text:
011.01.18}
}

@ARTICLE{Warshel:86,
  author = {Warshel, A. and Sussman, F. and King, G.},
  title = {Free Energy of Charges in Solvated Proteins: Microscopic Calculations
	Using a Reversible Charging Process},
  journal = {Biochemistry},
  year = {1986},
  volume = {25},
  pages = {8368},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Watanabe:Andersen:86,
  author = {Watanabe, K. and Anderesen, H. C.},
  title = {Molecula Dynamics Study of the Hydrophobic Interaction in an Aqueous
	Solution of Krypton},
  journal = {J. Phys. Chem.},
  year = {1986},
  volume = {90},
  pages = {795-802},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Watts2010,
  author = {K. Shawn Watts and Pranav Dalal and Robert B Murphy and Woody Sherman
	and Rich A Friesner and John C Shelley},
  title = {ConfGen: a conformational search method for efficient generation
	of bioactive conformers.},
  journal = {J Chem Inf Model},
  year = {2010},
  volume = {50},
  pages = {534--546},
  number = {4},
  month = {Apr},
  abstract = {We describe the methodology, parametrization, and application of a
	conformational search method, called ConfGen, designed to efficiently
	generate bioactive conformers. We define efficiency as the ability
	to generate a bioactive conformation within a small total number
	of conformations using a reasonable amount of computer time. The
	method combines physics-based force field calculations with empirically
	derived heuristics designed to achieve efficient searching and prioritization
	of the ligand's conformational space. While many parameter settings
	are supported, four modes spanning a range of speed and quality trades-offs
	are defined and characterized. The validation set used to test the
	method is composed of ligands from 667 crystal structures covering
	a broad array of target and ligand classes. With the fastest mode,
	ConfGen uses an average of 0.5 s per ligand and generates only 14.3
	conformers per ligand, at least one of which lies within 2.0 A root-mean-squared
	deviation of the crystal structure for 96\% of the ligands. The most
	computationally intensive mode raises this recovery rate to 99\%,
	while taking 8 s per ligand. Combining multiple search modes to "fill-in"
	holes in the conformation space or energy minimizing using an all-atom
	force field each lead to improvements in the recovery rates at higher
	resolutions. Overall, ConfGen is at least as good as competing programs
	at high resolution and demonstrates higher efficiency at resolutions
	sufficient for many downstream applications, such as pharmacophore
	modeling.},
  comment = {Ligand reorganization},
  doi = {10.1021/ci100015j},
  institution = {Schrodinger, LLC, 101 SW Main Street, Suite 1300, Portland, Oregon
	97204, USA.},
  keywords = {Computational Biology; Drug Evaluation, Preclinical; Ligands; Models,
	Molecular; Molecular Conformation; Software; Time Factors},
  owner = {emilio},
  pmid = {20373803},
  timestamp = {2010.09.08},
  url = {http://dx.doi.org/10.1021/ci100015j}
}

