the GI
	tract.

	We have examined selected physicochemical properties of compounds
	from the diaryltriazine/diarylpyrimidine (DATA/DAPY) classes of non-nucleoside
	reverse transcriptase inhibitors (NNRTIs) and explored possible correlations
	with their bioavailability. In simple aqueous solutions designed
	to mimic the gastrointestinal (GI) environment of a fasting individual,
	all NNRTIs demonstrated formation of aggregates as detected by dynamic
	light scattering and electron microscopy. Under various conditions
	mimicking physiological transitions in the GI environment, aggregate
	size distributions were shown to depend on compound concentration
	and pH. NNRTIs with good absorption were capable of forming aggregates
	with hydrodynamic radii of ≤100 nm at higher concentrations and over
	wide ranges of pH, while poorly absorbed inhibitors form aggregates
	with radii of ≥250 nm at concentrations above 0.01 mM, probably representing
	precipitate. We propose a model in which the uptake rate into systemic
	circulation depends on having hydrophobic drug aggregates of appropriate
	size available for absorption at different locations within the GI
	tract.},
  booktitle = {Journal of Medicinal Chemistry},
  comment = {doi: 10.1021/jm049439i},
  issn = {0022-2623},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2012.02.23},
  url = {http://dx.doi.org/10.1021/jm049439i}
}

@ARTICLE{Frenkel2009,
  author = {Yulia Volovik Frenkel and Emilio Gallicchio and Kalyan Das and Ronald
	M Levy and Eddy Arnold},
  title = {Molecular dynamics study of non-nucleoside reverse transcriptase
	inhibitor 4-[[4-[[4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl]amino]-2-pyrimidinyl]amino]benzonitrile
	(TMC278/rilpivirine) aggregates: correlation between amphiphilic
	properties of the drug and oral bioavailability.},
  journal = {J Med Chem},
  year = {2009},
  volume = {52},
  pages = {5896--5905},
  number = {19},
  month = {Oct},
  abstract = {The non-nucleoside reverse transcriptase inhibitor (NNRTI) TMC278/rilpivirine
	is an anti-AIDS therapeutic agent with high oral bioavailability
	despite its high hydrophobicity. Previous studies established a correlation
	between ability of the drug molecule to form stable, homogeneous
	populations of spherical nanoparticles (approximately 100-120 nm
	in diameter) at low pH in surfactant-independent fashion and good
	oral bioavailability. Here, we hypothesize that the drug is able
	to assume surfactant-like properties under physiologically relevant
	conditions, thus facilitating formation of nanostructures in the
	absence of other surfactants. The results of all-atom molecular dynamics
	simulations indeed show that protonated drug molecules behave as
	surfactants at the water/aggregate interface while neutral drug molecules
	assist aggregate packing via conformational variability. Our simulation
	results suggest that amphiphilic behavior at low pH and intrinsic
	flexibility influence drug aggregation and are believed to play critical
	roles in the favorable oral bioavailability of hydrophobic drugs.},
  doi = {10.1021/jm900282z},
  institution = {Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey
	08854, USA.},
  keywords = {Biological Availability; Hydrogen-Ion Concentration; Hydrophobicity;
	Molecular Conformation; Nanoparticles; Nitriles; Pyrimidines; Reverse
	Transcriptase Inhibitors; Surface Properties; Surface-Active Agents},
  owner = {emilio},
  pmid = {19739675},
  timestamp = {2010.07.14},
  url = {http://dx.doi.org/10.1021/jm900282z}
}

@ARTICLE{Friedman:75,
  author = {Friedman, H. L.},
  journal = {Mol. Phys.},
  year = {1975},
  volume = {29},
  pages = {1533-1538},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@BOOK{Frisch:Trucks:H-G:Gill:Wong:Pople:92,
  title = {Gaussian 92},
  publisher = {Gaussian Inc.},
  year = {1992},
  author = {Frisch, M. J. and Trucks, G. W. and Head-Gordon, M. and Gill, P.
	M. W. and Wong, M. W. and Foresman, J. B. and Johnson, B. G. and
	Schlegel, H. B. and Robb, M. A. and Replogle, E. S. and Gomperts,
	R. and Andres, J. L. and Raghavachari, K. and Binkley, J. S. and
	Gonzalez, C. and Martin, R. L. and Fox, D. J. and Defrees, D. J.
	and Baker, J. and Stewart, J. J. P. and Pople J. A.},
  address = {Pittsburgh PA},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@BOOK{Frisch:Trucks:Schlegel:Gill:Johnson:Pople:94,
  title = {Gaussian 94},
  publisher = {Gaussian Inc.},
  year = {1995},
  author = {Frisch, M. J. and Trucks, G. W. and Schlegel, H. B. and Gill, P.
	M. W. and Johnson, B. G. and Robb, M. A. and Cheeseman, J. R. and
	Keith, T. and Petersson, G. A. and Montgomery, J. A. and Raghavachari,
	K. and Al-Laham, M. A. and Zakrzewski, V. G. and Ortiz, J. V. and
	Foresman, J. B. and Cioslowski, J. and Stefanov, B. B. and Nanayakkara,
	A. and Challacombe, M. and Peng, C. Y. and Ayala, P. Y. and Chen,
	W. and Wong, M. W. and Andres, J. L. and Replogle, E. S. and Gomperts,
	R. and Martin, R. L. and Fox, D. J. and Binkley, J. S. and Defrees,
	D. J. and Baker, J. and Stewart, J. P. and Head-Gordon, M. and Gonzalez,
	C. and Pople, J. A.},
  address = {Pittsburgh PA},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Froloff1997,
  author = {N. Froloff and A. Windemuth and B. Honig},
  title = {On the calculation of binding free energies using continuum methods:
	application to MHC class I protein-peptide interactions.},
  journal = {Protein Sci},
  year = {1997},
  volume = {6},
  pages = {1293--1301},
  number = {6},
  month = {Jun},
  abstract = {This paper describes a methodology to calculate the binding free energy
	(delta G) of a protein-ligand complex using a continuum model of
	the solvent. A formal thermodynamic cycle is used to decompose the
	binding free energy into electrostatic and non-electrostatic contributions.
	In this cycle, the reactants are discharged in water, associated
	as purely nonpolar entities, and the final complex is then recharged.
	The total electrostatic free energies of the protein, the ligand,
	and the complex in water are calculated with the finite difference
	Poisson-Boltzmann (FDPB) method. The nonpolar (hydrophobic) binding
	free energy is calculated using a free energy-surface area relationship,
	with a single alkane/water surface tension coefficient (gamma aw).
	The loss in backbone and side-chain configurational entropy upon
	binding is estimated and added to the electrostatic and the nonpolar
	components of delta G. The methodology is applied to the binding
	of the murine MHC class I protein H-2Kb with three distinct peptides,
	and to the human MHC class I protein HLA-A2 in complex with five
	different peptides. Despite significant differences in the amino
	acid sequences of the different peptides, the experimental binding
	free energy differences (delta delta Gexp) are quite small (< 0.3
	and < 2.7 kcal/mol for the H-2Kb and HLA-A2 complexes, respectively).
	For each protein, the calculations are successful in reproducing
	a fairly small range of values for delta delta Gcalc (< 4.4 and <
	5.2 kcal/mol, respectively) although the relative peptide binding
	affinities of H-2Kb and HLA-A2 are not reproduced. For all protein-peptide
	complexes that were treated, it was found that electrostatic interactions
	oppose binding whereas nonpolar interactions drive complex formation.
	The two types of interactions appear to be correlated in that larger
	nonpolar contributions to binding are generally opposed by increased
	electrostatic contributions favoring dissociation. The factors that
	drive the binding of peptides to MHC proteins are discussed in light
	of our results.},
  doi = {10.1002/pro.5560060617},
  institution = {Department of Biochemistry and Molecular Biophysics, Columbia University,
	New York, New York 10032, USA.},
  keywords = {Animals; Computer Simulation; H-2 Antigens; HLA-A2 Antigen; Histocompatibility
	Antigens Class I; Humans; Mice; Models, Chemical; Peptides; Poisson
	Distribution; Protein Binding; Sensitivity and Specificity; Solvents;
	Static Electricity; Thermodynamics; Water},
  owner = {emilio},
  pmid = {9194189},
  timestamp = {2010.04.20},
  url = {http://dx.doi.org/10.1002/pro.5560060617}
}

@ARTICLE{Froloff:Windemuth:Honig:97,
  author = {Froloff, N. and Windemuth, A. and Honig, B.},
  title = {On the calculation of binding free energies using continuum methods:
	Application to {MHC} class {I} protein-peptide interactions},
  journal = {Protein Science},
  year = {1997},
  volume = {6},
  pages = {1293-1301},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Fujitani2005,
  author = {Hideaki Fujitani and Yoshiaki Tanida and Masakatsu Ito and Guha Jayachandran
	and Christopher D Snow and Michael R Shirts and Eric J Sorin and
	Vijay S Pande},
  title = {Direct calculation of the binding free energies of FKBP ligands.},
  journal = {J. Chem. Phys.},
  year = {2005},
  volume = {123},
  pages = {084108},
  number = {8},
  month = {Aug},
  abstract = {Direct calculations of the absolute free energies of binding for eight
	ligands to FKBP protein were performed using the Fujitsu BioServer
	massively parallel computer. Using the latest version of the general
	assisted model building with energy refinement (AMBER) force field
	for ligand model parameters and the Bennett acceptance ratio for
	computing free-energy differences, we obtained an excellent linear
	fit between the calculated and experimental binding free energies.
	The rms error from a linear fit is 0.4 kcal/mol for eight ligand
	complexes. In comparison with a previous study of the binding energies
	of these same eight ligand complexes, these results suggest that
	the use of improved model parameters can lead to more predictive
	binding estimates, and that these estimates can be obtained with
	significantly less computer time than previously thought. These findings
	make such direct methods more attractive for use in rational drug
	design.},
  doi = {10.1063/1.1999637},
  institution = {Fujitsu Laboratories Ltd., 10-1 Morinosato-Wakamiya, Atsugi 243-0197,
	Japan. fjtani@labs.fujitsu.com},
  keywords = {Biophysics; Chemistry, Physical; Dose-Response Relationship, Drug;
	Drug Design; Entropy; Humans; Ligands; Models, Chemical; Models,
	Theoretical; Molecular Conformation; Protein Binding; Protein Conformation;
	Tacrolimus Binding Proteins; Thermodynamics; Time Factors},
  owner = {emilio},
  pmid = {16164283},
  timestamp = {2010.04.29},
  url = {http://dx.doi.org/10.1063/1.1999637}
}

