text:
iron. Detailed
	analysis of the structure indicates that the tighter binding in the
	mutant reflects a shift in the conformational equilibrium of the
	substrate-free enzyme towards the conformation seen in the substrate
	complex rather than differences in the enzyme-substrate interactions.
	On this basis, we outline a sequence of events for the initial stages
	of the catalytic cycle. The Ala82Phe and Ala82Trp mutants are also
	very much more effective catalysts of indole hydroxylation than the
	wild-type enzyme, suggesting that they will be valuable starting
	points for the design of mutants to catalyse synthetically useful
	hydroxylation reactions.},
  doi = {10.1016/j.jmb.2007.08.015},
  institution = {Henry Wellcome Laboratories of Structural Biology, Department of
	Biochemistry, University of Leicester, Leicester LE1 9HN, UK.},
  keywords = {Bacillus megaterium; Bacterial Proteins; Binding Sites; Catalysis;
	Cytochrome P-450 Enzyme System; Heme; Hydroxylation; Kinetics; Lauric
	Acids; Mixed Function Oxygenases; Models, Molecular; Mutagenesis,
	Site-Directed; NADPH-Ferrihemoprotein Reductase; Protein Binding;
	Protein Conformation; Substrate Specificity},
  owner = {emilio},
  pii = {S0022-2836(07)01086-8},
  pmid = {17868686},
  review = {Mutant P450 to attempt remove the "distant" state.},
  timestamp = {2010.06.07},
  url = {http://dx.doi.org/10.1016/j.jmb.2007.08.015}
}

@ARTICLE{Hubbard2007a,
  author = {Roderick E Hubbard and Ijen Chen and Ben Davis},
  title = {Informatics and modeling challenges in fragment-based drug discovery.},
  journal = {Curr Opin Drug Discov Devel},
  year = {2007},
  volume = {10},
  pages = {289--297},
  number = {3},
  month = {May},
  abstract = {This review summarizes recent developments in fragment-based drug-discovery
	methods with an emphasis on informatics and modeling requirements.
	Fragment-based methods have become established as a powerful approach
	in structure-based lead discovery. A number of successful projects
	have been announced recently, where fragments have had a central
	role in hit generation and lead optimization, leading to candidates
	being considered for clinical trials. Despite these successes, there
	are still many opportunities for new development, such as improving
	the structural diversity of fragment libraries, strategies for fragment
	evolution, and methods for predicting fragment binding modes.},
  institution = {Structural Biology Laboratory, University of York, Heslington, York
	YO10 5YW, UK. r.hubbard@vernalis.com},
  keywords = {Binding Sites; Combinatorial Chemistry Techniques; Computer Simulation;
	Drug Design; Informatics; Ligands; Magnetic Resonance Spectroscopy;
	Models, Chemical; Models, Molecular; Molecular Structure; Molecular
	Weight; Pharmaceutical Preparations; Protein Binding; Protein Conformation;
	Proteins; Structure-Activity Relationship; Technology, Pharmaceutical},
  owner = {emilio},
  pmid = {17554855},
  timestamp = {2010.10.26}
}

@ARTICLE{Hummer:Garde:98,
  author = {Hummer, G. and Garde, S.},
  title = {Cavity Expulsion and Weak Dewetting of Hydrophobic Solutes in Water},
  journal = {Phys. Rev. Lett.},
  year = {1998},
  volume = {80},
  pages = {4193-4196},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hummer:Garde:Garcia:Paulaitis:Pratt:98,
  author = {Hummer, G. and Garde, S. and {Garc\'{\i}a}, A. E. and Paulaitis,
	M. E. and Pratt, L. R.},
  title = {Hydrophobic Effects on a Molecular Scale},
  journal = {Phys. Chem. B},
  year = {1998},
  volume = {102},
  pages = {10469-82},
  number = {51},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hummer:Pratt:96,
  author = {Hummer, G. and Garde, S. and Garc{\'{\i}}a, A. E. and Pohorille,
	A. and Pratt, L. R.},
  title = {An information theory model of hydrophobic interactions},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {1996},
  volume = {93},
  pages = {8951-8955},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hummer:96a,
  author = {Hummer, G. and Pratt, L. R. and Garcia, A.},
  journal = {J. Phys. Chem.},
  year = {1996},
  volume = {100},
  pages = {1206-1215},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hummer:97,
  author = {Hummer, G. and Pratt, L. R. and Garcia, A. E.},
  journal = {J. Chem. Phys.},
  year = {1997},
  volume = {107},
  pages = {9275-9277},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hummer:Soumpasis:Neumann:93,
  author = {Hummer, G. and Soumpasis, D. M. and Neumann. M.},
  journal = {Mol. Phys.},
  year = {1993},
  volume = {81},
  pages = {1155-1162},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hummer:Szabo:96,
  author = {Hummer, G. and Szabo, A.},
  journal = {J. Chem. Phys.},
  year = {1996},
  volume = {105},
  pages = {2004-2010},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hung2009,
  author = {Alvin W Hung and H. Leonardo Silvestre and Shijun Wen and Alessio
	Ciulli and Tom L Blundell and Chris Abell},
  title = {Application of fragment growing and fragment linking to the discovery
	of inhibitors of Mycobacterium tuberculosis pantothenate synthetase.},
  journal = {Angew Chem Int Ed Engl},
  year = {2009},
  volume = {48},
  pages = {8452--8456},
  number = {45},
  doi = {10.1002/anie.200903821},
  institution = {Department of Chemistry, University of Cambridge, UK.},
  keywords = {Enzyme Inhibitors; Humans; Models, Molecular; Mycobacterium tuberculosis;
	Peptide Synthases; Protein Conformation; Stereoisomerism},
  owner = {emilio},
  pmid = {19780086},
  timestamp = {2010.10.26},
  url = {http://dx.doi.org/10.1002/anie.200903821}
}

@ARTICLE{Hyun:Babu:Ichiye:95,
  author = {Hyun, J. K. and Babu, C. and Ichiye, T.},
  journal = {J. Phys. Chem.},
  year = {1995},
  volume = {99},
  pages = {5187-5195},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hyun:Ichiye:95,
  author = {Hyun, J. K. and Ichiye, T.},
  journal = {J. Phys. Chem.},
  year = {1995},
  volume = {101},
  pages = {3596-3604},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Hagler:Euler:Lifson:74,
  author = {H{\"{a}}gler, A. T. and Euler, E. and Lifson, S.},
  journal = {J. Am. Chem. Soc.},
  year = {1974},
  volume = {96},
  pages = {5319},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Im:Beglov:Roux:1998,
  author = {Wonpil Im and Dmitrii Beglov and Benoît Roux},
  title = {Continuum solvation model: Computation of electrostatic forces from
	numerical solutions to the Poisson-Boltzmann equation},
  journal = {Computer Physics Communications},
  year = {1998},
  volume = {111},
  pages = {59 - 75},
  number = {1-3},
  doi = {DOI: 10.1016/S0010-4655(98)00016-2},
  issn = {0010-4655},
  owner = {emilio},
  timestamp = {2011.01.18},
  url = {http://www.sciencedirect.com/science/article/B6TJ5-3VY62FH-6/2/08a00565050bf954f992540968a3ce23}
}

@ARTICLE{Im:Lee:Brooks:2003,
  author = {Im, W. and Lee, {M. S.} and Brooks, {C. L. III}},
  title = {Generalized born model with a simple smoothing function},
  journal = {J. Comp. Chem.},
  year = {2003},
  volume = {24},
  pages = {1691-1702},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Irisa:Nagayama:Hirata:93,
  author = {Irisa, M. and Nagayama, K. and Hirata, F.},
  title = {Extended Scaled Particle Theory for Dilute Solutions of Arbitrarily
	Shaped Solutes. An application to Solvation Free Energies of Hydrocarbons.},
  journal = {Chem. Phys. Lett.},
  year = {1993},
  volume = {207},
  pages = {430-5},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Ivery1997,
  author = {Ivery, M. T. and Weiler, L.},
  title = {Modeling the interaction between FK506 and FKBP12: a mechanism for
	formation of the calcineurin inhibitory complex},
  journal = {Bioorg. Med. Chem.},
  year = {1997},
  volume = {5},
  pages = {217--32},
  number = {2},
  abstract = {FK506 is a naturally occurring immunosuppressant whose mode of action
	involves formation of an initial complex with the cytosolic protein
	FKBP12. The composite surface of this complex then binds to and inhibits
	the protein phosphatase calcineurin (PP2B). To investigate why FK506
	does not inhibit calcineurin directly we have conducted molecular
	modeling and conformational studies on published structures of FK506
	both alone and in complex with FKBP12. From studies of the structure
	of FK506 in CDCl3 and Z-Arg32-ascomycin in water (a water soluble
	analogue of FK506) we suggest that the FK506 molecule can be viewed
	as consisting of three separate regions. The pipecolate region which
	extends from C24 to C10 including the pipecolate ring shows strongly
	conserved conformation in both solvents. The loop region which extends
	from C25 to C16 shows general conservation of the loop structure
	and the pyranose region made up of the pyranose ring and C15-C17
	which shows highly variable conformation depending on solvent. Comparison
	of the structure of Z-Arg32-ascomycin in water with structures of
	FK506 bound to FKBP12 indicate that the conformation of the pipecolate
	region is conserved during the binding process. The conformation
	of the loop region was generally conserved but a significant reduction
	(approximately 1.7 A) in the diameter of the loop in the bound structure
	was observed. The conformation of the pyranose ring and C15-C17 region
	was found to be significantly altered in the bound structure resulting
	in displacements of the C13 and C15 methoxyl groups of 2.8 and 3.5
	A, respectively. From computer models and molecular dynamics simulations
	of interactions between FK506 and FKBP12 we suggest that the conformational
	changes observed in bound FK506 are induced by the interaction between
	the 80's loop of FKBP12 and the pyranose ring of FKBP12. These interactions
	result in the formation of a complex with the both correct shape
	and surface polarity for interaction with calcineurin.},
  address = {Department of Chemistry, University of British Columbia, Vancouver,
	Canada.},
  comment = {Feb

	Modeling the interaction between FK506 and FKBP12: a mechanism for
	formation of the calcineurin inhibitory complex

	9061187

	Ivery, M T Weiler, L Research Support, Non-U.S. Gov't England Bioorganic
	& medicinal chemistry Bioorg Med Chem. 1997 Feb;5(2):217-32.

	eng},
  issn = {0968-0896 (Print) 0968-0896 (Linking)},
  keywords = {Calcineurin Calmodulin-Binding Proteins/*antagonists & inhibitors
	Carrier Proteins/*chemistry DNA-Binding Proteins/*chemistry Heat-Shock
	Proteins/*chemistry Immunosuppressive Agents/*chemistry Models, Molecular
	Molecular Structure Phosphoprotein Phosphatases/*antagonists & inhibitors
	Tacrolimus/*chemistry Tacrolimus Binding Proteins},
  owner = {mauro},
  refid = {61},
  timestamp = {2011.07.22},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9061187}
}

@ARTICLE{Ivetac2009,
  author = {Ivetac, Anthony and McCammon, J. Andrew},
  title = {Elucidating the Inhibition Mechanism of HIV-1 Non-Nucleoside Reverse
	Transcriptase Inhibitors through Multicopy Molecular Dynamics Simulations},
  journal = {Journal of Molecular Biology},
  year = {2009},
  volume = {388},
  pages = {644--658},
  number = {3},
  month = may,
  abstract = {Human immunodeficiency virus-1 reverse transcriptase (RT) inhibition
	is a major focus of current anti-AIDS drug discovery and development
	programs, comprising 17 of the 31 Food and Drug Administration-approved
	compounds. The emergence of the non-nucleoside RT inhibitor (NNRTI)
	class of compounds provides a highly specific and structurally diverse
	set of drugs, which act noncompetitively to perturb normal RT function.
	Despite a relatively rich set of crystallographic data of RT in various
	states, details of the allosteric modulation of RT dynamics by NNRTIs
	are lacking. Capturing this inhibitory mechanism could fuel the design
	of more effective inhibitors at the NNRTI site and also drive the
	identification of novel allosteric sites. To address this, we have
	performed multicopy molecular dynamics (MD) simulations of RT in
	the presence and absence of the NNRTI nevirapine (cumulative total
	simulation time, 360�ns). By comparing the collective motions of
	the MD and crystallographic structures, we demonstrate that the chief
	effect of NNRTIs is to constrain a key rigid-body motion between
	the "fingers" and "thumb" subdomains of the p66 subunit. We show
	that the NNRTI binding pocket (NNIBP) is proximal to the hinge points
	for this essential motion, and NNRTIs therefore act as "molecular
	wedges," sterically blocking the full range of motion. To explain
	how this impaired movement might result in the experimentally observed
	loss of polymerase activity, we show that the motion influences the
	geometry of key catalytic residues on opposite faces of the NNIBP.
	From a methodological point of view, our results suggest that the
	multicopy MD simulation approach is very useful when studying proteins
	that perform such large conformational changes.},
  issn = {0022-2836},
  keywords = {reverse transcriptase, molecular dynamics, simulation, HIV},
  owner = {emilio},
  timestamp = {2011.06.27},
  url = {http://www.sciencedirect.com/science/article/pii/S0022283609003349}
}