@ARTICLE{Weeks:Chandler:Andersen:71,
  author = {Weeks, J. D. and Chandler, D. and Andersen, H. C.},
  title = {Role of Repulsive Forces in Determining the Equilibrium Structure
	of Simple Liquids},
  journal = {J. Chem. Phys.},
  year = {1971},
  volume = {54},
  pages = {5237-47},
  number = {12},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Weeks:Selinger:1995,
  author = {Weeks, J. D. and Selinger, R. L. B. and Broughton, J. Q.},
  title = {Self-Consistent treatment of repulsive and attractive forces in nonuniform
	liquids},
  journal = {Phys. Rev. Lett.},
  year = {1995},
  volume = {75},
  pages = {2694},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Wei2002,
  author = {Binqing Q Wei and Walter A Baase and Larry H Weaver and Brian W Matthews
	and Brian K Shoichet},
  title = {A model binding site for testing scoring functions in molecular docking.},
  journal = {J. Mol. Biol.},
  year = {2002},
  volume = {322},
  pages = {339--355},
  number = {2},
  month = {Sep},
  abstract = {Prediction of interaction energies between ligands and their receptors
	remains a major challenge for structure-based inhibitor discovery.
	Much effort has been devoted to developing scoring schemes that can
	successfully rank the affinities of a diverse set of possible ligands
	to a binding site for which the structure is known. To test these
	scoring functions, well-characterized experimental systems can be
	very useful. Here, mutation-created binding sites in T4 lysozyme
	were used to investigate how the quality of atomic charges and solvation
	energies affects molecular docking. Atomic charges and solvation
	energies were calculated for 172,118 molecules in the Available Chemicals
	Directory using a semi-empirical quantum mechanical approach by the
	program AMSOL. The database was first screened against the apolar
	cavity site created by the mutation Leu99Ala (L99A). Compared to
	the electronegativity-based charges that are widely used, the new
	charges and desolvation energies improved ranking of known apolar
	ligands, and better distinguished them from more polar isosteres
	that are not observed to bind. To investigate whether the new charges
	had predictive value, the non-polar residue Met102, which forms part
	of the binding site, was changed to the polar residue glutamine.
	The structure of the resulting Leu99Ala and Met102Gln double mutant
	of T4 lysozyme (L99A/M102Q) was determined and the docking calculation
	was repeated for the new site. Seven representative polar molecules
	that preferentially docked to the polar versus the apolar binding
	site were tested experimentally. All seven bind to the polar cavity
	(L99A/M102Q) but do not detectably bind to the apolar cavity (L99A).
	Five ligand-bound structures of L99A/M102Q were determined by X-ray
	crystallography. Docking predictions corresponded to the crystallographic
	results to within 0.4A RMSD. Improved treatment of partial atomic
	charges and desolvation energies in database docking appears feasible
	and leads to better distinction of true ligands. Simple model binding
	sites, such as L99A and its more polar variants, may find broad use
	in the development and testing of docking algorithms.},
  institution = {Department of Molecular Pharmacology and Biological Chemistry, Northwestern
	University School of Medicine, Chicago, IL 60611-3008, USA.},
  keywords = {Algorithms; Amino Acid Substitution; Bacteriophage T4; Binding Sites;
	Calorimetry; Crystallography, X-Ray; Databases, Factual; Hydrophobicity;
	Ligands; Models, Molecular; Muramidase; Mutation; Protein Binding;
	Protein Conformation; Software},
  owner = {emilio},
  pii = {S0022283602007775},
  pmid = {12217695},
  timestamp = {2010.04.27}
}

@ARTICLE{Wei2004,
  author = {Binqing Q Wei and Larry H Weaver and Anna M Ferrari and Brian W Matthews
	and Brian K Shoichet},
  title = {Testing a flexible-receptor docking algorithm in a model binding
	site.},
  journal = {J Mol Biol},
  year = {2004},
  volume = {337},
  pages = {1161--1182},
  number = {5},
  month = {Apr},
  abstract = {Sampling receptor flexibility is challenging for database docking.
	We consider a method that treats multiple flexible regions of the
	binding site independently, recombining them to generate different
	discrete conformations. This algorithm scales linearly rather than
	exponentially with the receptor's degrees of freedom. The method
	was first evaluated for its ability to identify known ligands of
	a hydrophobic cavity mutant of T4 lysozyme (L99A). Some 200000 molecules
	of the Available Chemical Directory (ACD) were docked against an
	ensemble of cavity conformations. Surprisingly, the enrichment of
	known ligands from among a much larger number of decoys in the ACD
	was worse than simply docking to the apo conformation alone. Large
	decoys, accommodated in the larger cavity conformations sampled in
	the ensemble, were ranked better than known small ligands. The calculation
	was redone with an energy correction term that considered the cost
	of forming the larger cavity conformations. Enrichment improved,
	as did the balance between high-ranking large and small ligands.
	In a second retrospective test, the ACD was docked against a conformational
	ensemble of thymidylate synthase. Compared to docking against individual
	enzyme conformations, the flexible receptor docking approach improved
	enrichment of known ligands. Including a receptor conformational
	energy weighting term improved enrichment further. To test the method
	prospectively, the ACD database was docked against another cavity
	mutant of lysozyme (L99A/M102Q). A total of 18 new compounds predicted
	to bind this polar cavity and to change its conformation were tested
	experimentally; 14 were found to bind. The bound structures for seven
	ligands were determined by X-ray crystallography. The predicted geometries
	of these ligands all corresponded to the observed geometries to within
	0.7A RMSD or better. Significant conformational changes of the cavity
	were observed in all seven complexes. In five structures, part of
	the observed accommodations were correctly predicted; in two structures,
	the receptor conformational changes were unanticipated and thus never
	sampled. These results suggest that although sampling receptor flexibility
	can lead to novel ligands that would have been missed when docking
	a rigid structure, it is also important to consider receptor conformational
	energy.},
  doi = {10.1016/j.jmb.2004.02.015},
  institution = {Department of Pharmaceutical Chemistry, University of California,
	600 16th St, San Francisco, CA 94143-2240, USA.},
  keywords = {Algorithms; Bacteriophage T4; Binding Sites; Computer Simulation;
	Crystallography, X-Ray; Databases, Factual; Ligands; Models, Molecular;
	Muramidase; Pliability; Protein Binding},
  owner = {emilio},
  pii = {S0022283604001718},
  pmid = {15046985},
  timestamp = {2010.10.27},
  url = {http://dx.doi.org/10.1016/j.jmb.2004.02.015}
}