@UNPUBLISHED{Fukunishi:97,
  author = {Yoshifumi Fukunishi},
  year = {1997},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Gallicchio2012b,
  author = {Gallicchio, E.},
  title = {Role of Ligand Reorganization and Conformational Restraints on the
	Binding Free Energies of DAPY Non-Nucleoside Inhibitors to HIV Reverse
	Transcriptase},
  journal = {Molecular Biosciences},
  year = {2012},
  volume = {2},
  pages = {7-22},
  doi = {10.4236/cmb.2012.21002},
  owner = {emilio},
  timestamp = {2011.07.15},
  url = {http://dx.doi.org/10.4236/cmb.2012.21002}
}

@ARTICLE{Gallicchio:Andrec:Felts:Levy:2005,
  author = {Gallicchio, E. and Andrec, M. and Felts, A. K. and Levy, R. M.},
  title = {Temperature Weighted Histogram Analysis Method, Replica Exchange,
	and Transition Paths},
  journal = {J. Phys. Chem. B},
  year = {2005},
  volume = {109},
  pages = {6722--6731},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Gallicchio:Kubo:Levy:2000,
  author = {Gallicchio, E. and Kubo, M. M. and Levy, R. M.},
  title = {Enthalpy-Entropy and Cavity Decomposition of Alkane Hydration Free
	Energies: Numerical Results and Implications for Theories of Hydrophobic
	Solvation},
  journal = {J. Phys. Chem. B},
  year = {2000},
  volume = {104},
  pages = {6271-6285},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Gallicchio:Kubo:Levy:98,
  author = {Gallicchio, E. and Kubo, M. M. and Levy, R. M.},
  title = {Entropy-Enthalpy Compensation in Solvation and Ligand Binding Revisited},
  journal = {J. Am. Chem. Soc.},
  year = {1998},
  volume = {120},
  pages = {4526-27},
  number = {18},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Gallicchio2010,
  author = {Gallicchio, Emilio and Lapelosa, Mauro and Levy, Ronald M.},
  title = {Binding Energy Distribution Analysis Method ({BEDAM}) for Estimation
	of Protein-Ligand Binding Affinities},
  journal = {J. Chem. Theory Comput.},
  year = {2010},
  volume = {6},
  pages = {2961--2977},
  number = {9},
  month = sep,
  abstract = {The binding energy distribution analysis method (BEDAM) for the computation
	of receptor−ligand standard binding free energies with implicit solvation
	is presented. The method is based on a well-established statistical
	mechanics theory of molecular association. It is shown that, in the
	context of implicit solvation, the theory is homologous to the test
	particle method of solvation thermodynamics with the solute−solvent
	potential represented by the effective binding energy of the protein−ligand
	complex. Accordingly, in BEDAM the binding constant is computed by
	means of a weighted integral of the probability distribution of the
	binding energy obtained in the canonical ensemble in which the ligand
	is positioned in the binding site but the receptor and the ligand
	interact only with the solvent continuum. It is shown that the binding
	energy distribution encodes all of the physical effects of binding.
	The balance between binding enthalpy and entropy is seen in our formalism
	as a balance between favorable and unfavorable binding modes which
	are coupled through the normalization of the binding energy distribution
	function. An efficient computational protocol for the binding energy
	distribution based on the AGBNP2 implicit solvent model, parallel
	Hamiltonian replica exchange sampling, and histogram reweighting
	is developed. Applications of the method to a set of known binders
	and nonbinders of the L99A and L99A/M102Q mutants of T4 lysozyme
	receptor are illustrated. The method is able to discriminate without
	error binders from nonbinders, and the computed standard binding
	free energies of the binders are found to be in good agreement with
	experimental measurements. Analysis of the results reveals that the
	binding affinities of these systems reflect the contributions from
	multiple conformations spanning a wide range of binding energies.},
  comment = {doi: 10.1021/ct1002913},
  issn = {1549-9618},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2010.09.17},
  url = {http://dx.doi.org/10.1021/ct1002913}
}

@INBOOK{Gallicchio2011adv,
  chapter = {Recent Theoretical and Computational Advances for Modeling Protein-Ligand
	Binding Affinities},
  pages = {27-80},
  title = {Advances in Protein Chemistry and Structural Biology, vol. 85},
  publisher = {Academic Press},
  year = {2011},
  editor = {Christo Christov},
  author = {Emilio Gallicchio and Ronald M Levy},
  owner = {emilio},
  timestamp = {2011.09.28}
}

@UNPUBLISHED{Gallicchio:trypsin:SAMPL3:2012,
  author = {Emilio Gallicchio and Ronald M Levy},
  title = {Fragment screening and binding affinity estimation of the trypsin
	SAMPL3 dataset using the BEDAM method},
  note = {In preparation},
  owner = {emilio},
  timestamp = {2012.07.13}
}

@ARTICLE{Gallicchio2012a,
  author = {Gallicchio, E. and Levy, R. M.},
  title = {Prediction of SAMPL3 Host-Guest Affinities with the Binding Energy
	Distribution Analysis Method {(BEDAM)}},
  journal = {J Comp Aided Mol Design},
  year = {2012},
  volume = {Online First},
  doi = {10.1007/s10822-012-9552-3},
  owner = {emilio},
  timestamp = {2012.02.20},
  url = {http://dx.doi.org/10.1007/s10822-012-9552-3}
}

@ARTICLE{Gallicchio2011,
  author = {Gallicchio, Emilio and Levy, Ronald M},
  title = {Advances in all atom sampling methods for modeling protein-ligand
	binding affinities},
  journal = {Curr. Opin. Struct. Biol.},
  year = {2011},
  volume = {21},
  pages = {161--166},
  number = {2},
  month = apr,
  abstract = {Conformational dynamics plays a fundamental role in the regulation
	of molecular recognition processes. Conformational heterogeneity
	and entropy variations upon binding, although not always evident
	from the analysis of structural data, can substantially affect affinity
	and specificity. Computer modeling is able to provide some of the
	most direct insights into these aspects of molecular recognition.
	We review recent physics-based computational studies that employ
	advanced conformational sampling algorithms and effective potentials
	to model the three main classes of degrees of freedom relevant to
	the binding process: ligand positioning relative to the receptor,
	ligand and receptor internal reorganization, and hydration. Collectively
	these studies show that all of these elements are important for proper
	modeling of protein-ligand interactions.},
  issn = {0959-440X},
  owner = {emilio},
  timestamp = {2011.04.01},
  url = {http://www.sciencedirect.com/science/article/B6VS6-526YJJ9-1/2/0fde71fb14495534e8a5146128463e21}
}

@ARTICLE{Gallicchio2008,
  author = {Gallicchio, Emilio and Levy, Ronald M. and Parashar, Manish},
  title = {Asynchronous replica exchange for molecular simulations},
  journal = {J. Comp. Chem.},
  year = {2008},
  volume = {29},
  pages = {788--794},
  number = {5},
  abstract = {An asynchronous implementation of the replica exchange method that
	addresses some of the limitations of conventional synchronous replica
	exchange implementations is presented. In asynchronous replica exchange
	pairs of processors initiate and perform temperature replica exchanges
	independently from the other processors, thereby removing the need
	for processor synchronization found in conventional synchronous implementations.
	Illustrative calculations on a molecular system are presented that
	show that asynchronous replica exchange, contrary to the synchronous
	implementation, is able to utilize at nearly top efficiency loosely
	coupled pools of processors with heterogeneous speeds, such as those
	found in computational grids and CPU scavenging environments. It
	is also shown that employing non-nearest-neighbor temperature exchanges,
	which are straightforward to implement within the asynchronous algorithm,
	can lead to faster temperature equilibration across processors. �
	2007 Wiley Periodicals, Inc. J Comput Chem, 2008},
  owner = {emilio},
  timestamp = {2010.07.14},
  url = {http://dx.doi.org/10.1002/jcc.20839}
}