@ARTICLE{Jackson:Sternberg:95,
  author = {Jackson, R. M. and Sternberg, J. E.},
  title = {A continuum model for protein-protein interactions: applications
	to the docking problem},
  journal = {J. Mol. Biol.},
  year = {1995},
  volume = {250},
  pages = {258-275},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Jacobson:Kaminski:Friesner:Rapp:2002,
  author = {Jacobson, M. P. and Kaminski, G. A. and Friesner, R. A. and Rapp,
	C. S.},
  title = {Force Field Validation Using Protein Sidechain Prediction},
  journal = {J. Phys. Chem. B},
  year = {2002},
  volume = {106},
  pages = {11673-11680},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Jacobson:Pincus:Rapp:Day:Honig:Shaw:Friesner:2003,
  author = {Jacobson, M. P. and Pincus, D. L. and Rapp, C. S. and Day, T. J.
	F. and Honig, B. and Shaw, D. E. and Friesner, R. A.},
  title = {A Hierarchical Approach to All-Atom Loop Prediction},
  journal = {Proteins},
  year = {2003},
  note = {In press.},
  owner = {emilio},
  timestamp = {2010.11.02}
}

@INBOOK{JankeBook2002,
  chapter = {Statistical Analysis of Simulations: Data Correlations and Error
	Estimation},
  pages = {423-445},
  title = {Quantum Simulations of Complex Many-Body Systems: From Theory to
	Algorithms},
  publisher = {John von Neumann Institute for Computing, J\"{u}lich, Germany},
  year = {2002},
  editor = {J. Grotendorst, D. Marx, and A. Muramatsu},
  author = {Wolfhard Janke},
  owner = {emilio},
  timestamp = {2012.02.29}
}

@ARTICLE{Janssen:Lewi:Arnold:2005,
  author = {Janssen, {P. A. J.} and Lewi, {P. J.} and Arnold, E. and Daeyaert,
	F. and de Jonge, M. and Heeres, J. and Koymans, L. and Vinkers, M.
	and Guillemont, J. and Pasquier, E. and Kukla, M. and Ludovici, D.
	and Andries, K. and de B\`{e}thune, M.-P. and Pawels, R. and Das,
	K. and Clark Jr., {A. D.} and Frenkel, {Y. V.} and Hughes, {S. H.}
	and Medaer, B. and De Knaep, F. and Bohets, H. and De Clerck, F.
	and Lampo, A. and Williams, P. and Stoffels, P.},
  title = {In Search of a Novel Anti-HIV Drug: Multidisciplinary Coordination
	in the Discovery of 4-[[4-[[4-[(1E)-2-Cyanoethenyl]-2,6-dimethylphenyl]amino]-2-pyrimidinyl]amino]benzonitrile
	(R278474, Rilpivirine)},
  journal = {J. Med. Chem.},
  year = {2005},
  volume = {48},
  pages = {1901--1909},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Jayachandran2006,
  author = {Guha Jayachandran and Michael R Shirts and Sanghyun Park and Vijay
	S Pande},
  title = {Parallelized-over-parts computation of absolute binding free energy
	with docking and molecular dynamics.},
  journal = {J. Chem. Phys.},
  year = {2006},
  volume = {125},
  pages = {084901},
  number = {8},
  month = {Aug},
  abstract = {We present a technique for biomolecular free energy calculations that
	exploits highly parallelized sampling to significantly reduce the
	time to results. The technique combines free energies for multiple,
	nonoverlapping configurational macrostates and is naturally suited
	to distributed computing. We describe a methodology that uses this
	technique with docking, molecular dynamics, and free energy perturbation
	to compute absolute free energies of binding quickly compared to
	previous methods. The method does not require a priori knowledge
	of the binding pose as long as the docking technique used can generate
	reasonable binding modes. We demonstrate the method on the protein
	FKBP12 and eight of its inhibitors.},
  doi = {10.1063/1.2221680},
  institution = {Computer Science Department, Stanford University, Stanford, CA 94305,
	USA.},
  keywords = {Biophysics; Chemistry, Physical; Cluster Analysis; Computer Simulation;
	Humans; Ligands; Models, Chemical; Models, Statistical; Molecular
	Conformation; Probability; Protein Binding; Proteins; Tacrolimus
	Binding Protein 1A; Thermodynamics},
  owner = {emilio},
  pmid = {16965051},
  timestamp = {2010.04.29},
  url = {http://dx.doi.org/10.1063/1.2221680}
}

@ARTICLE{Jayachandran2007,
  author = {Guha Jayachandran and V. Vishal and Angel E García and Vijay S Pande},
  title = {Local structure formation in simulations of two small proteins.},
  journal = {J Struct Biol},
  year = {2007},
  volume = {157},
  pages = {491--499},
  number = {3},
  month = {Mar},
  abstract = {Massively parallel all-atom, explicit solvent molecular dynamics simulations
	were used to explore the formation and existence of local structure
	in two small alpha-helical proteins, the villin headpiece and the
	helical fragment B of protein A. We report on the existence of transient
	helices and combinations of helices in the unfolded ensemble, and
	on the order of formation of helices, which appears to largely agree
	with previous experimental results. Transient local structure is
	observed even in the absence of overall native structure. We also
	calculate sets of residue-residue pairs that are statistically predictive
	of the formation of given local structures in our simulations.},
  doi = {10.1016/j.jsb.2006.10.001},
  institution = {Computer Science Department, Stanford University, Stanford, CA 94305,
	USA.},
  keywords = {Computer Simulation; Protein Folding; Protein Structure, Secondary;
	Proteins},
  owner = {emilio},
  pii = {S1047-8477(06)00312-1},
  pmid = {17098444},
  timestamp = {2010.11.03},
  url = {http://dx.doi.org/10.1016/j.jsb.2006.10.001}
}

@ARTICLE{Jayram:89,
  author = {Jayram, B. and Fine, R. and Sharp, K. and Honig, B.},
  journal = {J. Phys. Chem.},
  year = {1989},
  volume = {93},
  pages = {4320-4326},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Jiang2009,
  author = {Jiang, Wei and Hodoscek, Milan and Roux, Beno\^{i}t},
  title = {Computation of Absolute Hydration and Binding Free Energy with Free
	Energy Perturbation Distributed Replica-Exchange Molecular Dynamics},
  journal = {J. Chem. Theory Comput.},
  year = {2009},
  volume = {5},
  pages = {2583--2588},
  number = {10},
  month = oct,
  abstract = {Distributed Replica (REPDSTR) is a powerful parallelization technique
	enabling simulations of a group of replicas in a parallel/parallel
	fashion, where each replica is distributed to different nodes of
	a large cluster [Theor. Chem. Acc. 2003, 109, 140]. Here, we use
	the framework provided by REPDSTR to combine a staged free energy
	perturbation protocol with replica-exchange molecular dynamics (FEP/REMD).
	The structure of REPDSTR, which allows multiple parallel input/output
	(I/O), facilitates the treatment of replica-exchange to couple the
	N window simulations corresponding to different values of the thermodynamic
	coupling parameters. As a result, each of the N synchronous window
	simulations benefit from the sampling carried out by the N-1 others.
	As illustrative examples of the FEP/REMD strategy, calculations of
	the absolute hydration and binding free energy of small molecules
	were performed using the biomolecular simulation program CHARMM adapted
	for the IBM Blue Gene/P platform. The computations show that a FEP/REMD
	strategy significantly improves the sampling and accelerates the
	convergence of absolute free energy computations.},
  comment = {doi: 10.1021/ct900223z},
  issn = {1549-9618},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2010.09.08},
  url = {http://dx.doi.org/10.1021/ct900223z}
}

@ARTICLE{Jiang2010,
  author = {Jiang, Wei and Roux, Beno\^{i}t},
  title = {Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics
	{(FEP/H-REMD)} for Absolute Ligand Binding Free Energy Calculations},
  journal = {J. Chem. Theory Comput.},
  year = {2010},
  volume = {6},
  pages = {2559--2565},
  month = jul,
  abstract = {Free Energy Perturbation with Replica Exchange Molecular Dynamics
	(FEP/REMD) offers a powerful strategy to improve the convergence
	of free energy computations. In particular, it has been shown previously
	that a FEP/REMD scheme allowing random moves within an extended replica
	ensemble of thermodynamic coupling parameters “λ” can improve the
	statistical convergence in calculations of absolute binding free
	energy of ligands to proteins [J. Chem. Theory Comput. 2009, 5, 2583].
	In the present study, FEP/REMD is extended and combined with an accelerated
	MD simulations method based on Hamiltonian replica-exchange MD (H-REMD)
	to overcome the additional problems arising from the existence of
	kinetically trapped conformations within the protein receptor. In
	the combined strategy, each system with a given thermodynamic coupling
	factor λ in the extended ensemble is further coupled with a set of
	replicas evolving on a biased energy surface with boosting potentials
	used to accelerate the interconversion among different rotameric
	states of the side chains in the neighborhood of the binding site.
	Exchanges are allowed to occur alternatively along the axes corresponding
	to the thermodynamic coupling parameter λ and the boosting potential,
	in an extended dual array of coupled λ- and H-REMD simulations. The
	method is implemented on the basis of new extensions to the REPDSTR
	module of the biomolecular simulation program CHARMM. As an illustrative
	example, the absolute binding free energy of p-xylene to the nonpolar
	cavity of the L99A mutant of the T4 lysozyme was calculated. The
	tests demonstrate that the dual λ-REMD and H-REMD simulation scheme
	greatly accelerates the configurational sampling of the rotameric
	states of the side chains around the binding pocket, thereby improving
	the convergence of the FEP computations.},
  comment = {doi: 10.1021/ct1001768},
  issn = {1549-9618},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2010.08.04},
  url = {http://dx.doi.org/10.1021/ct1001768}
}

@ARTICLE{Arnett:74,
  author = {Jones, F. M. and Arnett, E. M.},
  journal = {Prog. Phys. Org. Chem.},
  year = {1974},
  volume = {11},
  pages = {263},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Jones-Hertzog:Jorgensen:1997,
  author = {Jones-Hertzog, {D. K.} and Jorgensen, {W. L.}},
  title = {Binding affinities for sulfonamide inhibitors with human thrombin
	using {M}onte {C}arlo simulations with a linear response method},
  journal = {J. Med. Chem.},
  year = {1997},
  volume = {40},
  pages = {1539--1549},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Jorgensen2010,
  author = {Jorgensen, W. L.},
  title = {Drug discovery: Pulled from a protein's embrace},
  journal = {Nature},
  year = {2010},
  volume = {466},
  pages = {42--43},
  number = {7302},
  comment = {Jul 1

	Drug discovery: Pulled from a protein's embrace

	20596009

	Jorgensen, William L

	eng},
  issn = {1476-4687 (Electronic) 0028-0836 (Linking)},
  keywords = {Catalytic Domain *Computer-Aided Design Drug Design Drug Discovery/*methods
	Enzyme Inhibitors/*chemistry/*metabolism Flavonoids/chemistry/metabolism
	Ligands Luteolin/chemistry/metabolism Molecular Dynamics Simulation
	Plasmodium falciparum Protein Binding Protozoan Proteins/chemistry/metabolism
	Thermodynamics},
  owner = {mauro},
  refid = {16},
  timestamp = {2011.07.22},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=20596009}
}