@ARTICLE{Weiner:Kollman:Nguyen:Case:86,
  author = {Weiner, S. J. and Kollman, P. A. and Nguyen, D. T. and Case, D. A.},
  journal = {J. Comput. Chem.},
  year = {1986},
  volume = {7},
  pages = {230},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Weinstock:Narayanan:Baum:Levy:2008,
  author = {Weinstock, {D. S.} and Narayanan, C. and Baum, J. and Levy, {R. M.}},
  title = {Correlation Between 13C-alpha Chemical Shifts and Helix Content of
	Peptide Ensembles},
  journal = {Protein Science},
  year = {2008},
  volume = {17},
  pages = {950--954},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Weinstock:Narayanan:Baum:Levy:2007,
  author = {Weinstock, {D. S.} and Narayanan, C. and Felts, {A. K.} Andrec, M.
	and Levy, {R. M.} and Wu, {K.-P.} and Baum, J.},
  title = {Distinguishing among Structural Ensembles of the GB1 Peptide: REMD
	Simulations and NMR Experiments},
  journal = {J. Am. Chem. Soc.},
  year = {2007},
  volume = {129},
  pages = {4858--4859},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Weiser:Shenkin:Still:99,
  author = {Weiser, J. and Shenkin, P. S. and Still, C.},
  title = {Optimization of Gaussian Surface Calculations and Extension to Solvent-Accessible
	Surface Areas},
  journal = {J. Comp. Chem.},
  year = {1999},
  volume = {20},
  pages = {688-703},
  number = {7},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Wickner2005,
  author = {William Wickner and Randy Schekman},
  title = {Protein translocation across biological membranes.},
  journal = {Science},
  year = {2005},
  volume = {310},
  pages = {1452--1456},
  number = {5753},
  month = {Dec},
  abstract = {Subcellular compartments have unique protein compositions, yet protein
	synthesis only occurs in the cytosol and in mitochondria and chloroplasts.
	How do proteins get where they need to go? The first steps are targeting
	to an organelle and efficient translocation across its limiting membrane.
	Given that most transport systems are exquisitely substrate specific,
	how are diverse protein sequences recognized for translocation? Are
	they translocated as linear polypeptide chains or after folding?
	During translocation, how are diverse amino acyl side chains accommodated?
	What are the proteins and the lipid environment that catalyze transport
	and couple it to energy? How is translocation coordinated with protein
	synthesis and folding, and how are partially translocated transmembrane
	proteins released into the lipid bilayer? We review here the marked
	progress of the past 35 years and salient questions for future work.
	Subcellular compartments have unique protein compositions, yet protein
	synthesis only occurs in the cytosol and in mitochondria and chloroplasts.
	How do proteins get where they need to go? The first steps are targeting
	to an organelle and efficient translocation across its limiting membrane.
	Given that most transport systems are exquisitely substrate specific,
	how are diverse protein sequences recognized for translocation? Are
	they translocated as linear polypeptide chains or after folding?
	During translocation, how are diverse amino acyl side chains accommodated?
	What are the proteins and the lipid environment that catalyze transport
	and couple it to energy? How is translocation coordinated with protein
	synthesis and folding, and how are partially translocated transmembrane
	proteins released into the lipid bilayer? We review here the marked
	progress of the past 35 years and salient questions for future work.},
  doi = {10.1126/science.1113752},
  institution = {Department of Biological Chemistry, Dartmouth Medical School, 7200
	Vail Building, Hanover, NH 03755-3844, USA. Bill.Wickner@Dartmouth.edu},
  keywords = {Carrier Proteins, metabolism; Endoplasmic Reticulum, metabolism; Intracellular
	Membranes, metabolism; Mitochondria, metabolism; Peroxisomes, metabolism;
	Protein Biosynthesis; Protein Folding; Protein Transport},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pii = {310/5753/1452},
  pmid = {16322447},
  timestamp = {2011.07.15},
  url = {http://dx.doi.org/10.1126/science.1113752}
}