@ARTICLE{Gallicchio:Levy:2004,
  author = {Gallicchio, E. and Levy, {R. M.}},
  title = {{AGBNP}: an analytic implicit solvent model suitable for molecular
	dynamics simulations and high-resolution modeling},
  journal = {J. Comput. Chem.},
  year = {2004},
  volume = {25},
  pages = {479--499},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Gallicchio2009,
  author = {Gallicchio, Emilio and Paris, Kristina and Levy, Ronald M.},
  title = {The AGBNP2 Implicit Solvation Model},
  journal = {J. Chem. Theory Comput.},
  year = {2009},
  volume = {5},
  pages = {2544--2564},
  number = {9},
  month = sep,
  abstract = {The AGBNP2 implicit solvent model, an evolution of the Analytical
	Generalized Born plus NonPolar (AGBNP) model we have previously reported,
	is presented with the aim of modeling hydration effects beyond those
	described by conventional continuum dielectric representations. A
	new empirical hydration free energy component based on a procedure
	to locate and score hydration sites on the solute surface is introduced
	to model first solvation shell effects, such as hydrogen bonding,
	which are poorly described by continuum dielectric models. This new
	component is added to the generalized Born and nonpolar AGBNP terms.
	Also newly introduced is an analytical Solvent Excluded Volume (SEV)
	model which improves the solute volume description by reducing the
	effect of spurious high dielectric interstitial spaces present in
	conventional van der Waals representations. The AGBNP2 model is parametrized
	and tested with respect to experimental hydration free energies of
	small molecules and the results of explicit solvent simulations.
	Modeling the granularity of water is one of the main design principles
	employed for the first shell solvation function and the SEV model,
	by requiring that water locations have a minimum available volume
	based on the size of a water molecule. It is shown that the new volumetric
	model produces Born radii and surface areas in good agreement with
	accurate numerical evaluations of these quantities. The results of
	molecular dynamics simulations of a series of miniproteins show that
	the new model produces conformational ensembles in substantially
	better agreement with reference explicit solvent ensembles than the
	original AGBNP model with respect to both structural and energetics
	measures.},
  comment = {doi: 10.1021/ct900234u},
  issn = {1549-9618},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2010.04.23},
  url = {http://dx.doi.org/10.1021/ct900234u}
}

@ARTICLE{Gallicchio:Zhang:Levy:2002,
  author = {Gallicchio, E. and Zhang, L. Y. and Levy, R. M.},
  title = {The SGB/NP Hydration Free Energy Model Based on the Surface Generalized
	Born Solvent Reaction Field and Novel Non-Polar Hydration Free Energy
	Estimators},
  journal = {J. Comp. Chem.},
  year = {2002},
  volume = {23},
  pages = {517-529},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Gao2010,
  author = {Cen Gao and Min-Sun Park and Harry A Stern},
  title = {Accounting for ligand conformational restriction in calculations
	of protein-ligand binding affinities.},
  journal = {Biophys. J.},
  year = {2010},
  volume = {98},
  pages = {901--910},
  number = {5},
  month = {Mar},
  abstract = {The conformation adopted by a ligand on binding to a receptor may
	differ from its lowest-energy conformation in solution. In addition,
	the bound ligand is more conformationally restricted, which is associated
	with a configurational entropy loss. The free energy change due to
	these effects is often neglected or treated crudely in current models
	for predicting binding affinity. We present a method for estimating
	this contribution, based on perturbation theory using the quasi-harmonic
	model of Karplus and Kushick as a reference system. The consistency
	of the method is checked for small model systems. Subsequently we
	use the method, along with an estimate for the enthalpic contribution
	due to ligand-receptor interactions, to calculate relative binding
	affinities. The AMBER force field and generalized Born implicit solvent
	model is used. Binding affinities were estimated for a test set of
	233 protein-ligand complexes for which crystal structures and measured
	binding affinities are available. In most cases, the ligand conformation
	in the bound state was significantly different from the most favorable
	conformation in solution. In general, the correlation between measured
	and calculated ligand binding affinities including the free energy
	change due to ligand conformational change is comparable to or slightly
	better than that obtained by using an empirically-trained docking
	score. Both entropic and enthalpic contributions to this free energy
	change are significant.},
  comment = {Ligand reorganization},
  doi = {10.1016/j.bpj.2009.11.018},
  institution = {Department of Chemistry, University of Rochester, New York, USA.},
  keywords = {Hydro-Lyases; Ligands; Molecular Conformation; Molecular Weight; Proteins;
	Thermodynamics},
  owner = {emilio},
  pii = {S0006-3495(09)01746-9},
  pmid = {20197044},
  timestamp = {2010.09.08},
  url = {http://dx.doi.org/10.1016/j.bpj.2009.11.018}
}

@ARTICLE{Garcia:Sanbomatsu:2001,
  author = {Garc\'{\i}a, A. E. and Sanbomatsu, K. Y.},
  title = {Exploring the Energy Landscape of a $\beta$ Hairpin in Explicit Solvent},
  journal = {Proteins},
  year = {2001},
  volume = {42},
  pages = {345-354},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Garde:Pratt:96,
  author = {Garde, S. and Hummer, S. and Pratt, L. R.},
  title = {Origin of Entropy Convergence in Hydrophobic Hydration and Protein
	Folding},
  journal = {Phys. Rev. Lett.},
  year = {1996},
  volume = {77},
  pages = {4966},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Ge2010,
  author = {Xiaoxia Ge and Benoit Roux},
  title = {Absolute binding free energy calculations of sparsomycin analogs
	to the bacterial ribosome.},
  journal = {J. Phys. Chem. B},
  year = {2010},
  volume = {114},
  pages = {9525--9539},
  number = {29},
  month = {Jul},
  abstract = {The interactions of the 50S subunit of bacterial ribosome with antibiotic
	sparsomycin (SPS) and five analogs (AN) are investigated through
	the calculation of the standard (absolute) binding free energy and
	the characterization of conformational dynamics. The standard binding
	free energies of the complexes are computed using free energy perturbation
	molecular dynamics (FEP/MD) simulations with explicit solvent. Restraining
	potentials are applied and then released during the simulation to
	efficiently sample the changes in translational, orientational, and
	conformational freedom of the ligand and receptor upon binding. The
	biasing effects of the restraining potentials are rigorously removed.
	The loss of conformational freedom of the ligand upon binding is
	determined by introducing a potential of mean force (PMF) as a function
	of the root-mean-square deviation (rmsd) of the ligand relative to
	its conformation in the bound state. To reduce the size of the simulated
	system, the binding pocket of the ribosome is simulated in the framework
	of the generalized solvent boundary potential (GSBP). The number
	of solvent molecules in the buried binding site is treated via grand
	canonical Monte Carlo (GCMC) during the FEP/MD simulations. The correlation
	coefficient between the calculated and measured binding free energies
	is 0.96, and the experimentally observed ranking order for the binding
	affinities of the six ligands is reproduced. However, while the calculated
	affinities of the strong binders agree well with the experimental
	values, those for the weak binders are underestimated.},
  doi = {10.1021/jp100579y},
  institution = {Department of Physiology and Biophysics, Weill Medical College of
	Cornell University, New York, New York 10065, USA.},
  owner = {emilio},
  pmid = {20608691},
  timestamp = {2010.09.08},
  url = {http://dx.doi.org/10.1021/jp100579y}
}

@ARTICLE{Ge2010a,
  author = {Xiaoxia Ge and Benoit Roux},
  title = {Calculation of the standard binding free energy of sparsomycin to
	the ribosomal peptidyl-transferase P-site using molecular dynamics
	simulations with restraining potentials.},
  journal = {J Mol Recognit},
  year = {2010},
  volume = {23},
  pages = {128--141},
  number = {2},
  month = {Mar},
  abstract = {The standard (absolute) binding free energy of the antibiotic sparsomycin
	with the 50S bacteria ribosomal subunit is calculated using molecular
	dynamics (MD) free energy perturbation (FEP) simulations with restraining
	potentials developed by Wang et al. [Biophys. J. 91:2798-2814 (2006)].
	In the simulation protocol, restraining potentials are activated
	for the orientational and translational movements of the ligand relative
	to the binding site when it is decoupled from the binding pocket,
	and then released once the ligand fully interacts with the rest of
	the system. A reduced system is simulated to decrease the computational
	cost of the FEP/MD calculations and the effects of the surrounding
	atoms are incorporated using the generalized solvent boundary potential
	(GSBP) method. The loss of conformational freedom of the ligand upon
	binding is characterized using the potential of mean force (PMF)
	as a function of the root-mean-square deviation (RMSD) relative to
	the bound conformation. The number of water molecules in the binding
	pocket is allowed to fluctuate dynamically in response to the ligand
	during the calculations by combining FEP/MD with grand canonical
	Monte Carlo (GCMC) simulations. The calculated binding free energy
	is about -6 kcal/mol, which is in reasonable agreement with the experimental
	value. The information gleaned from this study provides new insight
	on the recognition of ribosome by sparsomycin and highlights the
	challenges in calculations of absolute binding free energies in these
	systems.},
  comment = {Ligand reorganization},
  doi = {10.1002/jmr.996},
  institution = {Department of Physiology and Biophysics, Weill Medical College of
	Cornell University, New York, NY, USA.},
  keywords = {Binding Sites; Ligands; Magnesium; Models, Molecular; Molecular Dynamics
	Simulation; Monte Carlo Method; Peptidyl Transferases; Protein Binding;
	Protein Conformation; Ribosome Subunits, Large, Bacterial; Sparsomycin;
	Thermodynamics},
  owner = {emilio},
  pmid = {20151411},
  timestamp = {2010.09.08},
  url = {http://dx.doi.org/10.1002/jmr.996}
}