@ARTICLE{Jorgensen2009,
  author = {William L Jorgensen},
  title = {Efficient drug lead discovery and optimization.},
  journal = {Acc Chem Res},
  year = {2009},
  volume = {42},
  pages = {724--733},
  number = {6},
  month = {Jun},
  abstract = {During the 1980s, advances in the abilities to perform computer simulations
	of chemical and biomolecular systems and to calculate free energy
	changes led to the expectation that such methodology would soon show
	great utility for guiding molecular design. Important potential applications
	included design of selective receptors, catalysts, and regulators
	of biological function including enzyme inhibitors. This time also
	saw the rise of high-throughput screening and combinatorial chemistry
	along with complementary computational methods for de novo design
	and virtual screening including docking. These technologies appeared
	poised to deliver diverse lead compounds for any biological target.
	As with many technological advances, realization of the expectations
	required significant additional effort and time. However, as summarized
	here, striking success has now been achieved for computer-aided drug
	lead generation and optimization. De novo design using both molecular
	growing and docking are illustrated for lead generation, and lead
	optimization features free energy perturbation calculations in conjunction
	with Monte Carlo statistical mechanics simulations for protein-inhibitor
	complexes in aqueous solution. The specific applications are to the
	discovery of non-nucleoside inhibitors of HIV reverse transcriptase
	(HIV-RT) and inhibitors of the binding of the proinflammatory cytokine
	MIF to its receptor CD74. A standard protocol is presented that includes
	scans for possible additions of small substituents to a molecular
	core, interchange of heterocycles, and focused optimization of substituents
	at one site. Initial leads with activities at low-micromolar concentrations
	have been advanced rapidly to low-nanomolar inhibitors.},
  doi = {10.1021/ar800236t},
  institution = {Department of Chemistry, Yale University, New Haven, Connecticut
	06520-8107, USA.},
  keywords = {Antigens, Differentiation, B-Lymphocyte; Binding Sites; Combinatorial
	Chemistry Techniques; Computer Simulation; Computer-Aided Design;
	Drug Discovery; Drug Evaluation, Preclinical; HIV Reverse Transcriptase;
	Histocompatibility Antigens Class II; Monte Carlo Method; Protein
	Binding; Reverse Transcriptase Inhibitors; Structure-Activity Relationship;
	Thermodynamics},
  owner = {emilio},
  pmid = {19317443},
  timestamp = {2010.06.02},
  url = {http://dx.doi.org/10.1021/ar800236t}
}

@ARTICLE{Jorgensen2004,
  author = {William L Jorgensen},
  title = {The many roles of computation in drug discovery.},
  journal = {Science},
  year = {2004},
  volume = {303},
  pages = {1813--1818},
  number = {5665},
  month = {Mar},
  abstract = {An overview is given on the diverse uses of computational chemistry
	in drug discovery. Particular emphasis is placed on virtual screening,
	de novo design, evaluation of drug-likeness, and advanced methods
	for determining protein-ligand binding.},
  doi = {10.1126/science.1096361},
  institution = {Department of Chemistry, Yale University, New Haven, CT 06520-8107,
	USA. william.jorgensen@yale.edu},
  keywords = {Computer Simulation; Computers; Drug Design; Drug Evaluation, Preclinical;
	Ligands; Models, Molecular; Molecular Structure; Pharmaceutical Preparations;
	Protein Binding; Proteins; Software},
  owner = {emilio},
  pii = {303/5665/1813},
  pmid = {15031495},
  timestamp = {2010.04.20},
  url = {http://dx.doi.org/10.1126/science.1096361}
}

@ARTICLE{Jorgensen:95,
  author = {Jorgensen, W. L.},
  journal = {J. Phys. Chem.},
  year = {1995},
  volume = {99},
  pages = {10667-10673},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Jorgensen1989,
  author = {Jorgensen, William L.},
  title = {Interactions between amides in solution and the thermodynamics of
	weak binding},
  journal = {Journal of the American Chemical Society},
  year = {1989},
  volume = {111},
  pages = {3770--3771},
  number = {10},
  month = may,
  abstract = {null},
  comment = {doi: 10.1021/ja00192a057},
  issn = {0002-7863},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2011.02.03},
  url = {http://dx.doi.org/10.1021/ja00192a057}
}

@ARTICLE{Jorgensen:89,
  author = {Jorgensen, W. L.},
  journal = {Acc. Chem. Res.},
  year = {1989},
  volume = {22},
  pages = {184},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Jorgensen:Blake:Buckner:89,
  author = {Jorgensen, W. L. and Blake, J. F. and Buckner, J. K.},
  title = {Free Energy of TIP4P water and the Free Energies of Hydration of
	CH$_4$ and Cl$^-$ from Statistical Perturbation Theory},
  journal = {Chem. Phys.},
  year = {1989},
  volume = {129},
  pages = {193},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Jorgensen:Buckner:Boudon:Rives:88,
  author = {Jorgensen, W. L. and Buckner, J. K. and Boudon, S. and Tirado-Rives,
	J.},
  title = {Efficient Computation of Absolute Free Energies of Binding by Computer
	Simulations. Application to the Methane Dimer in Water},
  journal = {J. Chem. Phys.},
  year = {1988},
  volume = {89},
  pages = {3742},
  number = {6},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Jorgensen:Chandrasekhar:Madura:83b,
  author = {Jorgensen, W. L. and Chandrasekhar, J. and Madura, J. D.},
  title = {Comparison of Simple Potential Functions for Simulating Liquid Water},
  journal = {J. Chem. Phys.},
  year = {1983},
  volume = {79},
  pages = {926-935},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Jorgensen:Chandrasekhar:Madura:83,
  author = {Jorgensen, W. L. and Chandrasekhar, J. and Madura, J. D. and Impey,
	R. W. and Klein, M. L.},
  title = {Comparison of Simple Potential Functions for Simulating Liquid Water},
  journal = {J. Chem. Phys.},
  year = {1983},
  volume = {79},
  pages = {926},
  number = {2},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Jorgensen:Gao:Ravimohan:85,
  author = {Jorgensen, W. L. and Gao, J. and Ravimohan, C.},
  title = {Monte Carlo Simulations of Alkanes in Water: Hydration Numbers and
	Hydrophobic Effect},
  journal = {J. of Phys. Chem.},
  year = {1985},
  volume = {89},
  pages = {3470},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Jorgensen:Madura:85,
  author = {Jorgensen, W. L. and Madura, J. D.},
  title = {TEMPERATURE AND SIZE DEPENDENCE FOR MONTE-CARLO SIMULATIONS OF TIP4P
	WATER},
  journal = {Mol. Phys.},
  year = {1985},
  volume = {56},
  pages = {1381-1392},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Jorgensen:Maxwell:96,
  author = {Jorgensen, W. L. and Maxwell, D. S. and Tirado-Rives, J.},
  title = {Developement and Testing of the OPLS All-Atom Force Field on Conformational
	Energetics and Properties of Organic Liquids},
  journal = {J. Am. Chem. Soc.},
  year = {1996},
  volume = {118},
  pages = {11225-11236},
  owner = {emilio},
  timestamp = {2010.11.02}
}

@ARTICLE{Jorgensen2008,
  author = {Jorgensen, William L. and Thomas, Laura L.},
  title = {Perspective on Free-Energy Perturbation Calculations for Chemical
	Equilibria},
  journal = {J. Chem. Theory Comput.},
  year = {2008},
  volume = {4},
  pages = {869--876},
  number = {6},
  month = jun,
  comment = {doi: 10.1021/ct800011m},
  issn = {1549-9618},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2010.04.30},
  url = {http://dx.doi.org/10.1021/ct800011m}
}

@ARTICLE{Jorgensen:Ulmschneider:Tirado-Rives:2004,
  author = {Jorgensen, {W. L.} and Ulmschneider, {J. P.} and Tirado-Rives, J.},
  title = {Free Energies of Hydration from a Generalized Born Model and an All-Atom
	Force Field},
  journal = {J. Phys. Chem. B},
  year = {2004},
  volume = {108},
  pages = {16264--16270},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Kaminski:2001,
  author = {G. A. Kaminski and R. A. Friesner and J. Tirado-{R}ives and W. L.
	Jorgensen},
  title = {Evaluation and reparameterization of the {OPLS-AA} force field for
	proteins via comparison with accurate quantum chemical calculations
	on peptides},
  journal = {J. Phys. Chem. B},
  year = {2001},
  volume = {105},
  pages = {6474--6487},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Kaminski:Jorgensen:94,
  author = {Kaminski, G. and Duffy, E. M. and Matsui, T. and Jorgensen, W. L.},
  title = {Free Energies of Hydration and Pure Liquid Properties of Hydrocarbons
	from the OPLS All-Atom Model},
  journal = {J. Phys. Chem.},
  year = {1994},
  volume = {98},
  pages = {13077},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@MISC{Kaminski:Jorgensen:98,
  author = {Kaminski, G. and Jorgensen, W. L.},
  note = {Personal communication.},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Kar2010,
  author = {Gozde Kar and Ozlem Keskin and Attila Gursoy and Ruth Nussinov},
  title = {Allostery and population shift in drug discovery.},
  journal = {Curr Opin Pharmacol},
  year = {2010},
  volume = {10},
  pages = {715--722},
  number = {6},
  month = {Dec},
  abstract = {Proteins can exist in a large number of conformations around their
	native states that can be characterized by an energy landscape. The
	landscape illustrates individual valleys, which are the conformational
	substates. From the functional standpoint, there are two key points:
	first, all functionally relevant substates pre-exist; and second,
	the landscape is dynamic and the relative populations of the substates
	will change following allosteric events. Allosteric events perturb
	the structure, and the energetic strain propagates and shifts the
	population. This can lead to changes in the shapes and properties
	of target binding sites. Here we present an overview of dynamic conformational
	ensembles focusing on allosteric events in signaling. We propose
	that combining equilibrium fluctuation concepts with genomic screens
	could help drug discovery.},
  doi = {10.1016/j.coph.2010.09.002},
  institution = {Center for Computational Biology and Bioinformatics and College of
	Engineering, Koc University Rumelifeneri Yolu, 34450 Sariyer Istanbul,
	Turkey.},
  owner = {emilio},
  pii = {S1471-4892(10)00138-4},
  pmid = {20884293},
  timestamp = {2011.01.18},
  url = {http://dx.doi.org/10.1016/j.coph.2010.09.002}
}

@ARTICLE{Karplus2010,
  author = {Martin Karplus},
  title = {Dynamical aspects of molecular recognition.},
  journal = {J Mol Recognit},
  year = {2010},
  volume = {23},
  pages = {102--104},
  number = {2},
  month = {Mar},
  doi = {10.1002/jmr.1018},
  institution = { Chemical Biology, 12 Oxford Street, Harvard University Cambridge,
	Massachusetts 02138, USA. marci@tammy.harvard.edu},
  keywords = {Binding Sites; Ligands; Protein Binding; Proteins; Thermodynamics},
  owner = {emilio},
  pmid = {20151415},
  timestamp = {2010.09.15},
  url = {http://dx.doi.org/10.1002/jmr.1018}
}

@ARTICLE{Kato:95,
  author = {Kato, M. and Makino, R. and Iizuka, T.},
  title = {Thermodynamic Aspects of the CO-binding Reaction to Cytochrome {P-450$_{\rm
	cam}$}. Relevance with their Biological Significance and Structure},
  journal = {Biochimica et Biophysica Acta},
  year = {1995},
  volume = {1246},
  pages = {178-184},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Kauzmann:59,
  author = {Kauzmann, W.},
  title = {Some factors in the interpretation of protein denaturation},
  journal = {Adv. in Prot. Chem.},
  year = {1959},
  volume = {14},
  pages = {1-63},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Khavrutskii2011,
  author = {Khavrutskii, Ilja V. and Wallqvist, Anders},
  title = {Improved Binding Free Energy Predictions from Single-Reference Thermodynamic
	Integration Augmented with Hamiltonian Replica Exchange},
  journal = {J. Chem. Theory Comput.},
  year = {2011},
  volume = {7},
  pages = {3001--3011},
  number = {9},
  month = aug,
  abstract = {Reliable predictions of relative binding free energies are essential
	in drug discovery, where chemists modify promising compounds with
	the aim of increasing binding affinity. Conventional thermodynamic
	integration (TI) approaches can estimate corresponding changes in
	binding free energies but suffer from inadequate sampling due to
	the ruggedness of the molecular energy surfaces. Here, we present
	an improved TI strategy for computing relative binding free energies
	of congeneric ligands. This strategy employs a specific, unphysical
	single-reference (SR) state and Hamiltonian replica exchange (HREX)
	to locally enhance sampling. We then apply this strategy to compute
	relative binding free energies of 12 ligands in the L99A mutant of
	T4 lysozyme. Besides the ligands, our approach enhances hindered
	rotations of the important V111 as well as V87 and L118 side chains.
	Concurrently, we devise practical strategies to monitor and improve
	HREX-SRTI efficiency. Overall, the HREX-SRTI results agree well (R2
	= 0.76, RMSE = 0.3 kcal/mol) with available experimental data. When
	optimized for efficiency, the HREX-SRTI precision matches that of
	experimental measurements.