@UNPUBLISHED{Wickstrom:2012,
  author = {Lauren Wickstrom and Emilio Gallicchio and Ronald M Levy},
  title = {Large scale binding affinity calculations on host-guest systems:
	Application to force field optimization},
  note = {In preparation},
  owner = {emilio},
  timestamp = {2012.06.21}
}

@UNPUBLISHED{Wickstrom:He:2013a,
  author = {Laren Wickstrom and Peng He and Emilio Gallicchio and Ronald M. Levy},
  title = {Kinetics of Conformational Reorganization in Alchemical Binding Free
	Energy Transformations},
  note = {In preparation.},
  owner = {emilio},
  timestamp = {2012.06.22}
}

@ARTICLE{Widom1982,
  author = {Widom, B.},
  title = {Potential-distribution theory and the statistical mechanics of fluids},
  journal = {J. Phys. Chem.},
  year = {1982},
  volume = {86},
  pages = {869--872},
  number = {6},
  month = mar,
  comment = {doi: 10.1021/j100395a005},
  issn = {0022-3654},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2010.04.30},
  url = {http://dx.doi.org/10.1021/j100395a005}
}

@ARTICLE{Widom:65,
  author = {Widom, B.},
  journal = {J. Chem. Phys.},
  year = {1965},
  volume = {43},
  pages = {3829},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Widom1963,
  author = {Widom, B.},
  title = {Some Topics in the Theory of Fluids},
  journal = {J. Chem. Phys.},
  year = {1963},
  volume = {39},
  pages = {2808--2812},
  number = {11},
  month = dec,
  owner = {emilio},
  publisher = {AIP},
  timestamp = {2010.04.30},
  url = {http://link.aip.org/link/?JCP/39/2808/1}
}

@ARTICLE{Widom:82,
  author = {Widom, B. J.},
  journal = {Chem. Phys.},
  year = {1982},
  volume = {86},
  pages = {869},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Wilhelm:77,
  author = {Wilhelm, E. and Battino, R. and Wilcock, R. J.},
  journal = {Chem. Rev.},
  year = {1977},
  volume = {77},
  pages = {219},
  number = {2},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Williams:Searle:Mackay:Gerhard:Maplestone:93,
  author = {Williams, D. H. and Searle, M. S. and Mackay, J. P. and Gerhard,
	U. and Maplestone, R. A.},
  title = {Toward an estimation of binding constants in aqueous solutions: Studies
	of associations of vancomycin group antibiotics.},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {1993},
  volume = {90},
  pages = {1172-78},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Wilson1995,
  author = {Wilson, K. P. and Yamashita, M. M. and Sintchak, M. D. and Rotstein,
	S. H. and Murcko, M. A. and Boger, J. and Thomson, J. A. and Fitzgibbon,
	M. J. and Black, J. R. and Navia, M. A.},
  title = {Comparative X-ray structures of the major binding protein for the
	immunosuppressant FK506 (tacrolimus) in unliganded form and in complex
	with FK506 and rapamycin},
  journal = {Acta Cryst. D Biol. Cryst.},
  year = {1995},
  volume = {51},
  pages = {511--521},
  number = {Pt 4},
  abstract = {FK506 (tacrolimus) is a natural product now approved in the US and
	Japan for organ transplantation. FK506, in complex with its 12 kDa
	cytosolic receptor (FKBP12), is a potent agonist of immunosuppression
	through the inhibition of the phosphatase activity of calcineurin.
	Rapamycin (sirolimus), which is itself an immunosuppressant by a
	different mechanism, completes with FK506 for binding to FKBP12 and
	thereby acts as an antagonist of calcineurin inhibition. We have
	solved the X-ray structure of unliganded FKBP12 and of FKBP12 in
	complex with FK506 and with rapamycin; these structures show localized
	differences in conformation and mobility in those regions of the
	protein that are known, by site-directed mutagenesis, to be involved
	in calcineurin inhibition. A comparison of 16 additional X-ray structures
	of FKBP12 in complex with FKBP12-binding ligands, where those structures
	were determined from different crystal forms with distinct packing
	arrangements, lends significance to the observed structural variability
	and suggests that it represents an intrinsic functional characteristic
	of the protein. Similar differences have been observed for FKBP12
	before, but were considered artifacts of crystal-packing interactions.
	We suggest that immunosuppressive ligands express their differential
	effects in part by modulating the conformation of FKBP12, in agreement
	with mutagenesis experiments on the protein, and not simply through
	differences in the ligand structures themselves.},
  address = {Vertex Pharmaceuticals Incorporated, Cambridge, MA 02139-4211, USA.},
  comment = {Jul 1