@ARTICLE{Chandler:94,
  author = {Gehlen, J. N. and Marchi, M. and Chandler, D.},
  title = {Dynamics Affecting the Primary Charge Transfer in Photosynthesis},
  journal = {Science},
  year = {1994},
  volume = {263},
  pages = {499},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Gelis2007,
  author = {Ioannis Gelis and Alexandre M J J Bonvin and Dimitra Keramisanou
	and Marina Koukaki and Giorgos Gouridis and Spyridoula Karamanou
	and Anastassios Economou and Charalampos G Kalodimos},
  title = {Structural basis for signal-sequence recognition by the translocase
	motor SecA as determined by NMR.},
  journal = {Cell},
  year = {2007},
  volume = {131},
  pages = {756--769},
  number = {4},
  month = {Nov},
  abstract = {Recognition of signal sequences by cognate receptors controls the
	entry of virtually all proteins to export pathways. Despite its importance,
	this process remains poorly understood. Here, we present the solution
	structure of a signal peptide bound to SecA, the 204 kDa ATPase motor
	of the Sec translocase. Upon encounter, the signal peptide forms
	an alpha-helix that inserts into a flexible and elongated groove
	in SecA. The mode of binding is bimodal, with both hydrophobic and
	electrostatic interactions mediating recognition. The same groove
	is used by SecA to recognize a diverse set of signal sequences. Impairment
	of the signal-peptide binding to SecA results in significant translocation
	defects. The C-terminal tail of SecA occludes the groove and inhibits
	signal-peptide binding, but autoinhibition is relieved by the SecB
	chaperone. Finally, it is shown that SecA interconverts between two
	conformations in solution, suggesting a simple mechanism for polypeptide
	translocation.},
  doi = {10.1016/j.cell.2007.09.039},
  institution = {Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.},
  keywords = {Adenosine Triphosphatases, chemistry/genetics/metabolism; Amino Acid
	Sequence; Bacterial Proteins, chemistry/genetics/metabolism; Membrane
	Transport Proteins, chemistry/genetics/metabolism; Models, Molecular;
	Molecular Sequence Data; Nuclear Magnetic Resonance, Biomolecular;
	Nucleic Acid Conformation; Peptides, chemistry/metabolism; Protein
	Binding; Protein Sorting Signals; Protein Structure, Secondary; Protein
	Structure, Tertiary; Sequence Alignment; Static Electricity},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pii = {S0092-8674(07)01269-X},
  pmid = {18022369},
  timestamp = {2011.07.15},
  url = {http://dx.doi.org/10.1016/j.cell.2007.09.039}
}

@ELECTRONIC{Geyer2009,
  author = {C. J. Geyer},
  year = {2009},
  title = {Trust Region Optimization, {R} package 0.1-2.},
  note = {http://www.stat.umn.edu/geyer/trust/},
  owner = {emilio},
  timestamp = {2011.11.24}
}

@TECHREPORT{Geyer1994,
  author = {Charles J. Geyer},
  title = {Estimating Normalizing Constants and Reweighting Mixtures in Markov
	Chain Monte Carlo},
  institution = {University of Minnesota, School of Statistics},
  year = {1994},
  comment = {From Zhiqiang},
  owner = {emilio},
  timestamp = {2011.11.06}
}

@ARTICLE{Ghosh:Rapp:Friesner:98,
  author = {Ghosh, A. and Rapp, C. S. and Friesner, R. A.},
  title = {Generalized {B}orn model based on a surface integral formulation},
  journal = {J. Phys. Chem. B},
  year = {1998},
  volume = {102},
  pages = {10983-10990},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Gill1988,
  author = {R. Gill and Y. Vardi and J. Wellner},
  title = {Large sample theory of empirical distributions in biased sampling
	models},
  journal = {Annals of Statistics},
  year = {1988},
  volume = {16},
  pages = {1069-1112},
  comment = {From Zhiqiang},
  owner = {emilio},
  timestamp = {2011.11.06}
}

@ARTICLE{Gilli:94,
  author = {Gilli, P. and Ferretti, L. and Gilli, G. and Borea, P. A.},
  title = {Enthalpy-entropy compensation in Drug-Receptor Binding},
  journal = {J. Phys. Chem.},
  year = {1994},
  volume = {98},
  pages = {1515-1518},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Gilli:95,
  author = {Gilli, P. and Ferretti, V. and Gilli, G. and Borea, P. A.},
  title = {Enthalpy-entropy compensation in drug receptor binding},
  journal = {J. Phys. Chem.},
  year = {1994},
  volume = {98},
  pages = {1515-1518},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Gilson:95,
  author = {Gilson, M. K.},
  journal = {Curr. Opin. Struct. Biol.},
  year = {1995},
  volume = {5},
  pages = {216-223},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Gilson:Given:Bush:McCammon:97,
  author = {Gilson, M. K. and Given, J. A. and Bush, B. L. and McCammon, J. A.},
  title = {The Statistical-Thermodynamic Basis for Computation of Binding Affinities:
	A Critical Review },
  journal = {Biophys. J.},
  year = {1997},
  volume = {72},
  pages = {1047-1069},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Gilson2007,
  author = {Michael K Gilson and Huan-Xiang Zhou},
  title = {Calculation of protein-ligand binding affinities.},
  journal = {Annu. Rev. Biophys. Biomol. Struct.},
  year = {2007},
  volume = {36},
  pages = {21--42},
  abstract = {Accurate methods of computing the affinity of a small molecule with
	a protein are needed to speed the discovery of new medications and
	biological probes. This paper reviews physics-based models of binding,
	beginning with a summary of the changes in potential energy, solvation
	energy, and configurational entropy that influence affinity, and
	a theoretical overview to frame the discussion of specific computational
	approaches. Important advances are reported in modeling protein-ligand
	energetics, such as the incorporation of electronic polarization
	and the use of quantum mechanical methods. Recent calculations suggest
	that changes in configurational entropy strongly oppose binding and
	must be included if accurate affinities are to be obtained. The linear
	interaction energy (LIE) and molecular mechanics Poisson-Boltzmann
	surface area (MM-PBSA) methods are analyzed, as are free energy pathway
	methods, which show promise and may be ready for more extensive testing.
	Ultimately, major improvements in modeling accuracy will likely require
	advances on multiple fronts, as well as continued validation against
	experiment.},
  doi = {10.1146/annurev.biophys.36.040306.132550},
  institution = {Center for Advanced Research in Biotechnology, University of Maryland
	Biotechnology Institute, Rockville, Maryland 20850, USA. gilson@umbi.umd.edu},
  keywords = {Biophysics; Drug Design; Electrolytes; Entropy; Hydrogen-Ion Concentration;
	Ligands; Models, Theoretical; Molecular Conformation; Protein Binding;
	Protein Conformation; Proteins; Quantum Theory; Software; Thermodynamics},
  owner = {emilio},
  pmid = {17201676},
  timestamp = {2010.04.20},
  url = {http://dx.doi.org/10.1146/annurev.biophys.36.040306.132550}
}

@ARTICLE{Gouda2003,
  author = {Hiroaki Gouda and Irwin D Kuntz and David A Case and Peter A Kollman},
  title = {Free energy calculations for theophylline binding to an RNA aptamer:
	Comparison of MM-PBSA and thermodynamic integration methods.},
  journal = {Biopolymers},
  year = {2003},
  volume = {68},
  pages = {16--34},
  number = {1},
  month = {Jan},
  abstract = {We have applied the molecular mechanics Poisson-Boltzmann surface
	area (MM-PBSA) method (J. Srinivasan, T. E. Cheatham, P. Cieplak,
	P. A. Kollman, and D. A. Case, Journal of the American Chemical Society,
	1998, Vol. 120, pp. 9401-9409) to study the interaction of an RNA
	aptamer with theophylline and its analogs. The MM-PBSA free energy
	analysis provides a reasonable absolute binding free energy for the
	RNA aptamer-theophylline complex formation. Energetic analysis reveals
	that the van der Waals interaction and the nonpolar contribution
	to solvation provide the basis for the favorable absolute free energy
	of complex. This trend is similar to other protein-ligand interactions
	studied previously. The MM-PBSA method also ranks the relative binding
	energies of five theophylline analogs approximately correctly, but
	not as well as the more conventional thermodynamic integration calculations,
	which were carried out to convert theophylline into its analogs.
	The comparison of MM-PBSA with TI suggests that the MM-PBSA method
	has some difficulties with the first-solvation-shell energetics.},
  doi = {10.1002/bip.10270},
  institution = {Department of Pharmaceutical Chemistry, University of California,
	San Francisco, CA 94143, USA.},
  keywords = {Binding Sites; Hydrogen Bonding; Magnetic Resonance Spectroscopy;
	Models, Molecular; Nucleic Acid Conformation; RNA; Theophylline;
	Thermodynamics},
  owner = {emilio},
  pmid = {12579577},
  timestamp = {2010.04.21},
  url = {http://dx.doi.org/10.1002/bip.10270}
}