	Reliable predictions of relative binding free energies are essential
	in drug discovery, where chemists modify promising compounds with
	the aim of increasing binding affinity. Conventional thermodynamic
	integration (TI) approaches can estimate corresponding changes in
	binding free energies but suffer from inadequate sampling due to
	the ruggedness of the molecular energy surfaces. Here, we present
	an improved TI strategy for computing relative binding free energies
	of congeneric ligands. This strategy employs a specific, unphysical
	single-reference (SR) state and Hamiltonian replica exchange (HREX)
	to locally enhance sampling. We then apply this strategy to compute
	relative binding free energies of 12 ligands in the L99A mutant of
	T4 lysozyme. Besides the ligands, our approach enhances hindered
	rotations of the important V111 as well as V87 and L118 side chains.
	Concurrently, we devise practical strategies to monitor and improve
	HREX-SRTI efficiency. Overall, the HREX-SRTI results agree well (R2
	= 0.76, RMSE = 0.3 kcal/mol) with available experimental data. When
	optimized for efficiency, the HREX-SRTI precision matches that of
	experimental measurements.},
  booktitle = {Journal of Chemical Theory and Computation},
  comment = {doi: 10.1021/ct2003786},
  issn = {1549-9618},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2011.09.27},
  url = {http://dx.doi.org/10.1021/ct2003786}
}

@ARTICLE{Khavrutskii2010,
  author = {Khavrutskii, Ilja V. and Wallqvist, Anders},
  title = {Computing Relative Free Energies of Solvation Using Single Reference
	Thermodynamic Integration Augmented with Hamiltonian Replica Exchange},
  journal = {Journal of Chemical Theory and Computation},
  year = {2010},
  volume = {6},
  pages = {3427--3441},
  number = {11},
  month = nov,
  abstract = {This paper introduces an efficient single-topology variant of Thermodynamic
	Integration (TI) for computing relative transformation free energies
	in a series of molecules with respect to a single reference state.
	The presented TI variant that we refer to as Single-Reference TI
	(SR-TI) combines well-established molecular simulation methodologies
	into a practical computational tool. Augmented with Hamiltonian Replica
	Exchange (HREX), the SR-TI variant can deliver enhanced sampling
	in select degrees of freedom. The utility of the SR-TI variant is
	demonstrated in calculations of relative solvation free energies
	for a series of benzene derivatives with increasing complexity. Of
	note, the SR-TI variant with the HREX option provides converged results
	in a challenging case of an amide molecule with a high (13−15 kcal/mol)
	barrier for internal cis/trans interconversion using simulation times
	of only 1 to 4 ns.},
  comment = {doi: 10.1021/ct1003302},
  issn = {1549-9618},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2011.01.13},
  url = {http://dx.doi.org/10.1021/ct1003302}
}

@ARTICLE{Kim2011,
  author = {Jaegil Kim and Thomas Keyes and John E Straub},
  title = {Communication: Iteration-free, weighted histogram analysis method
	in terms of intensive variables.},
  journal = {J Chem Phys},
  year = {2011},
  volume = {135},
  pages = {061103},
  number = {6},
  month = {Aug},
  abstract = {We present an iteration-free weighted histogram method in terms of
	intensive variables that directly determines the inverse statistical
	temperature, β(S) = ∂S/∂E, with S the microcanonical entropy. The
	method eliminates iterative evaluations of the partition functions
	intrinsic to the conventional approach and leads to a dramatic acceleration
	of the posterior analysis of combining statistically independent
	simulations with no loss in accuracy. The synergistic combination
	of the method with generalized ensemble weights provides insights
	into the nature of the underlying phase transitions via signatures
	in β(S) characteristic of finite size systems. The versatility and
	accuracy of the method is illustrated for the Ising and Potts models.},
  doi = {10.1063/1.3626150},
  institution = {Department of Chemistry, Boston University, Boston, Massachusetts
	02215, USA. jaegilkim89@gmail.com},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {21842919},
  timestamp = {2012.02.06},
  url = {http://dx.doi.org/10.1063/1.3626150}
}

@ARTICLE{Kim2010b,
  author = {Jaegil Kim and Thomas Keyes and John E Straub},
  title = {Generalized replica exchange method.},
  journal = {J Chem Phys},
  year = {2010},
  volume = {132},
  pages = {224107},
  number = {22},
  month = {Jun},
  abstract = {We present a powerful replica exchange method, particularly suited
	to first-order phase transitions associated with the backbending
	in the statistical temperature, by merging an optimally designed
	generalized ensemble sampling with replica exchanges. The key ingredients
	of our method are parametrized effective sampling weights, smoothly
	joining ordered and disordered phases with a succession of unimodal
	energy distributions by transforming unstable or metastable energy
	states of canonical ensembles into stable ones. The inverse mapping
	between the sampling weight and the effective temperature provides
	a systematic way to design the effective sampling weights and determine
	a dynamic range of relevant parameters. Illustrative simulations
	on Potts spins with varying system size and simulation conditions
	demonstrate a comprehensive sampling for phase-coexistent states
	with a dramatic acceleration of tunneling transitions. A significant
	improvement over the power-law slowing down of mean tunneling times
	with increasing system size is obtained, and the underlying mechanism
	for accelerated tunneling is discussed.},
  doi = {10.1063/1.3432176},
  institution = {Department of Chemistry, Boston University, Boston, Massachusetts
	02215, USA. jaegil@bu.edu},
  keywords = {Hot Temperature; Models, Theoretical; Phase Transition; Thermodynamics},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {20550390},
  timestamp = {2012.02.06},
  url = {http://dx.doi.org/10.1063/1.3432176}
}

@ARTICLE{Kim2009a,
  author = {Jaegil Kim and Thomas Keyes and John E Straub},
  title = {Replica exchange statistical temperature Monte Carlo.},
  journal = {J Chem Phys},
  year = {2009},
  volume = {130},
  pages = {124112},
  number = {12},
  month = {Mar},
  abstract = {The replica exchange statistical temperature Monte Carlo algorithm
	(RESTMC) is presented, extending the single-replica STMC algorithm
	[J. Kim, J. E. Straub, and T. Keyes, Phys. Rev. Lett. 97, 050601
	(2006)] to alleviate the slow convergence of the conventional temperature
	replica exchange method (t-REM) with increasing system size. In contrast
	to the Gibbs-Boltzmann sampling at a specific temperature characteristic
	of the standard t-REM, RESTMC samples a range of temperatures in
	each replica and achieves a flat energy sampling employing the generalized
	sampling weight, which is automatically determined via the dynamic
	modification of the replica-dependent statistical temperature. Faster
	weight determination, through the dynamic update of the statistical
	temperature, and the flat energy sampling, maximizing energy overlaps
	between neighboring replicas, lead to a considerable acceleration
	in the convergence of simulations even while employing significantly
	fewer replicas. The performance of RESTMC is demonstrated and quantitatively
	compared with that of the conventional t-REM under varying simulation
	conditions for Lennard-Jones 19, 31, and 55 atomic clusters, exhibiting
	single- and double-funneled energy landscapes.},
  doi = {10.1063/1.3095422},
  institution = {Department of Chemistry, Boston University, Boston, Massachusetts
	02215, USA. jaegil@bu.edu},
  keywords = {Algorithms; Models, Chemical; Monte Carlo Method; Temperature; Thermodynamics},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {19334813},
  timestamp = {2012.02.06},
  url = {http://dx.doi.org/10.1063/1.3095422}
}

@ARTICLE{Kim2010,
  author = {Jaegil Kim and John E Straub},
  title = {Generalized simulated tempering for exploring strong phase transitions.},
  journal = {J. Chem. Phys.},
  year = {2010},
  volume = {133},
  pages = {154101},
  number = {15},
  month = {Oct},
  __markedentry = {[mauro]},
  abstract = {An extension of the simulation tempering algorithm is proposed. It
	is shown to be particularly suited to the exploration of first-order
	phase transition systems characterized by the backbending or S-loop
	in the statistical temperature or a microcanonical caloric curve.
	A guided Markov process in an auxiliary parameter space systematically
	combines a set of parametrized Tsallis-weight ensemble simulations,
	which are targeted to transform unstable or metastable energy states
	of canonical ensembles into stable ones and smoothly join ordered
	and disordered phases across phase transition regions via a succession
	of unimodal energy distributions. The inverse mapping between the
	sampling weight and the effective temperature enables an optimal
	selection of relevant Tsallis-weight parameters. A semianalytic expression
	for the biasing weight in parameter space is adaptively updated "on
	the fly" during the simulation to achieve rapid convergence. Accelerated
	tunneling transitions with a comprehensive sampling for phase-coexistent
	states are explicitly demonstrated in systems subject to strong hysteresis
	including Potts and Ising spin models and a 147 atom Lennard-Jones
	cluster.},
  doi = {10.1063/1.3503503},
  institution = {Department of Chemistry, Boston University, Boston, Massachusetts
	02215, USA. jaegilkim89@gmail.com},
  keywords = {Algorithms; Computer Simulation; Markov Chains; Models, Chemical;
	Phase Transition; Thermodynamics},
  language = {eng},
  medline-pst = {ppublish},
  owner = {mauro},
  pmid = {20969364},
  timestamp = {2011.09.24},
  url = {http://dx.doi.org/10.1063/1.3503503}
}

@ARTICLE{Kim2009,
  author = {Jaegil Kim and John E Straub},
  title = {Optimal replica exchange method combined with Tsallis weight sampling.},
  journal = {J Chem Phys},
  year = {2009},
  volume = {130},
  pages = {144114},
  number = {14},
  month = {Apr},
  abstract = {A unified framework integrating the generalized ensemble sampling
	associated with the Tsallis weight [C. Tsallis, J. Stat. Phys. 52,
	479 (1988)] and the replica exchange method (REM) has been proposed
	to accelerate the convergence of the conventional temperature REM
	(t-REM). Using the effective temperature formulation of the Tsallis
	weight sampling, it is shown that the average acceptance probability
	for configurational swaps between neighboring replicas in the combination
	of Tsallis weight sampling and REM (Tsallis-REM) is directly proportional
	to an overlap integral of the energy distributions of neighboring
	replicas as in the t-REM. Based on this observation, we suggest a
	robust method to select optimal Tsallis parameters in the conventional
	parametrization scheme and present new parametrization schemes for
	the Tsallis-REM, which significantly improves the acceptance of configurational
	swaps by systematically modulating energy overlaps between neighboring
	replicas. The distinguished feature of our method is that all relevant
	parameters in the Tsallis-REM are automatically determined from the
	equilibrium phase simulation using the t-REM. The overall performance
	of our method is explicitly demonstrated for various simulation conditions
	for the Lennard-Jones 31 atom clusters, exhibiting a double-funneled
	energy landscape.},
  doi = {10.1063/1.3108523},
  institution = {Department of Chemistry, Boston University, Boston, Massachusetts
	02215, USA. jaegil@bu.edu},
  keywords = {Algorithms; Computer Simulation; Models, Molecular; Molecular Conformation;
	Thermodynamics},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {19368436},
  timestamp = {2012.02.06},
  url = {http://dx.doi.org/10.1063/1.3108523}
}