	Comparative X-ray structures of the major binding protein for the
	immunosuppressant FK506 (tacrolimus) in unliganded form and in complex
	with FK506 and rapamycin

	15299838

	Wilson, K P Yamashita, M M Sintchak, M D Rotstein, S H Murcko, M A
	Boger, J Thomson, J A Fitzgibbon, M J Black, J R Navia, M A Denmark
	Acta crystallographica. Section D, Biological crystallography Acta
	Crystallogr D Biol Crystallogr. 1995 Jul 1;51(Pt 4):511-21.

	eng},
  issn = {0907-4449 (Print) 0907-4449 (Linking)},
  owner = {mauro},
  refid = {62},
  timestamp = {2011.07.22},
  url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15299838}
}

@ARTICLE{Winn2002,
  author = {Peter J Winn and Susanna K Ludemann and Ralph Gauges and Valere Lounnas
	and Rebecca C Wade},
  title = {Comparison of the dynamics of substrate access channels in three
	cytochrome P450s reveals different opening mechanisms and a novel
	functional role for a buried arginine.},
  journal = {Proc Natl Acad Sci U S A},
  year = {2002},
  volume = {99},
  pages = {5361--5366},
  number = {8},
  month = {Apr},
  abstract = {Understanding the mechanism and specificity of substrate binding in
	the cytochrome P450 (P450) superfamily is an important step toward
	explaining its key role in drug metabolism, toxicity, xenobiotic
	degradation, and several biosynthetic pathways. Here we investigate
	the ligand exit pathways and mechanisms of P450cam (CYP101), P450BM-3
	(CYP102), and P450eryF (CYP107A1) by using random expulsion molecular
	dynamics and classical molecular dynamics simulations. Although several
	different pathways are found for each protein, one pathway is common
	to all three. The mechanism of ligand exit along this pathway is,
	however, quite different in the three different proteins. For P450cam,
	small backbone conformational changes, in combination with aromatic
	side chain rotation, allow for the passage of the rather rigid, compact,
	and hydrophobic substrate, camphor. In P450BM-3, larger transient
	backbone changes are observed on ligand exit. R47, situated at the
	entrance to the channel, appears important in guiding negatively
	charged fatty acid substrates in and out of the active site. In P450eryF,
	an isolated buried arginine, R185, stabilized by four hydrogen bonds
	to backbone carbonyl oxygen atoms, is located in the exit channel
	and is identified as having a particularly unusual functionality,
	dynamically gating channel opening. The results for these three P450s
	suggest that the channel opening mechanisms are adjusted to the physico-chemical
	properties of the substrate and can kinetically modulate protein-substrate
	specificity.},
  doi = {10.1073/pnas.082522999},
  institution = {European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg,
	Germany.},
  keywords = {Arginine; Bacterial Proteins; Binding Sites; Camphor; Camphor 5-Monooxygenase;
	Carbon; Cytochrome P-450 Enzyme System; Erythromycin; Hydrogen Bonding;
	Kinetics; Ligands; Mixed Function Oxygenases; Models, Chemical; Models,
	Molecular; NADPH-Ferrihemoprotein Reductase; Oxygen; Protein Binding;
	Software; Substrate Specificity; Thermodynamics; Time Factors},
  owner = {emilio},
  pii = {99/8/5361},
  pmid = {11959989},
  timestamp = {2010.09.07},
  url = {http://dx.doi.org/10.1073/pnas.082522999}
}

@ARTICLE{Wodak2007,
  author = {Wodak, Shoshana J.},
  title = {From the Mediterranean coast to the shores of Lake Ontario: CAPRI's
	premiere on the American continent},
  journal = {Proteins},
  year = {2007},
  volume = {69},
  pages = {697--698},
  number = {4},
  issn = {1097-0134},
  owner = {emilio},
  publisher = {Wiley Subscription Services, Inc., A Wiley Company},
  timestamp = {2011.10.15},
  url = {http://dx.doi.org/10.1002/prot.21805}
}