@ARTICLE{Grant:Pickup:95,
  author = {Grant, J. A. and Pickup, B. T.},
  title = {A Gaussian Description of Molecular Shape},
  journal = {J. Phys. Chem.},
  year = {1995},
  volume = {99},
  pages = {3503-3510},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Grant:Pickup:Sykes:Kitchen:Nicholls:2007,
  author = {Grant, {J. A.} amd Pickup, {B. T.} and Sykes, {M. J.} amd Kitchen,
	{C. A.} and Nicholls, A.},
  title = {The Gaussian Generalized Born model: application to small molecules},
  journal = {Phys. Chem. Chem. Phys.},
  year = {2007},
  volume = {9},
  pages = {4913-4922},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Grant:Pickup:Nicholls:2001,
  author = {Grant, {J. W.} and Pickup, {B. T.} and Nicholls, A.},
  title = {A smooth permittivity function for Poisson-Boltzmann solvation methods},
  journal = {J. Comp. Chem.},
  year = {2001},
  volume = {22},
  pages = {608-640},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Graves2005,
  author = {Alan P Graves and Ruth Brenk and Brian K Shoichet},
  title = {Decoys for docking.},
  journal = {J. Med. Chem.},
  year = {2005},
  volume = {48},
  pages = {3714--3728},
  number = {11},
  month = {Jun},
  abstract = {Molecular docking is widely used to predict novel lead compounds for
	drug discovery. Success depends on the quality of the docking scoring
	function, among other factors. An imperfect scoring function can
	mislead by predicting incorrect ligand geometries or by selecting
	nonbinding molecules over true ligands. These false-positive hits
	may be considered "decoys". Although these decoys are frustrating,
	they potentially provide important tests for a docking algorithm;
	the more subtle the decoy, the more rigorous the test. Indeed, decoy
	databases have been used to improve protein structure prediction
	algorithms and protein-protein docking algorithms. Here, we describe
	20 geometric decoys in five enzymes and 166 "hit list" decoys-i.e.,
	molecules predicted to bind by our docking program that were tested
	and found not to do so-for beta-lactamase and two cavity sites in
	lysozyme. Especially in the cavity sites, which are very simple,
	these decoys highlight particular weaknesses in our scoring function.
	We also consider the performance of five other widely used docking
	scoring functions against our geometric and hit list decoys. Intriguingly,
	whereas many of these other scoring functions performed better on
	the geometric decoys, they typically performed worse on the hit list
	decoys, often highly ranking molecules that seemed to poorly complement
	the model sites. Several of these "hits"from the other scoring functions
	were tested experimentally and found, in fact, to be decoys. Collectively,
	these decoys provide a tool for the development and improvement of
	molecular docking scoring functions. Such improvements may, in turn,
	be rapidly tested experimentally against these and related experimental
	systems, which are well-behaved in assays and for structure determination.},
  doi = {10.1021/jm0491187},
  institution = {Department of Pharmaceutical Chemistry, University of California
	San Francisco, 1700 4th Street, San Francisco, California 94143-2550,
	USA.},
  keywords = {Acetylcholinesterase; Algorithms; Binding Sites; Ligands; Models,
	Molecular; Protein Binding; Purine-Nucleoside Phosphorylase; Quantitative
	Structure-Activity Relationship; Tetrahydrofolate Dehydrogenase;
	Thrombin; Thymidylate Synthase},
  owner = {emilio},
  pmid = {15916423},
  timestamp = {2010.04.27},
  url = {http://dx.doi.org/10.1021/jm0491187}
}

@BOOK{Green:52,
  title = {The Molecular Theory of Fluids},
  publisher = {North-Holland},
  year = {1952},
  author = {Green, H. S.},
  address = {Amsterdam},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Greengard:Rokhlin:89,
  author = {Greengard, L. and Rokhlin, V.},
  journal = {Physica A},
  year = {1989},
  volume = {29},
  pages = {139-152},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Groot1992,
  author = {Groot, Robert D.},
  title = {The association constant of a flexible molecule and a single atom:
	Theory and simulation},
  journal = {J. Chem. Phys.},
  year = {1992},
  volume = {97},
  pages = {3537--3549},
  number = {5},
  month = sep,
  keywords = {MOLECULES, ATOMS, ASSOCIATION, SIMULATION, CALCULATION METHODS, FREE
	ENERGY, PERTURBATION THEORY, FLEXIBILITY, COMPLEXES, EQUILIBRIUM,
	DISSOCIATION, COUPLING CONSTANTS, SOLVENTS, CHAINS},
  owner = {emilio},
  publisher = {AIP},
  timestamp = {2011.02.08},
  url = {http://link.aip.org/link/?JCP/97/3537/1}
}

@ARTICLE{Grunwald:84,
  author = {Grunwald, A.},
  title = {Thermodynamic Properties, Propensity Laws, and Solvent Models in
	Solutions in Self-Associating Solvents. Application to Aqueous Alcohol
	Solutions.},
  journal = {J. Am. Chem. Soc.},
  year = {1984},
  volume = {106},
  pages = {5414-5420},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Grunwald:Steel:95,
  author = {Grunwald, E. and Steel, C.},
  title = {Solvent Reorganization and Thermodynamic Enthalpy-Entropy Compensation},
  journal = {J. Am. Chem. Soc.},
  year = {1995},
  volume = {117},
  pages = {5687-5692},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Guallar2004,
  author = {Guallar, Victor and Friesner, Richard A.},
  title = {Cytochrome P450CAM Enzymatic Catalysis cycle: a Quantum Mechanics/Molecular
	Mechanics Study},
  journal = {J. Am. Chem. Soc.},
  year = {2004},
  volume = {126},
  pages = {8501--8508},
  number = {27},
  month = jul,
  abstract = {The catalytic pathway of cytochrome P450cam is studied by means of
	a hybrid quantum mechanics/molecular mechanics method. Our results
	reveal an active role of the enzyme in the different catalytic steps.
	The protein initially controls the energy gap between the high- and
	low-spin states in the substrate binding process, allowing thermodynamic
	reduction by putidaredoxin reductase and molecular oxygen addition.
	A second electron reduction activates the delivery of protons to
	the active site through a selective interaction of Thr252 and the
	distal oxygen causing the O−O cleavage. Finally, the protein environment
	catalyzes the substrate hydrogen atom abstraction step with a remarkably
	low free energy barrier (∼8 kcal/mol). Our results are consistent
	with the effect of mutations on the enzymatic efficacy and provide
	a satisfactory explanation for the experimental failure to trap the
	proposed catalytically competent species, a ferryl Fe(IV) heme.},
  comment = {doi: 10.1021/ja036123b},
  issn = {0002-7863},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2011.01.18},
  url = {http://dx.doi.org/10.1021/ja036123b}
}

@ARTICLE{Guardia:Rey:Padro:91,
  author = {Guardia, E. and Rey, R. and Padro, J. A.},
  journal = {J. Chem. Phys.},
  year = {1991},
  volume = {95},
  pages = {2823-2828},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Guillot:Guissani:93,
  author = {Guillot, B. and Guissani, Y.},
  title = {Computer Simulation Study of the Temperature Dependence of the Hydrophobic
	Hydration.},
  journal = {J. Chem. Phys.},
  year = {1993},
  volume = {99},
  pages = {8075},
  number = {10},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Guillot:Guissani:Bratos:91,
  author = {Guillot, B. and Guissani, Y. and Bratos, S.},
  title = {A Computer Simulation Study of the Hydrophobic Hydration of Rare
	Gases and Methane. I. Thermodynamic and Structural Properties},
  journal = {J. Chem. Phys.},
  year = {1991},
  volume = {95},
  pages = {3643},
  number = {5},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{vanGunsteren:Berendsen:77,
  author = {van Gunsteren, W. F. and Berendsen, H. J. C.},
  journal = {Mol. Phys.},
  year = {1977},
  volume = {34},
  pages = {1311},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Guthrie2009,
  author = {Guthrie, J. Peter},
  title = {A Blind Challenge for Computational Solvation Free Energies: Introduction
	and Overview},
  journal = {J. Phys. Chem. B},
  year = {2009},
  volume = {113},
  pages = {4501--4507},
  number = {14},
  month = apr,
  abstract = {The accompanying set of papers arose from a recent blind challenge
	to computational solvation energies. The challenge was based on a
	set of 63 drug-like molecules for which solvation energies could
	be extracted from the literature. While the results are encouraging,
	there is still need for improvement.

	The accompanying set of papers arose from a recent blind challenge
	to computational solvation energies. The challenge was based on a
	set of 63 drug-like molecules for which solvation energies could
	be extracted from the literature. While the results are encouraging,
	there is still need for improvement.},
  booktitle = {The Journal of Physical Chemistry B},
  comment = {doi: 10.1021/jp806724u},
  issn = {1520-6106},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2012.02.09},
  url = {http://dx.doi.org/10.1021/jp806724u}
}

@ARTICLE{Guvench2009a,
  author = {Olgun Guvench and Alexander D MacKerell},
  title = {Computational evaluation of protein-small molecule binding.},
  journal = {Curr. Opin. Struct. Biol.},
  year = {2009},
  volume = {19},
  pages = {56--61},
  number = {1},
  month = {Feb},
  abstract = {Determining protein-small molecule binding affinity is a key component
	of present-day rational drug discovery. To circumvent the time, labor,
	and materials costs associated with experimental protein-small molecule
	binding assays, a variety of structure-based computational methods
	have been developed for determining protein-small molecule binding
	affinities. These methods can be placed in one of two classes: accurate
	but slow (Class 1), and fast but approximate (Class 2). Class 1 methods,
	which explicitly take into account protein flexibility and include
	an atomic-level description of solvation, are capable of quantitatively
	reproducing experimental protein-small molecule absolute binding
	free energies. However, Class 1 computational requirements make screening
	thousands to millions of small molecules against a protein, as required
	for rational drug design, infeasible for the foreseeable future.
	Class 2 methods, on the contrary, are sufficiently fast to perform
	such inhibitor screening, yet they suffer from limited descriptions
	of protein flexibility and solvation, which in turn limit their ability
	to select and rank-order small molecules by computed binding affinities.
	This review presents an overview of Class 1 and Class 2 methods,
	and avenues of research in Class 2 methods aimed at bringing them
	closer to Class 1 accuracy.},
  doi = {10.1016/j.sbi.2008.11.009},
  institution = {Department of Pharmaceutical Sciences, School of Pharmacy, University
	of Maryland, Baltimore, 20 Penn Street, Baltimore, MD 21201, United
	States.},
  keywords = {Animals; Binding Sites; Computer Simulation; Drug Design; Humans;
	Protein Conformation; Proteins},
  owner = {emilio},
  pii = {S0959-440X(08)00174-7},
  pmid = {19162472},
  timestamp = {2010.04.20},
  url = {http://dx.doi.org/10.1016/j.sbi.2008.11.009}
}