@ARTICLE{King:Warshel:90,
  author = {King, G. and Warshel, A.},
  journal = {J. Chem. Phys.},
  year = {1990},
  volume = {93},
  pages = {8682-8692},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Warshel:89,
  author = {King, G. and Warshel, A.},
  title = {A surface constrained all-atom solvent model for effective simulations
	of polar solutions},
  journal = {J. Chem. Phys.},
  year = {1989},
  volume = {91},
  pages = {3647},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Kitchen:Hirata:Kofke:Westbrook:Yormush:Levy:90,
  author = {Kitchen, D. B and Hirata, F. and D. A. Kofke, D. A. and Westbrook,
	J. D. and Yormush, M. and Levy, R. M. },
  journal = {J. Comput. Chem.},
  year = {1990},
  volume = {11},
  pages = {1169-1180},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Kitchen:Hirata:Westbrook:Levy:90,
  author = {Kitchen, D. B. and Hirata, F. and Westbrook, J. D. and Levy, R. M.
	and Kofke, D. and Yarmush, M.},
  journal = {J. Comput. Chem.},
  year = {1990},
  volume = {11},
  pages = {1169},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Knight2009a,
  author = {Jennifer L Knight and Charles L Brooks},
  title = {Lambda-dynamics free energy simulation methods.},
  journal = {J. Comput. Chem.},
  year = {2009},
  volume = {30},
  pages = {1692--1700},
  number = {11},
  month = {Aug},
  abstract = {Free energy calculations are fundamental to obtaining accurate theoretical
	estimates of many important biological phenomena including hydration
	energies, protein-ligand binding affinities and energetics of conformational
	changes. Unlike traditional free energy perturbation and thermodynamic
	integration methods, lambda-dynamics treats the conventional "lambda"
	as a dynamic variable in free energy simulations and simultaneously
	evaluates thermodynamic properties for multiple states in a single
	simulation. In the present article, we provide an overview of the
	theory of lambda-dynamics, including the use of biasing and restraining
	potentials to facilitate conformational sampling. We review how lambda-dynamics
	has been used to rapidly and reliably compute relative hydration
	free energies and binding affinities for series of ligands, to accurately
	identify crystallographically observed binding modes starting from
	incorrect orientations, and to model the effects of mutations upon
	protein stability. Finally, we suggest how lambda-dynamics may be
	extended to facilitate modeling efforts in structure-based drug design.},
  doi = {10.1002/jcc.21295},
  institution = {Department of Chemistry, University of Michigan, 930 N. University
	Ann Arbor, Michigan 48109, USA.},
  keywords = {Computer Simulation; Drug Design; Drug Resistance; Hepacivirus; Ligands;
	Models, Biological; Protease Inhibitors; Protein Binding; Proteins;
	Thermodynamics},
  owner = {emilio},
  pmid = {19421993},
  timestamp = {2010.09.23},
  url = {http://dx.doi.org/10.1002/jcc.21295}
}

@ARTICLE{Kohl1988,
  author = {N. E. Kohl and E. A. Emini and W. A. Schleif and L. J. Davis and
	J. C. Heimbach and R. A. Dixon and E. M. Scolnick and I. S. Sigal},
  title = {Active human immunodeficiency virus protease is required for viral
	infectivity.},
  journal = {Proc Natl Acad Sci U S A},
  year = {1988},
  volume = {85},
  pages = {4686--4690},
  number = {13},
  month = {Jul},
  abstract = {Retroviral proteins are synthesized as polyprotein precursors that
	undergo proteolytic cleavages to yield the mature viral proteins.
	The role of the human immunodeficiency virus (HIV) protease in the
	viral replication cycle was examined by use of a site-directed mutation
	in the protease gene. The HIV protease gene product was expressed
	in Escherichia coli and observed to cleave HIV gag p55 to gag p24
	and gag p17 in vitro. Substitution of aspartic acid residue 25 (Asp-25)
	of this protein with an asparagine residue did not affect the expression
	of the protein, but it eliminated detectable in vitro proteolytic
	activity against HIV gag p55. A mutant HIV provirus was constructed
	that contained the Asn-25 mutation within the protease gene. SW480
	human colon carcinoma cells transfected with the Asn-25 mutant proviral
	DNA produced virions that contained gag p55 but not gag p24, whereas
	virions from cells transfected with the wild-type DNA contained both
	gag p55 and gag p24. The mutant virions were not able to infect MT-4
	lymphoid cells. In contrast, these cells were highly sensitive to
	infection by the wild-type virions. These results demonstrate that
	the HIV protease is an essential viral enzyme and, consequently,
	an attractive target for anti-HIV drugs.},
  institution = { Dohme Research Laboratories, West Point, PA 19486.},
  keywords = {Asparagine; Binding Sites; Endopeptidases; Gene Products, gag; HIV;
	HIV Protease; Protein Precursors; Proviruses; Recombinant Fusion
	Proteins; Retroviridae Proteins; Viral Proteins; Virulence; Virus
	Replication},
  owner = {emilio},
  pmid = {3290901},
  timestamp = {2010.07.14}
}

@ARTICLE{Kollman:93,
  author = {Kollman, P.},
  journal = {Chem. Rev.},
  year = {1993},
  volume = {93},
  pages = {2395},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Kollman:96,
  author = {Kollman, P. A.},
  journal = {Accts. Chem. Res.},
  year = {1996},
  volume = {29},
  pages = {461-469},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Kollman2000,
  author = {P. A. Kollman and I. Massova and C. Reyes and B. Kuhn and S. Huo
	and L. Chong and M. Lee and T. Lee and Y. Duan and W. Wang and O.
	Donini and P. Cieplak and J. Srinivasan and D. A. Case and T. E.
	Cheatham},
  title = {Calculating structures and free energies of complex molecules: combining
	molecular mechanics and continuum models.},
  journal = {Acc. Chem. Res.},
  year = {2000},
  volume = {33},
  pages = {889--897},
  number = {12},
  month = {Dec},
  abstract = {A historical perspective on the application of molecular dynamics
	(MD) to biological macromolecules is presented. Recent developments
	combining state-of-the-art force fields with continuum solvation
	calculations have allowed us to reach the fourth era of MD applications
	in which one can often derive both accurate structure and accurate
	relative free energies from molecular dynamics trajectories. We illustrate
	such applications on nucleic acid duplexes, RNA hairpins, protein
	folding trajectories, and protein-ligand, protein-protein, and protein-nucleic
	acid interactions.},
  institution = {Department of Pharmaceutical Chemistry, University of California,
	San Francisco, California 94143, USA.},
  keywords = {Base Sequence; DNA; Models, Molecular; Molecular Structure; Proteins;
	RNA; Thermodynamics},
  owner = {emilio},
  pii = {ar000033j},
  pmid = {11123888},
  timestamp = {2010.04.21}
}

@ARTICLE{Kolossvary1997,
  author = {Kolossvary, Istvan},
  title = {Evaluation of the Molecular Configuration Integral in All Degrees
	of Freedom for the Direct Calculation of Conformational Free Energies:
	Prediction of the Anomeric Free Energy of Monosaccharides},
  journal = {The Journal of Physical Chemistry A},
  year = {1997},
  volume = {101},
  pages = {9900--9905},
  number = {51},
  month = dec,
  abstract = {A novel theoretical approach is presented for the direct calculation
	of conformational free energies without the need for expensive free
	energy simulations and the use of computational alchemy. It is shown
	that conformational search combined with advanced Monte Carlo integration
	can tackle the daunting problem of solving the molecular configuration
	integral in all degrees of freedom, affording a direct method to
	calculate accurate conformational free energies. The new algorithm
	termed mode integration (MINTA) was applied here to explain anharmonic
	effects in cycloheptane and to predict the A value of cyclohexane
	derivatives and the anomeric free energy of carbohydrates (tetrahydropyran
	derivatives and pyranose monosaccharides) using a continuum solvation
	model.},
  comment = {doi: 10.1021/jp972794i},
  issn = {1089-5639},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2011.02.07},
  url = {http://dx.doi.org/10.1021/jp972794i}
}

@ARTICLE{Kong2003,
  author = {Kong, A. and McCullagh, P. and Meng, X.-L. and Nicolae, D. and Tan,
	Z.},
  title = {A theory of statistical models for Monte Carlo integration},
  journal = {Journal of the Royal Statistical Society B},
  year = {2003},
  volume = {65},
  pages = {585-618},
  comment = {From Zhiqiang},
  owner = {emilio},
  timestamp = {2011.11.06}
}

@ARTICLE{Kratky:81,
  author = {Kratky, K. W.},
  title = {Intersecting disks (and spheres) and statistical mechanics. I. Mathematical
	basis},
  journal = {J. Statist. Phys.},
  year = {1981},
  volume = {25},
  pages = {619-634},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{KroegherSmith:Rizzo:Jorgensen:Smith:2003,
  author = {Kroeger Smith, {M. B.} and Hose, {B. M.} and Hawkins, A. and Lipchock,
	J. and Farnsworth, {D. W.} and Rizzo, {R. C.} and Tirado-Rives, J.
	and Arnold, E. and Zhang, W. and Hughes, {S. H.} and Jorgensen, {W.
	L.} and Michejda, {C. J.} and Smith Jr., {R. H.}},
  title = {Molecular Modeling Calculations of HIV-1 Reverse Transcriptase Nonnucleoside
	Inhibitors: Correlation of Binding Energy with Biological Activity
	for Novel 2-Aryl-Substituted Benzimidazole Analogues},
  journal = {J. Med. Chem.},
  year = {2003},
  volume = {46},
  pages = {1940--1947},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Krug:Hunter:Geiger:76,
  author = {Krug, R. R. and Hunter, W. G. and Geiger, R. A.},
  title = {Enthalpy-Entropy Compensation. 1. Some Fundamental Statistical Problems
	Associated with the Analysis of vant'Hoff and Arrehenius Data},
  journal = {J. Phys. Chem.},
  year = {1976},
  volume = {80},
  pages = {2335},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Kubo:Gallicchio:97,
  author = {Kubo, M. F. and Gallicchio, E. and Levy, R. M.},
  title = {Thermodynamic Decomposition of Hydration Free Energies by Computer
	Simulation: Application to Amines, Oxides and Sulfides},
  journal = {J. Phys. Chem.},
  year = {1997},
  volume = {101},
  pages = {10527-10534},
  number = {49},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Kumar:Kollman:Rosenberg:1992,
  author = {Kumar, S. and Bouzida, D. and Swendsen, R. H. and Kollman, P. A.
	and Rosenberg, J. M.},
  title = {The Weighted Histogram Analysis Method for free-energy calculations
	on biomolecules. I. The method.},
  journal = {J. Comput. Chem.},
  year = {1992},
  volume = {13},
  pages = {1011-1021},
  owner = {emilio},
  timestamp = {2011.02.08}
}

@ARTICLE{Kuroki:92,
  author = {Kuroki, R. and Nitta, K. and Yutani, K.},
  title = {Thermodynamic Changes in the Binding of {Ca}$^{2+}$ to a Mutant Human
	Lysozyme (D86/92)},
  journal = {J. of Biological Chemistry},
  year = {1992},
  volume = {267},
  pages = {24297-24301},
  number = {34},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Labute:2008,
  author = {Labute, P.},
  title = {The generalized Born/volume integral implicit solvent model: Estimation
	of the free energy of hydration using London dispersion instead of
	atomic surface area},
  journal = {J. Comp. Chem.},
  year = {2008},
  volume = {29},
  pages = {1693--1698},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Jorgensen:97,
  author = {Lamb, M. L. and Jorgensen, W. L.},
  title = {Computational Approaches to Molecular Recognition},
  journal = {Curr. Op. Chem. Biol.},
  year = {1997},
  volume = {1},
  pages = {449-457},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Lange2008,
  author = {Oliver F Lange and Nils-Alexander Lakomek and Christophe Fares and
	Gunnar F Schroder and Korvin F A Walter and Stefan Becker and Jens
	Meiler and Helmut Grubmuller and Christian Griesinger and Bert L
	de Groot},
  title = {Recognition dynamics up to microseconds revealed from an RDC-derived
	ubiquitin ensemble in solution.},
  journal = {Science},
  year = {2008},
  volume = {320},
  pages = {1471--1475},
  number = {5882},
  month = {Jun},
  abstract = {Protein dynamics are essential for protein function, and yet it has
	been challenging to access the underlying atomic motions in solution
	on nanosecond-to-microsecond time scales. We present a structural
	ensemble of ubiquitin, refined against residual dipolar couplings
	(RDCs), comprising solution dynamics up to microseconds. The ensemble
	covers the complete structural heterogeneity observed in 46 ubiquitin
	crystal structures, most of which are complexes with other proteins.
	Conformational selection, rather than induced-fit motion, thus suffices
	to explain the molecular recognition dynamics of ubiquitin. Marked
	correlations are seen between the flexibility of the ensemble and
	contacts formed in ubiquitin complexes. A large part of the solution
	dynamics is concentrated in one concerted mode, which accounts for
	most of ubiquitin's molecular recognition heterogeneity and ensures
	a low entropic complex formation cost.},
  comment = {Receptor reorganization},
  doi = {10.1126/science.1157092},
  institution = {Department of Theoretical and Computational Biophysics, Max Planck
	Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen,
	Germany.},
  keywords = {Amino Acid Motifs; Animals; Anisotropy; Chemistry, Physical; Crystallography,
	X-Ray; Entropy; Kinetics; Models, Molecular; Nuclear Magnetic Resonance,
	Biomolecular; Physicochemical Phenomena; Protein Binding; Protein
	Conformation; Protein Structure, Tertiary; Solutions; Ubiquitin;
	Xenopus laevis},
  owner = {emilio},
  pii = {320/5882/1471},
  pmid = {18556554},
  timestamp = {2010.09.08},
  url = {http://dx.doi.org/10.1126/science.1157092}
}

@ARTICLE{Lansdon2010,
  author = {Eric B Lansdon and Katherine M Brendza and Magdeleine Hung and Ruth
	Wang and Susmith Mukund and Debi Jin and Gabriel Birkus and Nilima
	Kutty and Xiaohong Liu},
  title = {Crystal structures of HIV-1 reverse transcriptase with etravirine
	(TMC125) and rilpivirine (TMC278): implications for drug design.},
  journal = {J Med Chem},
  year = {2010},
  volume = {53},
  pages = {4295--4299},
  number = {10},
  month = {May},
  abstract = {Diarylpyrimidine (DAPY) non-nucleoside reverse transcriptase inhibitors
	(NNRTIs) have inherent flexibility, helping to maintain activity
	against a wide range of resistance mutations. Crystal structures
	were determined with wild-type and K103N HIV-1 reverse transcriptase
	with etravirine (TMC125) and rilpivirine (TMC278). These structures
	reveal a similar binding mode for TMC125 and TMC278, whether bound
	to wild-type or K103N RT. Comparison to previously published structures
	reveals differences in binding modes for TMC125 and differences in
	protein conformation for TMC278.},
  doi = {10.1021/jm1002233},
  institution = {Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California
	94404, USA. eric.lansdon@gilead.com},
  keywords = {Binding Sites; Crystallography, X-Ray; Drug Design; HIV Reverse Transcriptase,
	antagonists /&/ inhibitors/chemistry/genetics; HIV-1, enzymology;
	Models, Molecular; Mutation; Nitriles, chemistry; Protein Binding;
	Protein Conformation; Pyridazines, chemistry; Pyrimidines, chemistry},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {20438081},
  timestamp = {2012.02.22},
  url = {http://dx.doi.org/10.1021/jm1002233}
}

@ARTICLE{Lapelosa2010,
  author = {Mauro Lapelosa and Gail Ferstandig Arnold and Emilio Gallicchio and
	Eddy Arnold and Ronald M Levy},
  title = {Antigenic characteristics of rhinovirus chimeras designed in silico
	for enhanced presentation of {HIV-1} gp41 epitopes},
  journal = {J .Mol. Biol.},
  year = {2010},
  volume = {397},
  pages = {752--766},
  number = {3},
  month = {Apr},
  abstract = {The development of an effective AIDS vaccine remains the most promising
	long-term strategy to combat human immunodeficiency virus (HIV)/AIDS.
	Here, we report favorable antigenic characteristics of vaccine candidates
	isolated from a combinatorial library of human rhinoviruses displaying
	the ELDKWA epitope of the gp41 glycoprotein of HIV-1. The design
	principles of this library emerged from the application of molecular
	modeling calculations in conjunction with our knowledge of previously
	obtained ELDKWA-displaying chimeras, including knowledge of a chimera
	with one of the best 2F5-binding characteristics obtained to date.
	The molecular modeling calculations identified the energetic and
	structural factors affecting the ability of the epitope to assume
	conformations capable of fitting into the complementarity determining
	region of the ELDKWA-binding, broadly neutralizing human mAb 2F5.
	Individual viruses were isolated from the library following competitive
	immunoselection and were tested using ELISA and fluorescence quenching
	experiments. Dissociation constants obtained using both techniques
	revealed that some of the newly isolated chimeras bind 2F5 with greater
	affinity than previously identified chimeric rhinoviruses. Molecular
	dynamics simulations of two of these same chimeras confirmed that
	their HIV inserts were partially preorganized for binding, which
	is largely responsible for their corresponding gains in binding affinity.
	The study illustrates the utility of combining structure-based experiments
	with computational modeling approaches for improving the odds of
	selecting vaccine component designs with preferred antigenic characteristics.
	The results obtained also confirm the flexibility of HRV as a presentation
	vehicle for HIV epitopes and the potential of this platform for the
	development of vaccine components against AIDS.},
  doi = {10.1016/j.jmb.2010.01.064},
  institution = {BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway,
	NJ 08854, USA.},
  keywords = {AIDS Vaccines; Antibodies, Monoclonal; Antigens, Viral; Drug Design;
	Enzyme-Linked Immunosorbent Assay; Epitopes; HIV Antibodies; HIV
	Envelope Protein gp41; HIV-1; Humans; Neutralization Tests; Peptide
	Library; Protein Conformation; Rhinovirus},
  owner = {emilio},
  pii = {S0022-2836(10)00119-1},
  pmid = {20138057},
  timestamp = {2010.09.11},
  url = {http://dx.doi.org/10.1016/j.jmb.2010.01.064}
}

@ARTICLE{Lapelosa2009,
  author = {Mauro Lapelosa and Emilio Gallicchio and Gail Ferstandig Arnold and
	Eddy Arnold and Ronald M Levy},
  title = {In silico vaccine design based on molecular simulations of rhinovirus
	chimeras presenting HIV-1 gp41 epitopes.},
  journal = {J. Mol. Biol.},
  year = {2009},
  volume = {385},
  pages = {675--691},
  number = {2},
  month = {Jan},
  abstract = {A cluster of promising epitopes for the development of human immunodeficiency
	virus (HIV) vaccines is located in the membrane-proximal external
	region (MPER) of the gp41 subunit of the HIV envelope spike structure.
	The crystal structure of the peptide corresponding to the so-called
	ELDKWA epitope (HIV-1 HxB2 gp41 residues 662-668), in complex with
	the corresponding broadly neutralizing human monoclonal antibody
	2F5, provides a target for structure-based vaccine design strategies
	aimed at finding macromolecular carriers that are able to present
	this MPER-derived epitope with optimal antigenic activity. To this
	end, a series of replica exchange molecular dynamics computer simulations
	was conducted to characterize the distributions of conformations
	of ELDKWA-based epitopes inserted into a rhinovirus carrier and to
	identify those with the highest fraction of conformations that are
	able to bind 2F5. The length, hydrophobic character, and precise
	site of insertion were found to be critical for achieving structural
	similarity to the target crystal structure. A construct with a high
	degree of complementarity to the corresponding determinant region
	of 2F5 was obtained. This construct was employed to build a high-resolution
	structural model of the complex between the 2F5 antibody and the
	chimeric human rhinovirus type 14:HIV-1 ELDKWA virus particle. Additional
	simulations, which were conducted to study the conformational propensities
	of the ELDKWA region in solution, confirm the hypothesis that the
	ELDKWA region of gp41 is highly flexible and capable of assuming
	helical conformations (as in the postfusion helical bundle structure)
	and beta-turn conformations (as in the complex with the 2F5 antibody).
	These results also suggest that the ELDKWA epitope can be involved
	in intramolecular--and likely intermolecular--hydrophobic interactions.
	This tendency offers an explanation for the observation that mutations
	decreasing the hydrophobic character of the MPER in many cases result
	in conformational changes that increase the affinity of this region
	for the 2F5 antibody.},
  doi = {10.1016/j.jmb.2008.10.089},
  institution = {BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway,
	NJ 08854, USA.},
  keywords = {AIDS Vaccines; Antibodies, Monoclonal; Drug Design; Epitopes; HIV
	Antibodies; HIV Envelope Protein gp41; Humans; Models, Molecular;
	Protein Conformation; Protein Structure, Tertiary; Rhinovirus},
  owner = {emilio},
  pii = {S0022-2836(08)01402-2},
  pmid = {19026659},
  timestamp = {2010.09.11},
  url = {http://dx.doi.org/10.1016/j.jmb.2008.10.089}
}

@ARTICLE{Lapelosa2011,
  author = {Lapelosa, Mauro and Gallicchio, Emilio and Levy, Ronald M.},
  title = {Conformational Transitions and Convergence of Absolute Binding Free
	Energy Calculations},
  journal = {J. Chem. Theory Comput.},
  year = {2012},
  volume = {8},
  pages = {47--60},
  abstract = {The Binding Energy Distribution Analysis Method (BEDAM) is employed
	to compute the standard binding free energies of a series of ligands
	to a FK506 binding protein (FKBP12) with implicit solvation. Binding
	free energy estimates are in reasonably good agreement with experimental
	affinities. The conformations of the complexes identified by the
	simulations are in good agreement with crystallographic data, which
	was not used to restrain ligand orientations. The BEDAM method is
	based on ?-hopping Hamiltonian parallel Replica Exchange (HREM) molecular
	dynamics conformational sampling, the OPLS-AA/AGBNP2 effective potential,
	and multi-state free energy estimators (MBAR). Achieving converged
	and accurate results depends on all of these elements of the calculation.
	Convergence of the binding free energy is tied to the level of convergence
	of binding energy distributions at critical intermediate states where
	bound and unbound states are at equilibrium, and where the rate of
	binding/unbinding conformational transitions is maximal. This finding
	mirrors similar observations in the context of order/disorder transitions
	as for example in protein folding. Insights concerning the physical
	mechanism of ligand binding and unbinding are obtained. Convergence
	for the largest FK506 ligand is achieved only after imposing strict
	conformational restraints, which however require accurate prior structural
	knowledge of the structure of the complex. The analytical AGBNP2
	model is found to underestimate the magnitude of the hydrophobic
	driving force towards binding in these systems characterized by loosely
	packed protein-ligand binding interfaces. Rescoring of the binding
	energies using a numerical surface area model corrects this deficiency.
	This study illustrates the complex interplay between energy models,
	exploration of conformational space, and free energy estimators needed
	to obtain robust estimates from binding free energy calculations.

	The Binding Energy Distribution Analysis Method (BEDAM) is employed
	to compute the standard binding free energies of a series of ligands
	to a FK506 binding protein (FKBP12) with implicit solvation. Binding
	free energy estimates are in reasonably good agreement with experimental
	affinities. The conformations of the complexes identified by the
	simulations are in good agreement with crystallographic data, which
	was not used to restrain ligand orientations. The BEDAM method is
	based on ?-hopping Hamiltonian parallel Replica Exchange (HREM) molecular
	dynamics conformational sampling, the OPLS-AA/AGBNP2 effective potential,
	and multi-state free energy estimators (MBAR). Achieving converged
	and accurate results depends on all of these elements of the calculation.
	Convergence of the binding free energy is tied to the level of convergence
	of binding energy distributions at critical intermediate states where
	bound and unbound states are at equilibrium, and where the rate of
	binding/unbinding conformational transitions is maximal. This finding
	mirrors similar observations in the context of order/disorder transitions
	as for example in protein folding. Insights concerning the physical
	mechanism of ligand binding and unbinding are obtained. Convergence
	for the largest FK506 ligand is achieved only after imposing strict
	conformational restraints, which however require accurate prior structural
	knowledge of the structure of the complex. The analytical AGBNP2
	model is found to underestimate the magnitude of the hydrophobic
	driving force towards binding in these systems characterized by loosely
	packed protein-ligand binding interfaces. Rescoring of the binding
	energies using a numerical surface area model corrects this deficiency.
	This study illustrates the complex interplay between energy models,
	exploration of conformational space, and free energy estimators needed
	to obtain robust estimates from binding free energy calculations.},
  booktitle = {Journal of Chemical Theory and Computation},
  comment = {doi: 10.1021/ct200684b},
  issn = {1549-9618},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2011.12.12},
  url = {http://dx.doi.org/10.1021/ct200684b}
}

@ARTICLE{Lawrenz2009,
  author = {Morgan Lawrenz and Riccardo Baron and J. Andrew McCammon},
  title = {Independent-Trajectories Thermodynamic-Integration Free-Energy Changes
	for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus
	Neuraminidase Inhibition by Peramivir.},
  journal = {J Chem Theory Comput},
  year = {2009},
  volume = {5},
  pages = {1106--1116},
  number = {4},
  month = {Apr},
  abstract = {Free-energy changes are essential physicochemical quantities for understanding
	most biochemical processes. Yet, the application of accurate thermodynamic-integration
	(TI) computation to biological and macromolecular systems is limited
	by finite-sampling artifacts. In this paper, we employ independent-trajectories
	thermodynamic-integration (IT-TI) computation to estimate improved
	free-energy changes and their uncertainties for (bio)molecular systems.
	IT-TI aids sampling statistics of the thermodynamic macrostates for
	flexible associating partners by ensemble averaging of multiple,
	independent simulation trajectories. We study peramivir (PVR) inhibition
	of the H5N1 avian influenza virus neuraminidase flexible receptor
	(N1). Binding site loops 150 and 119 are highly mobile, as revealed
	by N1-PVR 20-ns molecular dynamics. Due to such heterogeneous sampling,
	standard TI binding free-energy estimates span a rather large free-energy
	range, from a 19\% underestimation to a 29\% overestimation of the
	experimental reference value (-62.2 +/- 1.8 kJ mol(-1)). Remarkably,
	our IT-TI binding free-energy estimate (-61.1 +/- 5.4 kJ mol(-1))
	agrees with a 2\% relative difference. In addition, IT-TI runs provide
	a statistics-based free-energy uncertainty for the process of interest.
	Using approximately 800 ns of overall sampling, we investigate N1-PVR
	binding determinants by IT-TI alchemical modifications of PVR moieties.
	These results emphasize the dominant electrostatic contribution,
	particularly through the N1 E277-PVR guanidinium interaction. Future
	drug development may be also guided by properly tuning ligand flexibility
	and hydrophobicity. IT-TI will allow estimation of relative free
	energies for systems of increasing size, with improved reliability
	by employing large-scale distributed computing.},
  doi = {10.1021/ct800559d},
  institution = {ological Physics, Department of Pharmacology, and Howard Hughes Medical
	Institute, University of California San Diego, La Jolla, California
	92093-0365.},
  owner = {emilio},
  pmid = {19461872},
  timestamp = {2010.09.23},
  url = {http://dx.doi.org/10.1021/ct800559d}
}