@ARTICLE{Hunenberger:Helms:Narayana:Taylor:McCammon:99,
  author = {H\"{u}nenberger, P. H. and Helms, V. and Narayana, N. and Taylor,
	S. S. and McCammon, J. A.},
  title = {Determinants of Ligand Binding to cAMP-Dependent Protein Kinase},
  journal = {Biochemistry},
  year = {1999},
  volume = {38},
  pages = {2358-2366},
  number = {8},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hagen:Kim:Berne:2006,
  author = {Hagen, M. and Kim, B. and Liu, P. and Berne, {B. J.}},
  title = {Serial Replica Exchange},
  journal = {J. Phys. Chem. B},
  year = {2006},
  volume = {111},
  pages = {1416--1423},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Haines2001,
  author = {Haines, Donovan C. and Tomchick, Diana R. and Machius, Mischa and
	Peterson, Julian A.},
  title = {Pivotal Role of Water in the Mechanism of P450BM-3},
  journal = {Biochemistry},
  year = {2001},
  volume = {40},
  pages = {13456--13465},
  number = {45},
  month = nov,
  abstract = {Cytochrome P450s constitute a superfamily of enzymes that catalyze
	the oxidation of a vast number of structurally and chemically diverse
	hydrophobic substrates. Herein, we describe the crystal structure
	of a complex between the bacterial P450BM-3 and the novel substrate
	N-palmitoylglycine at a resolution of 1.65 A, which reveals previously
	unrecognizable features of active site reorganization upon substrate
	binding. N-Palmitoylglycine binds with higher affinity than any other
	known substrate and reacts with a higher turnover number than palmitic
	acid but with unaltered regiospecificity along the fatty acid moiety.
	Substrate binding induces conformational changes in distinct regions
	of the enzyme including part of the I-helix adjacent to the active
	site. These changes cause the displacement by about 1 A of the pivotal
	water molecule that ligands the heme iron, resulting in the low-spin
	to high-spin conversion of the iron. The water molecule is trapped
	close to the heme group, which allows it to partition between the
	iron and the new binding site. This partitioning explains the existence
	of a high-spinlow-spin equilibrium after substrate binding. The close
	proximity of the water molecule to the heme iron indicates that it
	may also participate in the proton-transfer cascade that leads to
	heterolytic bond scission of oxygen in P450BM-3.},
  comment = {doi: 10.1021/bi011197q},
  issn = {0006-2960},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2011.01.18},
  url = {http://dx.doi.org/10.1021/bi011197q}
}

@ARTICLE{Hajduk2007,
  author = {Philip J Hajduk and Jonathan Greer},
  title = {A decade of fragment-based drug design: strategic advances and lessons
	learned.},
  journal = {Nat. Rev. Drug. Discov.},
  year = {2007},
  volume = {6},
  pages = {211--219},
  number = {3},
  month = {Mar},
  abstract = {Since the early 1990s, several technological and scientific advances
	- such as combinatorial chemistry, high-throughput screening and
	the sequencing of the human genome - have been heralded as remedies
	to the problems facing the pharmaceutical industry. The use of these
	technologies in some form is now well established at most pharmaceutical
	companies; however, the return on investment in terms of marketed
	products has not met expectations. Fragment-based drug design is
	another tool for drug discovery that has emerged in the past decade.
	Here, we describe the development and evolution of fragment-based
	drug design, analyse the role that this approach can have in combination
	with other discovery technologies and highlight the impact that fragment-based
	methods have made in progressing new medicines into the clinic.},
  doi = {10.1038/nrd2220},
  institution = {Pharmaceutical Discovery Division, Abbott Laboratories, Abbott Park,
	Illinois 60064, USA. philip.hajduk@abbott.com},
  keywords = {Decision Making, Organizational; Drug Design; Drug Industry; Ligands;
	Molecular Structure; Technology, Pharmaceutical; Time Factors},
  owner = {emilio},
  pii = {nrd2220},
  pmid = {17290284},
  timestamp = {2010.10.26},
  url = {http://dx.doi.org/10.1038/nrd2220}
}

@ARTICLE{Hamelberg2004a,
  author = {Donald Hamelberg and J. Andrew McCammon},
  title = {Standard free energy of releasing a localized water molecule from
	the binding pockets of proteins: double-decoupling method.},
  journal = {J Am Chem Soc},
  year = {2004},
  volume = {126},
  pages = {7683--7689},
  number = {24},
  month = {Jun},
  abstract = {Localized water molecules in the binding pockets of proteins play
	an important role in noncovalent association of proteins and small
	drug compounds. At times, the dominant contribution to the binding
	free energy comes from the release of localized water molecules in
	the binding pockets of biomolecules. Therefore, to quantify the energetic
	importance of these water molecules for drug design purposes, we
	have used the double-decoupling approach to calculate the standard
	free energy of tying up a water molecule in the binding pockets of
	two protein complexes. The double-decoupling approach is based on
	the underlying principle of statistical thermodynamics. We have calculated
	the standard free energies of tying up the water molecule in the
	binding pockets of these complexes to be favorable. These water molecules
	stabilize the protein-drug complexes by interacting with the ligands
	and binding pockets. Our results offer ideas that could be used in
	optimizing protein-drug interactions, by designing ligands that are
	capable of targeting localized water molecules in protein binding
	sites. The resulting free energy of ligand binding could benefit
	from the potential free energy gain accompanying the release of these
	water molecules. Furthermore, we have examined the theoretical background
	of the double-decoupling method and its connection to the molecular
	dynamics thermodynamic integration techniques.},
  doi = {10.1021/ja0377908},
  institution = {Department of Chemistry and Biochemistry, University of California,
	San Diego, La Jolla, California 92093-0365, USA. dhamelbe@mccammon.ucsd.edu},
  keywords = {Binding Sites; Computer Simulation; Crystallography, X-Ray; Diamines;
	HIV Protease; Ligands; Macromolecular Substances; Models, Chemical;
	Oligopeptides; Protease Inhibitors; Proteins; Thermodynamics; Trypsin;
	Water},
  owner = {emilio},
  pmid = {15198616},
  timestamp = {2010.09.17},
  url = {http://dx.doi.org/10.1021/ja0377908}
}

@ARTICLE{Hansson:Aqvist:1995,
  author = {Hansson, T. and {\AA}qvist, J.},
  title = {Estimation of binding free energies for {HIV} proteinase inhibitors
	by molecular dynamics simulations},
  journal = {Prot. Engineering},
  year = {1995},
  volume = {8},
  pages = {1137--1144},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hansson1998,
  author = {Hansson, T. and Marelius, J. and Aqvist, J.},
  title = {Ligand binding affinity prediction by linear interaction energy methods},
  journal = {J. Comput.-Aided Mol. Des.},
  year = {1998},
  volume = {12},
  pages = {27-35},
  number = {1},
  abstract = {A recent method for estimating ligand binding affinities is extended.
	This method employs averages of interaction potential energy terms
	from molecular dynamics simulations or other thermal conformational
	sampling techniques. Incorporation of systematic deviations from
	electrostatic linear response, derived from free energy perturbation
	studies, into the absolute binding free energy expression significantly
	enhances the accuracy of the approach. This type of method may be
	useful for computational prediction of ligand binding strengths,
	e.g., in drug design applications.},
  address = {Department of Molecular Biology, Uppsala University, Sweden.},
  comment = {Jan

	Ligand binding affinity prediction by linear interaction energy methods

	9570087

	0920-654X (Print) 0920-654X (Linking) In Vitro Journal Article Research
	Support, Non-U.S. Gov't},
  keywords = {Binding Sites Computer Simulation *Drug Design Kinetics *Ligands Models,
	Chemical Proteins/chemistry/metabolism Static Electricity Thermodynamics},
  owner = {mauro},
  refid = {45},
  timestamp = {2011.07.22},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9570087}
}

@ARTICLE{Hasel:Henderson:Still:88,
  author = {Hasel, W. and Henderson, T. F. and Still, W. C.},
  journal = {Tetrahedron Comput. Methodol.},
  year = {1988},
  volume = {1},
  pages = {103-116},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hassan:2004,
  author = {Hassan, {S. A.}},
  title = {Intermolecular Potentials of Mean Force of Amino Acid Side Chain
	Interactions in Aqueous Medium},
  journal = {J. Phys. Chem. B},
  year = {2004},
  volume = {108},
  pages = {19501--19509},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hawkins:Cramer:Trhular:97,
  author = {Hawkins, G. D. and Cramer, C. J. and Truhlar, D. G.},
  title = {Parametrized Model for Aqueous Free Energies of Solvation Using Geometry-Dependent
	Atomic Surface Tensions with Implicit Electrostatics},
  journal = {J. Phys. Chem. B},
  year = {1997},
  volume = {101},
  pages = {7147-57},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hawkins:Cramer:Truhlar:96,
  author = {Hawkins, G. D. and Cramer, C. J. and Truhlar, D. G.},
  title = {Parametrized Models of Aqueous Free Energies of Solvation Based on
	Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium},
  journal = {J. Phys. Chem.},
  year = {1996},
  volume = {100},
  pages = {19824-19839},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Head1997,
  author = {Head, Martha S. and Given, James A. and Gilson, Michael K.},
  title = {Mining Minima: Direct Computation of Conformational Free Energy},
  journal = {The Journal of Physical Chemistry A},
  year = {1997},
  volume = {101},
  pages = {1609--1618},
  number = {8},
  month = feb,
  abstract = {We describe a novel, two-step method for directly computing the conformational
	free energy of a molecule. In the first step, a finite set of low-energy
	conformations is identified, and its contribution to the configuration
	integral is evaluated by a straightforward Monte Carlo technique.
	The method of finding energy minima incorporates certain features
	of the global-underestimator method and of a genetic algorithm. In
	the second step, the contribution to the configuration integral due
	to conformations not included in the initial integration is determined
	by Metropolis Monte Carlo sampling. Applications to alanine oligopeptides
	and to three cyclic urea inhibitors of HIV protease are presented.},
  comment = {doi: 10.1021/jp963817g},
  issn = {1089-5639},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2011.02.05},
  url = {http://dx.doi.org/10.1021/jp963817g}
}