@ARTICLE{Lawrenz2011,
  author = {Lawrenz, Morgan and Baron, Riccardo and Wang, Yi and McCammon, J.
	Andrew},
  title = {Effects of Biomolecular Flexibility on Alchemical Calculations of
	Absolute Binding Free Energies},
  journal = {Journal of Chemical Theory and Computation},
  year = {2011},
  pages = {EarlyView},
  month = jun,
  abstract = {The independent trajectory thermodynamic integration (IT-TI) approach
	( Lawrenz, M. , et al. J. Chem. Theory. Comput. 2009, 5, 1106 − 1116
	) for free energy calculations with distributed computing is employed
	to study two distinct cases of protein–ligand binding: first, the
	influenza surface protein N1 neuraminidase bound to the inhibitor
	oseltamivir, and second, the Mycobacterium tuberculosis enzyme RmlC
	complexed with the molecule CID 77074. For both systems, finite molecular
	dynamics (MD) sampling and varied molecular flexibility give rise
	to IT-TI free energy distributions that are remarkably centered on
	the target experimental values, with a spread directly related to
	protein, ligand, and solvent dynamics. Using over 2 μs of total MD
	simulation, alternative protocols for the practical, general implementation
	of IT-TI are investigated, including the optimal use of distributed
	computing, the total number of alchemical intermediates, and the
	procedure to perturb electrostatics and van der Waals interactions.
	A protocol that maximizes predictive power and computational efficiency
	is proposed. IT-TI outperforms traditional TI predictions and allows
	a straightforward evaluation of the reliability of free energy estimates.
	Our study has broad implications for the use of distributed computing
	in free energy calculations of macromolecular systems.},
  comment = {doi: 10.1021/ct200230v},
  issn = {1549-9618},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2011.06.29},
  url = {http://dx.doi.org/10.1021/ct200230v}
}

@ARTICLE{Lazaridis:98,
  author = {Lazaridis, T.},
  title = {Inhomogeneous Fluid Approach to Solvation Thermodyanmics. I. Theory},
  journal = {J. Phys. Chem. B},
  year = {1998},
  volume = {102},
  pages = {3531-41},
  number = {18},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Lazaridis:Archontis:Karlplus:95,
  author = {Lazaridis, T. and Archontis, G. and Karplus, M.},
  title = {Enthalpic contribution to protein stability: atom-based calculations
	and statistcal mechanics.},
  journal = {Adv. Prot. Chem.},
  year = {1995},
  volume = {47},
  pages = {262-344},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Lazaridis:Karplus:2000,
  author = {Lazaridis, T. and Karplus, M.},
  title = {Effective energy functions for protein structure prediction},
  journal = {Curr. Opin. Struct. Biol.},
  year = {2000},
  volume = {10},
  pages = {139-145},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Lazaridis:Karplus:99,
  author = {Lazaridis, T. and Karplus, M.},
  title = {Discrimination of the native from misfolded protein models with an
	energy function including implicit solvation},
  journal = {J. Mol. Biol.},
  year = {1999},
  volume = {288},
  pages = {477-487},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Lazaridis:Karplus:99p,
  author = {Lazaridis, T. and Karplus, M.},
  title = {Effective Energy Function for Protein in Solution},
  journal = {Proteins},
  year = {1999},
  volume = {35},
  pages = {133-152},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Lazaridis:Karplus:96,
  author = {Lazaridis, T. and Karplus, M.},
  title = {Orientational correlations and entropy in liquid water},
  journal = {J. Chem. Phys.},
  year = {1996},
  volume = {105},
  pages = {4294},
  number = {10},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Lazaridis:Paulaitis:94,
  author = {Lazaridis, T. and Paulaitis, M. E.},
  title = {Simulation Studies of the Hydration Entropy of Simple Hydrophobic
	Solutes},
  journal = {J. Phys. Chem.},
  year = {1994},
  volume = {98},
  pages = {635-642},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Lazaridis:Paulaitis:92,
  author = {Lazaridis, T. and Paulaitis, M. E.},
  title = {Entropy of hydrophobic hydration: A New Statistical Mechanics Formulation},
  journal = {J. Phys. Chem.},
  year = {1992},
  volume = {96},
  pages = {3847-3855},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Leach2006,
  author = {Andrew R Leach and Brian K Shoichet and Catherine E Peishoff},
  title = {Prediction of protein-ligand interactions. Docking and scoring: successes
	and gaps.},
  journal = {J Med Chem},
  year = {2006},
  volume = {49},
  pages = {5851--5855},
  number = {20},
  month = {Oct},
  doi = {10.1021/jm060999m},
  institution = {GlaxoSmithKline Pharmaceuticals, 1250 South Collegeville Road, Collegeville,
	Pennsylvania 19426, USA.},
  keywords = {Binding Sites; Drug Design; Ligands; Models, Molecular; Protein Binding;
	Proteins; Quantitative Structure-Activity Relationship},
  owner = {emilio},
  pmid = {17004700},
  timestamp = {2010.04.22},
  url = {http://dx.doi.org/10.1021/jm060999m}
}

@ARTICLE{Lee:94,
  author = {Lee, B.},
  title = {Solvent Reorganization Contribution to the Transfer Thermodynamics
	of Small Nonpolar Molecules},
  journal = {Biophysical Chemistry},
  year = {1994},
  volume = {51},
  pages = {271},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Lee:91,
  author = {Lee, B.},
  title = {Isoenthalpic and Isoentropic Temperatures and the Thermodynamics
	of Protein Denaturation},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {1991},
  volume = {88},
  pages = {5154-5158},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Lee:91b,
  author = {Lee, B.},
  title = {Sovent Reorganization Contribution to the Transfer Thermodynamics
	of Small Nonpolar Molecules},
  journal = {Biopolymers},
  year = {1991},
  volume = {31},
  pages = {993-1008},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Lee:85,
  author = {Lee, B.},
  title = {The Physical Origin of the Low Solubility of Nonpolar Solutes in
	Water},
  journal = {Biopolymers},
  year = {1985},
  volume = {24},
  pages = {813-23},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Lee:85b,
  author = {Lee, B.},
  title = {A procedure for calculating thermodynamic functions of cavity formation
	from the pure solvent simulation data},
  journal = {J. Chem. Phys.},
  year = {1985},
  volume = {83},
  pages = {2421-25},
  number = {5},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Lee:Richards:1971,
  author = {Lee, B. and Richards, {F. M.}},
  title = {The interpretation of protein structures: Estimation of static accessibility},
  journal = {J. Mol. Biol.},
  year = {1971},
  volume = {55},
  pages = {379-400},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Lee:Warshel:92,
  author = {Lee, F. S. and Warshel, A.},
  journal = {J. Chem. Phys.},
  year = {1992},
  volume = {97},
  pages = {3100-3109},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Lee:Duan:Kollman:2000,
  author = {Lee, M. R. and Duan, Y. and Kollman, P. A.},
  title = {Use of MM-PB/SA in estimating the free energies of proteins: Application
	to native, intermediates, and unfolded villin headpiece},
  journal = {Proteins},
  year = {2000},
  volume = {39},
  pages = {309-316},
  number = {4},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Lee:Feig:Salsbury:Brooks:2003,
  author = {Lee, M. S. and Feig, M. and Salsbury Jr., F. R. and Brooks III, C.
	L.},
  title = {New analytic approximation to the standard molecular volume definition
	and its application to generalized Born calculations},
  journal = {J. Comp. Chem.},
  year = {2003},
  volume = {24},
  pages = {1348-1356},
  number = {11},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Lee2006,
  author = {Michael S Lee and Mark A Olson},
  title = {Calculation of absolute protein-ligand binding affinity using path
	and endpoint approaches.},
  journal = {Biophys. J},
  year = {2006},
  volume = {90},
  pages = {864--877},
  number = {3},
  month = {Feb},
  abstract = {A comparative analysis is provided of rigorous and approximate methods
	for calculating absolute binding affinities of two protein-ligand
	complexes: the FKBP protein bound with small molecules 4-hydroxy-2-butanone
	and FK506. Our rigorous approach is an umbrella sampling technique
	where a potential of mean force is determined by pulling the ligand
	out of the protein active site over several simulation windows. The
	results of this approach agree well with experimentally observed
	binding affinities. Also assessed is a commonly used approximate
	endpoint approach, which separately estimates enthalpy, solvation
	free energy, and entropy. We show that this endpoint approach has
	numerous variations, all of which are prone to critical shortcomings.
	For example, conventional harmonic and quasiharmonic entropy estimation
	procedures produce disparate results for the relatively simple protein-ligand
	systems studied in this work.},
  doi = {10.1529/biophysj.105.071589},
  institution = {Department of Cell Biology and Biochemistry, U.S. Army Medical Research
	Institute of Infectious Diseases, Frederick, Maryland 21702, USA.
	michael.lee@amedd.army.mil},
  keywords = {Binding Sites; Biophysics; Butanones; Carrier Proteins; Computer Simulation;
	Crystallography, X-Ray; Entropy; Hot Temperature; Hydrogen Bonding;
	Kinetics; Ligands; Models, Molecular; Molecular Structure; Protein
	Binding; Protein Conformation; Proteins; Solvents; Tacrolimus; Thermodynamics},
  owner = {emilio},
  pii = {S0006-3495(06)72274-3},
  pmid = {16284269},
  timestamp = {2010.04.20},
  url = {http://dx.doi.org/10.1529/biophysj.105.071589}
}

@ARTICLE{Lee:Salsbury:Brooks:2002,
  author = {Lee, M. S. and Salsbury, F. R. and Brooks III, C. L.},
  title = {Novel Generalized Born Methods},
  journal = {J. Chem. Phys.},
  year = {2002},
  volume = {116},
  pages = {10606},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Lee:Chu:Bolger:Warshel:92,
  author = {Lee, {F. S.} and Chu, {Z. T.} and Bolger, {M. B.} and Warshel, A.},
  title = {Calculation of Antibody-antigen interactions: microscopic and semi-microscopic
	evaluation of the free energies of binding of phosphorylcholine analogs
	to {McPC603}},
  journal = {Prot. Eng.},
  year = {1992},
  volume = {5},
  pages = {215--228},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{deLeeuw:80,
  author = {de Leeuw, S. W. and Perram, J. W. and Smith, E. R.},
  journal = {Proc. Royal Soc. London Ser. A},
  year = {1980},
  volume = {373},
  pages = {27-56},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Leiros2004b,
  author = {Hanna-Kirsti Schrøder Leiros and Bjørn Olav Brandsdal and Ole Andreas
	Andersen and Vibeke Os and Ingar Leiros and Ronny Helland and Jacek
	Otlewski and Nils Peder Willassen and Arne O Smalås},
  title = {Trypsin specificity as elucidated by LIE calculations, X-ray structures,
	and association constant measurements.},
  journal = {Protein Sci},
  year = {2004},
  volume = {13},
  pages = {1056--1070},
  number = {4},
  month = {Apr},
  abstract = {The variation in inhibitor specificity for five different amine inhibitors
	bound to CST, BT, and the cold-adapted AST has been studied by use
	of association constant measurements, structural analysis of high-resolution
	crystal structures, and the LIE method. Experimental data show that
	AST binds the 1BZA and 2BEA inhibitors 0.8 and 0.5 kcal/mole more
	strongly than BT. However, structural interactions and orientations
	of the inhibitors within the S1 site have been found to be virtually
	identical in the three enzymes studied. For example, the four water
	molecules in the inhibitor-free structures of AST and BT are channeled
	into similar positions in the S1 site, and the nitrogen atom(s) of
	the inhibitors are found in two cationic binding sites denoted Position1
	and Position2. The hydrophobic binding contributions for all five
	inhibitors, estimated by the LIE calculations, are also in the same
	order (-2.1 +/- 0.2 kcal/mole) for all three enzymes. Our hypothesis
	is therefore that the observed variation in inhibitor binding arises
	from different electrostatic interactions originating from residues
	outside the S1 site. This is well illustrated by AST, in which Asp
	150 and Glu 221B, despite some distance from the S1 binding site,
	lower the electrostatic potential of the S1 site and thus enhance
	substrate binding. Because the trends in the experimentally determined
	binding energies were reproduced by the LIE calculations after adding
	the contribution from long-range interactions, we find this method
	very suitable for rational studies of protein-substrate interactions.},
  doi = {10.1110/ps.03498604},
  institution = {University of Tromsø, N-9037 Tromsø, Norway.},
  keywords = {Animals; Binding Sites; Cattle; Crystallography, X-Ray; Humans; Models,
	Molecular; Molecular Structure; Protein Structure, Tertiary; Serine
	Endopeptidases; Serine Proteinase Inhibitors; Structure-Activity
	Relationship; Substrate Specificity},
  owner = {emilio},
  pii = {13/4/1056},
  pmid = {15044735},
  timestamp = {2010.10.27},
  url = {http://dx.doi.org/10.1110/ps.03498604}
}

@ARTICLE{Levitt:87,
  author = {Levitt, M.},
  journal = {NATO Asi. Ser. A},
  year = {1987},
  volume = {126},
  pages = {197-205},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Levy:91,
  author = {Levy, R. M. and Belhadj, M. and Kitchen, D. B.},
  journal = {J. Chem. Phys.},
  year = {1991},
  volume = {95},
  pages = {3627-3633},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Levy:Gallicchio:98,
  author = {Levy, R. M. and Gallicchio, E.},
  title = {Computer Simulations with Explicit Solvent: Recent Progress in the
	Thermodynamic Decomposition of Free Energies and in Modeling Electrostatic
	Effects},
  journal = {Annu. Rev. Phys. Chem.},
  year = {1998},
  volume = {49},
  pages = {531-67},
  owner = {emilio},
  timestamp = {2010.11.02}
}

@ARTICLE{Levy1984,
  author = {Ronald M. Levy and Martin Karplus and Joseph Kushick and David Perahia},
  title = {Evaluation of the Configurational Entropy for Proteins: Application
	to Molecular Dynamics Simulations of an $\alpha$-Helix},
  journal = {Macromolecules},
  year = {1984},
  volume = {17},
  pages = {1370-1374},
  owner = {emilio},
  timestamp = {2011.02.05}
}

@ARTICLE{Levy:Zhang:Gallicchio:Felts:2003,
  author = {Ronald M Levy and Linda Y Zhang and Emilio Gallicchio and Anthony
	K Felts},
  title = {On the nonpolar hydration free energy of proteins: surface area and
	continuum solvent models for the solute-solvent interaction energy.},
  journal = {J. Am. Chem. Soc.},
  year = {2003},
  volume = {125},
  pages = {9523--9530},
  number = {31},
  month = {Aug},
  abstract = {Implicit solvent hydration free energy models are an important component
	of most modern computational methods aimed at protein structure prediction,
	binding affinity prediction, and modeling of conformational equilibria.
	The nonpolar component of the hydration free energy, consisting of
	a repulsive cavity term and an attractive van der Waals solute-solvent
	interaction term, is often modeled using estimators based on the
	solvent exposed solute surface area. In this paper, we analyze the
	accuracy of linear surface area models for predicting the van der
	Waals solute-solvent interaction energies of native and non-native
	protein conformations, peptides and small molecules, and the desolvation
	penalty of protein-protein and protein-ligand binding complexes.
	The target values are obtained from explicit solvent simulations
	and from a continuum solvent van der Waals interaction energy model.
	The results indicate that the standard surface area model, while
	useful on a coarse-grained scale, may not be accurate or transferable
	enough for high resolution modeling studies of protein folding and
	binding. The continuum model constructed in the course of this study
	provides one path for the development of a computationally efficient
	implicit solvent nonpolar hydration free energy estimator suitable
	for high-resolution structural and thermodynamic modeling of biological
	macromolecules.},
  doi = {10.1021/ja029833a},
  institution = {Department of Chemistry and Chemical Biology, Rutgers University,
	Piscataway, New Jersey 08854, USA. ronlevy@lutece.rutgers.edu},
  keywords = {Amino Acid Sequence; Computer Simulation; Models, Chemical; Molecular
	Sequence Data; Oligopeptides; Protein Binding; Solvents; Surface
	Properties; Thermodynamics; Water},
  owner = {emilio},
  pmid = {12889983},
  timestamp = {2010.07.08},
  url = {http://dx.doi.org/10.1021/ja029833a}
}

@ARTICLE{Levy:Belhadj:Kitchen:1991,
  author = {Levy, {R. M.} and Belhadj, M. and Kitchen, {D. B.}},
  title = {Gaussian fluctuation formula for electrostatic free-energy changes
	in solution},
  journal = {J. Chem. Phys.},
  year = {1991},
  volume = {95},
  pages = {3627--3633},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Li2007,
  author = {Li, Zheng and Lazaridis, Themis},
  title = {Water at biomolecular binding interfaces},
  journal = {Phys. Chem. Chem. Phys.},
  year = {2007},
  volume = {9},
  pages = {573--581},
  number = {5},
  abstract = {Water molecules are often found at the binding interface of biomolecular
	complexes mediating the interaction between polar groups viahydrogen
	bonds, or simply filling space providing van der Waals interactions.
	Recent studies have demonstrated the importance of taking such water
	molecules into account in docking and binding affinity prediction.
	Here, we review the recent experimental and theoretical work aimed
	at quantifying the influence of interfacial water on the thermodynamic
	properties of binding. We highlight especially our recent results
	obtained by inhomogeneous fluid solvation theory in several systems
	and the prediction of the thermodynamic consequences of displacement
	of the bound water molecule by ligand modification. Finally, we discuss
	possible directions for further progress in this field.},
  issn = {1463-9076},
  owner = {emilio},
  publisher = {The Royal Society of Chemistry},
  timestamp = {2010.09.17},
  url = {http://dx.doi.org/10.1039/B612449F}
}

@ARTICLE{Li2006,
  author = {Li, Zheng and Lazaridis, Themis},
  title = {Thermodynamics of Buried Water Clusters at a Protein-Ligand Binding
	Interface},
  journal = {J. Phys. Chem. B},
  year = {2006},
  volume = {110},
  pages = {1464--1475},
  number = {3},
  month = jan,
  abstract = {The structure of the complex of cyclophilin A (CypA) with cyclosporin
	A (CsA, 1) shows a cluster of four water molecules buried at the
	binding interface, which is rearranged when CsA is replaced by (5-hydroxynorvaline)-2-cyclosporin
	(2). The thermodynamic contributions of each bound water molecule
	in the two complexes are explored with the inhomogeneous fluid solvation
	theory and molecular dynamics simulations. Water (WTR) 133 in complex
	1 contributes little to the binding affinity, while WTR6 and 7 in
	complex 2 play an essential role in mediating protein−ligand binding
	with a hydrogen bond network. The calculations reveal that the rearrangement
	of the water molecules contributes favorably to the binding affinity,
	even though one of them is displaced going from ligand 1 to 2. Another
	favorable contribution comes from the larger protein−ligand interactions
	of ligand 2. However, these favorable contributions are not sufficient
	to overcome the unfavorable desolvation free energy change and the
	conformational entropy of the hydroxylpropyl group of ligand 2 in
	the complex, leading to a lower binding affinity of ligand 2. These
	physical insights may be useful in the development of improved scoring
	functions for binding affinity prediction.},
  comment = {doi: 10.1021/jp056020a},
  issn = {1520-6106},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2010.09.17},
  url = {http://dx.doi.org/10.1021/jp056020a}
}

@INPROCEEDINGS{Li:2007:CIG:1272366.1272404,
  author = {Li, Zhen and Parashar, Manish},
  title = {A computational infrastructure for grid-based asynchronous parallel
	applications},
  booktitle = {Proceedings of the 16th international symposium on High performance
	distributed computing},
  year = {2007},
  series = {HPDC '07},
  pages = {229--230},
  address = {New York, NY, USA},
  publisher = {ACM},
  acmid = {1272404},
  doi = {http://doi.acm.org/10.1145/1272366.1272404},
  isbn = {978-1-59593-673-8},
  keywords = {asynchronous, parallel, shared-space},
  location = {Monterey, California, USA},
  numpages = {2},
  owner = {emilio},
  timestamp = {2011.02.03},
  url = {http://doi.acm.org/10.1145/1272366.1272404}
}

@INPROCEEDINGS{Li:Parashar:2007,
  author = {Zhen Li and Parashar, M.},
  title = {Grid-based asynchronous replica exchange},
  booktitle = {Grid Computing, 2007 8th IEEE/ACM International Conference on},
  year = {2007},
  pages = {201 -208},
  month = {sept.},
  abstract = {Replica exchange is a powerful sampling algorithm and can be effectively
	used for applications such as simulating the structure, function,
	folding, and dynamics of proteins and drug design. However, Grid-based
	implementations of the algorithm present significant challenges due
	to its synchronization and communication requirements. This paper
	presents an asynchronous formulation of the replica exchange algorithm
	and the design and implementation of a Grid-based asynchronous replica
	exchange engine (GARE). GARE is based on CometG, a decentralized
	computational infrastructure for Desktop Grid environments that provides
	a scalable communication and interaction substrate and presents a
	virtual semantically specialized shared space abstraction. It enables
	the dynamic and asynchronous interactions required by the algorithm
	to be simply expressed and efficiently implemented. The design and
	implementation of GARE/CometG and the replica exchange simulations
	that it enables are presented. Experimental evaluations using the
	PlanetLab |1| wide-area test bed as well as a campus Grid environment
	arc presented.},
  doi = {10.1109/GRID.2007.4354134},
  keywords = {CometG decentralized computational infrastructure;asynchronous formulation;desktop
	grid environment;grid-based asynchronous replica exchange engine;grid-based
	asynchronous replica exchange simulation algorithm;sampling algorithm;virtual
	semantically-specialized shared space abstraction;digital simulation;grid
	computing;synchronisation;virtual reality;},
  owner = {emilio},
  timestamp = {2011.02.03}
}

@ARTICLE{Liebeschuetz2012,
  author = {Liebeschuetz, John and Hennemann, Jana and Olsson, Tjelvar and Groom,
	Colin},
  title = {The good, the bad and the twisted: a survey of ligand geometry in
	protein crystal structures},
  journal = {J. Comp. Aided Mol. Des.},
  year = {2012},
  pages = {Online First},
  note = {10.1007/s10822-011-9538-6},
  abstract = {The protein databank now contains the structures of over 11,000 ligands
	bound to proteins. These structures are invaluable in applied areas
	such as structure-based drug design, but are also the substrate for
	understanding the energetics of intermolecular interactions with
	proteins. Despite their obvious importance, the careful analysis
	of ligands bound to protein structures lags behind the analysis of
	the protein structures themselves. We present an analysis of the
	geometry of ligands bound to proteins and highlight the role of small
	molecule crystal structures in enabling molecular modellers to critically
	evaluate a ligand model’s quality and investigate protein-induced
	strain.},
  affiliation = {The Cambridge Crystallographic Data Centre (CCDC), 12 Union Road,
	Cambridge, CB2 1EZ UK},
  issn = {0920-654X},
  keyword = {Chemistry and Materials Science},
  owner = {emilio},
  publisher = {Springer Netherlands},
  timestamp = {2012.02.28},
  url = {http://dx.doi.org/10.1007/s10822-011-9538-6}
}

@ARTICLE{Lill2007,
  author = {Markus A Lill},
  title = {Multi-dimensional QSAR in drug discovery.},
  journal = {Drug Discov Today},
  year = {2007},
  volume = {12},
  pages = {1013--1017},
  number = {23-24},
  month = {Dec},
  abstract = {Quantitative structure-activity relationships (QSAR) is an area of
	computational research that builds virtual models to predict quantities
	such as the binding affinity or the toxic potential of existing or
	hypothetical molecules. Although a wealth of experimental data emphasizes
	the active role of the target protein in the binding process, QSAR
	studies are frequently restricted to the properties of the small-molecule
	ligand

license: MIT

license_type: permissive

branch_name: refs/heads/master

gha_license_id: MIT

gha_language: TeX

extension: bib