@ARTICLE{Heeres:Arnold:Janssen:2005,
  author = {Heeres, J. and de Jonge, M. and Koymans, {L. M. H.} and Daeyaert,
	{F. F. D.} and Vinkers, M. and Van Aken, {K. J. A.} and Arnold, E.
	and Das, K. and Kilonda, A. and Hoornaert, G. J. and Compernolle,
	F. and Cegla, M. and Azzam, {R. A.} and Andries, K. and de B\`{e}thune,
	M.-P. and Azjin, H. and Pauwels, R. and Lewi, {P. J.} and Janssen,
	{P. A. J.}},
  title = {Design, Synthesis, and SAR of a Novel Pyrazinone Series with Non-Nucleoside
	HIV-1 Reverse Transcriptase Inhibitory Activity},
  journal = {J. Med. Chem.},
  year = {2005},
  volume = {48},
  pages = {1910--1918},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hegde2006,
  author = {Ramanujan S Hegde and Harris D Bernstein},
  title = {The surprising complexity of signal sequences.},
  journal = {Trends Biochem Sci},
  year = {2006},
  volume = {31},
  pages = {563--571},
  number = {10},
  month = {Oct},
  abstract = {Most secreted and many membrane proteins contain cleavable N-terminal
	signal sequences that mediate their targeting to and translocation
	across the endoplasmic reticulum or bacterial cytoplasmic membrane.
	Recent studies have identified many exceptions to the widely held
	view that signal sequences are simple, degenerate and interchangeable.
	Growing evidence indicates that signal sequences contain information
	that specifies the choice of targeting pathway, the efficiency of
	translocation, the timing of cleavage and even postcleavage functions.
	As a consequence, signal sequences can have important roles in modulating
	protein biogenesis. Based on a synthesis of studies in numerous experimental
	systems, we propose that substrate-specific sequence elements embedded
	in a conserved domain structure impart unique and physiologically
	important functionality to signal sequences.},
  doi = {10.1016/j.tibs.2006.08.004},
  institution = {Cell Biology and Metabolism Branch, National Institute of Child Health
	and Human Development, National Institutes of Health, Bethesda, MD
	20892, USA. hegder@mail.nih.gov},
  keywords = {Animals; Endoplasmic Reticulum, metabolism; Humans; Membrane Proteins,
	chemistry/metabolism/physiology; Models, Biological; Protein Conformation;
	Protein Processing, Post-Translational, physiology; Protein Sorting
	Signals, physiology; Protein Transport, physiology},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pii = {S0968-0004(06)00226-X},
  pmid = {16919958},
  timestamp = {2011.07.15},
  url = {http://dx.doi.org/10.1016/j.tibs.2006.08.004}
}

@ARTICLE{Hermann:72,
  author = {R. B. Hermann},
  journal = {J. Phys. Chem.},
  year = {1972},
  volume = {76},
  pages = {2754},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hermans1986,
  author = {Jan Hermans and Shankar Subramaniam},
  title = {The free energy of xenon binding to myoglobin from molecular dynamics
	simulation},
  journal = {Isr. J. Chem.},
  year = {1986},
  volume = {27},
  pages = {225-227},
  owner = {emilio},
  timestamp = {2010.04.21}
}

@ARTICLE{Hermans:Wang:97,
  author = {Hermans, J. and Wang, L.},
  title = {Inclusion of Loss of Translational and Rotational Freedom in Theoretical
	Estimates of Free Energies of Binding. Application to a Complex of
	Benzene and Mutant T4 Lysozyme},
  journal = {J. Am. Chem. Soc.},
  year = {1997},
  volume = {119},
  pages = {2707-2714},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@BOOK{Hill:56,
  title = {Statistical Mechanics: Principles and Selected Applications},
  publisher = {McGraw-Hill},
  year = {1956},
  author = {Hill, T. L.},
  address = {New York},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Himmel:Levy:Arnold:2006,
  author = {Himmel, {D. M.} and Sarafianos, {S. G.} and Dharmasena, S. and Hossain,
	{M. M.} and McCoy-Simandle, K. and Ilina, T. and Clark Jr., {A. D.}
	and Knight, {J. L.} and Julias, {J. G.} and Clark, {P. K.} and Krogh-Jespersen,
	K. and Levy, {R. M.} and Hughes, {S. H.} and Parniak, {M. A.} and
	Arnold, E.},
  title = {Structure of a Complex of {HIV-1} Reverse Transcriptase with the
	{RNase H} Inhibitor {DHBNH} Bound at a Novel Site on the Enzyme},
  year = {2006},
  note = {Submitted for publication.},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hirata:88,
  author = {Hirata, F. and Rejfern, P. and Levy, R. M.},
  journal = {J. Quantum Chem.},
  year = {1988},
  volume = {15},
  pages = {179-188},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Ho:Kukla:1995,
  author = {Ho, W. and Kukla, {M. J.} and Breslin, {H. J.} and Ludovici, {D.
	W.} and Grous, {P. P.} and Diamond, {C. J.} and Miranda, M. and Rodgers,
	{J. D.} and Ho, {C. Y.} and De Clercq, E. and Pauwels, R. and Andries,
	K. and Janssen, {M. A. C} and Janssen, {P. A. J.}},
  title = {Synthesis and anti-{HIV-1} activity of 4,5,6,7-tetrahydro-5-methylimidazo-[4,5,1-jk][1,4]benzodiazepin-2(1H)-one
	(TIBO) derivatives},
  journal = {J. Med. Chem.},
  year = {1995},
  volume = {38},
  pages = {794--802},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@BOOK{Hockney:Eastwood:89,
  title = {Computer Simulations Using Particles},
  publisher = {Adam Hilger},
  year = {1989},
  author = {Hockney, R. W. and Eastwood, J. W.},
  address = {Bristol},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Holt1993,
  author = {Holt, Dennis A. and Luengo, Juan I. and Yamashita, Dennis S. and
	Oh, Hye Ja and Konialian, Arda L. and Yen, Hwa Kwo and Rozamus, Leonard
	W. and Brandt, Martin and Bossard, Mary J.},
  title = {Design, synthesis, and kinetic evaluation of high-affinity FKBP ligands
	and the X-ray crystal structures of their complexes with FKBP12},
  journal = {J. Am. Chem. Soc.},
  year = {1993},
  volume = {115},
  pages = {9925-9938},
  number = {22},
  abstract = {null},
  comment = {Design, synthesis, and kinetic evaluation of high-affinity FKBP ligands
	and the X-ray crystal structures of their complexes with FKBP12

	doi: 10.1021/ja00075a008},
  issn = {0002-7863},
  owner = {mauro},
  refid = {52},
  timestamp = {2011.07.22},
  url = {http://dx.doi.org/10.1021/ja00075a008}
}

@ARTICLE{Honig:Sharp:Yang:93,
  author = {Honig, B. and Sharp, K. and Yang, {A.-S.}},
  title = {Macroscopic Models of Aqueous Solutions: Biological and Chemical
	Applications},
  journal = {J. Phys. Chem.},
  year = {1993},
  volume = {97},
  pages = {1101-9},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Honig:Yang:95,
  author = {Honig, B. and Yang, A.-S.},
  title = {Free Energy Balance in Protein Folding},
  journal = {Ad. Prot. Chem.},
  year = {1995},
  volume = {46},
  pages = {27-58},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hoover:1985,
  author = {Hoover, {W. G.}},
  title = {Canonical dynamics: Equilibrium phase-space distributions},
  journal = {Phys. Rev. A},
  year = {1985},
  volume = {31},
  pages = {1695-1697},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hopkins:Stuart:1996,
  author = {Hopkins, {A. L.} and Ren, J. and Esnouf, {R. M.} and Willcox, {B.
	E.} and Jones, {E. Y.} and Ross, C. and Miyasaka, T. and Walker,
	{R. T.} and Tanaka, H. and Stammers, D.K. and Stuart, {D. I.}},
  title = {Complexes of HIV-1 reverse transcriptase with inhibitors of the HEPT
	series reveal conformational changes relevant to the design of potent
	non-nucleoside inhibitors},
  journal = {J. Med. Chem.},
  year = {1996},
  volume = {39},
  pages = {1589--1600},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hornak2007,
  author = {Viktor Hornak and Carlos Simmerling},
  title = {Targeting structural flexibility in HIV-1 protease inhibitor binding.},
  journal = {Drug Discov Today},
  year = {2007},
  volume = {12},
  pages = {132--138},
  number = {3-4},
  month = {Feb},
  abstract = {HIV-1 protease remains an important anti-AIDS drug target. Although
	it has been known that ligand binding induces large conformational
	changes in the protease, the dynamic aspects of binding have been
	largely ignored. Several computational models describing protease
	dynamics have been reported recently. These have reproduced experimental
	observations, and have also explained how ligands gain access to
	the binding site through dynamic behavior of the protease. Specifically,
	the transitions between three different conformations of the protein
	have been modeled in atomic detail. Two of these forms were determined
	by crystallography, and the third was implied by NMR experiments.
	Based on these computational models, it has been suggested that binding
	of inhibitors in allosteric sites might affect protease flexibility
	and disrupt its function.},
  doi = {10.1016/j.drudis.2006.12.011},
  institution = {Stony Brook University, Center for Structural Biology, Stony Brook,
	NY 11794-5155, USA.},
  keywords = {Acquired Immunodeficiency Syndrome; Computer Simulation; Crystallography;
	Drug Delivery Systems; Drug Design; Drug Resistance, Viral; HIV Protease;
	HIV Protease Inhibitors; HIV-1; Ligands; Magnetic Resonance Spectroscopy;
	Models, Molecular; Protein Binding; Protein Conformation},
  owner = {emilio},
  pii = {S1359-6446(06)00493-4},
  pmid = {17275733},
  timestamp = {2010.07.14},
  url = {http://dx.doi.org/10.1016/j.drudis.2006.12.011}
}

@ARTICLE{Houstin:Rossky:89,
  author = {Houstin, S. E. and Rossky, P. J.},
  journal = {J. Phys. Chem.},
  year = {1989},
  volume = {93},
  pages = {7888-7893},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Howkins:96,
  author = {Howkins, G. D. and Cramer, C. J. and Truhlar, D. G.},
  journal = {J. Phys. Chem.},
  year = {1996},
  volume = {100},
  pages = {19824-19834},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hritz2009,
  author = {Jozef Hritz and Chris Oostenbrink},
  title = {Efficient free energy calculations for compounds with multiple stable
	conformations separated by high energy barriers.},
  journal = {J. Phys. Chem. B},
  year = {2009},
  volume = {113},
  pages = {12711--12720},
  number = {38},
  month = {Sep},
  abstract = {Compounds with high intramolecular energy barriers represent challenging
	targets for free energy calculations because of the difficulty to
	obtain sufficient conformational sampling. Existing approaches are
	therefore computationally very demanding, thus preventing practical
	applications for such compounds. We present an enhanced sampling-one
	step perturbation method (ES-OS) to tackle this problem in a highly
	efficient way. A single molecular dynamics simulation of a judiciously
	chosen reference state (using two sets of soft-core interactions)
	is sufficient to determine conformational distributions of chemically
	similar compounds and the free energy differences between them. The
	ES-OS method is applied to a set of five biologically relevant 8-substituted
	GTP analogs having high energy barriers between the anti and the
	syn conformations of the base with respect to the ribose part. The
	reliability of ES-OS is verified by comparing the results to Hamiltonian
	replica exchange simulations of GTP and 8-Br-GTP and the experimentally
	determined 3J(C4,H1') coupling constant for GMP in water. Additional
	simulations in vacuum and octanol allow us to calculate differences
	in the solvation free energies and in lipophilicities (log P). Free
	energy contributions from individual conformational regions are also
	calculated, and their relationship with the overall free energy is
	derived leading to a set of multiconformational free energy formulas.
	These relationships are of general applicability and can be used
	in free energy calculations for a more diverse set of compounds.},
  doi = {10.1021/jp902968m},
  institution = {Leiden Amsterdam Center for Drug Research, Division of Molecular
	Toxicology, VU University Amsterdam, The Netherlands.},
  keywords = {Computer Simulation; Guanosine Triphosphate; Molecular Conformation;
	Thermodynamics},
  owner = {emilio},
  pmid = {19722597},
  timestamp = {2010.07.08},
  url = {http://dx.doi.org/10.1021/jp902968m}
}

@ARTICLE{Hritz2008a,
  author = {Jozef Hritz and Chris Oostenbrink},
  title = {Hamiltonian replica exchange molecular dynamics using soft-core interactions.},
  journal = {J. Chem. Phys.},
  year = {2008},
  volume = {128},
  pages = {144121},
  number = {14},
  month = {Apr},
  abstract = {To overcome the problem of insufficient conformational sampling within
	biomolecular simulations, we have developed a novel Hamiltonian replica
	exchange molecular dynamics (H-REMD) scheme that uses soft-core interactions
	between those parts of the system that contribute most to high energy
	barriers. The advantage of this approach over other H-REMD schemes
	is the possibility to use a relatively small number of replicas with
	locally larger differences between the individual Hamiltonians. Because
	soft-core potentials are almost the same as regular ones at longer
	distances, most of the interactions between atoms of perturbed parts
	will only be slightly changed. Rather, the strong repulsion between
	atoms that are close in space, which in many cases results in high
	energy barriers, is weakened within higher replicas of our proposed
	scheme. In addition to the soft-core interactions, we proposed to
	include multiple replicas using the same Hamiltonian/level of softness.
	We have tested the new protocol on the GTP and 8-Br-GTP molecules,
	which are known to have high energy barriers between the anti and
	syn conformation of the base with respect to the sugar moiety. During
	two 25 ns MD simulations of both systems the transition from the
	more stable to the less stable (but still experimentally observed)
	conformation is not seen at all. Also temperature REMD over 50 replicas
	for 1 ns did not show any transition at room temperature. On the
	other hand, more than 20 of such transitions are observed in H-REMD
	using six replicas (at three different Hamiltonians) during 6.8 ns
	per replica for GTP and 12 replicas (at six different Hamiltonians)
	during 8.7 ns per replica for 8-Br-GTP. The large increase in sampling
	efficiency was obtained from an optimized H-REMD scheme involving
	soft-core potentials, with multiple simulations using the same level
	of softness. The optimization of the scheme was performed by fast
	mimicking [J. Hritz and C. Oostenbrink, J. Chem. Phys. 127, 204104
	(2007)].},
  doi = {10.1063/1.2888998},
  institution = {Leiden Amsterdam Center for Drug Research, Division of Molecular
	Toxicology, Vrije Universiteit, Amsterdam NL-1081 HV, The Netherlands.},
  keywords = {Biopolymers; Computer Simulation; Energy Transfer; Models, Chemical;
	Models, Molecular; Molecular Conformation},
  owner = {emilio},
  pmid = {18412437},
  timestamp = {2010.07.08},
  url = {http://dx.doi.org/10.1063/1.2888998}
}

@ARTICLE{Huang:Chandler:2002,
  author = {Huang, D. M. and Chandler, D.},
  title = {The Hydrophobic Effect and the Influence of Solute-Solvent attractions},
  journal = {J. Phys. Chem. B},
  year = {2002},
  volume = {106},
  pages = {2047-2053},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Huang:Chandler:2000,
  author = {Huang, D. M. and Chandler, D.},
  title = {Temperature and length sclae dependence of hydrophobic effects and
	their possible implications for protein folding},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {2000},
  volume = {97},
  pages = {8324-8327},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Huang2006,
  author = {Niu Huang and Chakrapani Kalyanaraman and John J Irwin and Matthew
	P Jacobson},
  title = {Physics-based scoring of protein-ligand complexes: enrichment of
	known inhibitors in large-scale virtual screening.},
  journal = {J. Chem. Inf. Model.},
  year = {2006},
  volume = {46},
  pages = {243--253},
  number = {1},
  abstract = {We demonstrate that using an all-atom molecular mechanics force field
	combined with an implicit solvent model for scoring protein-ligand
	complexes is a promising approach for improving inhibitor enrichment
	in the virtual screening of large compound databases. The rescoring
	method is evaluated by the extent to which known binders for nine
	diverse, therapeutically relevant enzymes are enriched against a
	background of approximately 100,000 drug-like decoys. The improvement
	in enrichment is most robust and dramatic within the top 1\% of the
	ranked database, that is, the first thousand compounds; below the
	first few percent of the ranked database, there is little overall
	improvement. The improved early enrichment is likely due to the more
	realistic treatment of ligand and receptor desolvation in the rescoring
	procedure. We also present anecdotal but encouraging results assessing
	the ability of the rescoring method to predict specificity of inhibitors
	for structurally related proteins.},
  doi = {10.1021/ci0502855},
  institution = {Department of Pharmaceutical Chemistry, University of California
	San Francisco, Genentech Hall, 94143-2240, USA.},
  keywords = {Biophysical Phenomena; Biophysics; Computer Simulation; Drug Evaluation,
	Preclinical; Enzyme Inhibitors; Enzymes; Folic Acid Antagonists;
	Ligands; Models, Molecular; Protein Binding; Structure-Activity Relationship;
	Tetrahydrofolate Dehydrogenase},
  owner = {emilio},
  pmid = {16426060},
  timestamp = {2010.04.22},
  url = {http://dx.doi.org/10.1021/ci0502855}
}

@ARTICLE{Huang2007,
  author = {Wei-Cheng Huang and Andrew C G Westlake and Jean-Didier Maréchal
	and M. Gordon Joyce and Peter C E Moody and Gordon C K Roberts},
  title = {Filling a hole in cytochrome P450 BM3 improves substrate binding
	and catalytic efficiency.},
  journal = {J Mol Biol},
  year = {2007},
  volume = {373},
  pages = {633--651},
  number = {3},
  month = {Oct},
  abstract = {Cytochrome P450BM3 (CYP102A1) from Bacillus megaterium, a fatty acid
	hydroxylase, is a member of a very large superfamily of monooxygenase
	enzymes. The available crystal structures of the enzyme show non-productive
	binding of substrates with their omega-end distant from the iron
	in a hydrophobic pocket at one side of the active site. We have constructed
	and characterised mutants in which this pocket is filled by large
	hydrophobic side-chains replacing alanine at position 82. The mutants
	having phenylalanine or tryptophan at this position have very much
	(approximately 800-fold) greater affinity for substrate, with a greater
	conversion of the haem iron to the high-spin state, and similarly
	increased catalytic efficiency. The enzyme as isolated contains bound
	palmitate, reflecting this much higher affinity. We have determined
	the crystal structure of the haem domain of the Ala82Phe mutant with
	bound palmitate; this shows that the substrate is binding differently
	from the wild-type enzyme but still distant from the haem

repository: radical-papers/radical-references

repo_name: radical-papers/radical-references