@ARTICLE{Wong2011,
  author = {Kin-Yiu Wong and Tai-Sung Lee and Darrin M York},
  title = {Active participation of Mg ion in the reaction coordinate of RNA
	self-cleavage catalyzed by the hammerhead ribozyme.},
  journal = {J Chem Theory Comput},
  year = {2011},
  volume = {7},
  pages = {1--3},
  number = {1},
  month = {Jan},
  doi = {10.1021/ct100467t},
  institution = {Department of Chemistry, University of Minnesota, 207 Pleasant St.
	SE, Minneapolis, MN 55455, USA.},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {21379373},
  timestamp = {2011.07.15},
  url = {http://dx.doi.org/10.1021/ct100467t}
}

@ARTICLE{Wong2009,
  author = {Sergio Wong and Rommie E Amaro and J. Andrew McCammon},
  title = {MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein-Protein
	Interface.},
  journal = {J Chem Theory Comput},
  year = {2009},
  volume = {5},
  pages = {422--429},
  number = {2},
  month = {Feb},
  abstract = {The calculation of protein interaction energetics is of fundamental
	interest, yet accurate quantities are difficult to obtain due to
	the complex and dynamic nature of protein interfaces. This is further
	complicated by the presence of water molecules, which can exhibit
	transient interactions of variable duration and strength with the
	protein surface. The T-cell receptor (TCR) and its staphylococcal
	enterotoxin 3 (SEC3) binding partner are well-characterized examples
	of a protein-protein interaction system exhibiting interfacial plasticity,
	cooperativity, and additivity among mutants. Specifically engineered
	mutants induce intercalating interfacial water molecules, which subsequently
	enhance protein-protein binding affinity. In this work, we perform
	a set of molecular mechanics (MM) Poisson-Boltzmann (PB) surface
	area (SA) calculations on the wild type and two mutant TCR-SEC3 systems
	and show that the method is able to discriminate between weak and
	strong binders only when key explicit water molecules are included
	in the analysis. The results presented here point to the promise
	of MM-PBSA toward rationalizing molecular recognition at protein-protein
	interfaces, while establishing a general approach to handle explicit
	interfacial water molecules in such calculations.},
  comment = {Water},
  doi = {10.1021/ct8003707},
  institution = {Department of Chemistry and Biochemistry, Center for Theoretical
	Biological Physics, Department of Pharmacology, and Howard Hughes
	Medical Institute, University of California at San Diego, La Jolla,
	California 92093-0365.},
  owner = {emilio},
  pmid = {19461869},
  timestamp = {2010.09.09},
  url = {http://dx.doi.org/10.1021/ct8003707}
}

@ARTICLE{Woo2005,
  author = {Hyung-June Woo and Beno\^{i}t Roux},
  title = {Calculation of absolute protein-ligand binding free energy from computer
	simulations.},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {2005},
  volume = {102},
  pages = {6825--6830},
  number = {19},
  month = {May},
  abstract = {A general methodology for calculating the equilibrium binding constant
	of a flexible ligand to a protein receptor is formulated on the basis
	of potentials of mean force. The overall process is decomposed into
	several stages that can be computed separately: the free ligand in
	the bulk is first restrained into the conformation it adopts in the
	bound state, position, and orientation by applying biasing potentials,
	then it is translated into the binding site, where it is released
	completely. The conformational restraining potential is based on
	the root-mean-square deviation of the peptide coordinates relative
	to its average conformation in the bound complex. Free energy contributions
	from each stage are calculated by means of free energy perturbation
	potential of mean force techniques by using appropriate order parameters.
	The present approach avoids the need to decouple the ligand from
	its surrounding (bulk solvent and receptor protein) as is traditionally
	performed in the double-decoupling scheme. It is believed that the
	present formulation will be particularly useful when the solvation
	free energy of the ligand is very large. As an application, the equilibrium
	binding constant of the phosphotyrosine peptide pYEEI to the Src
	homology 2 domain of human Lck has been calculated. The results are
	in good agreement with experimental values.},
  doi = {10.1073/pnas.0409005102},
  institution = {Department of Physiology and Biophysics, Weill Medical College of
	Cornell University, 1300 York Avenue, New York, NY 10021, USA.},
  keywords = {Binding Sites; Computational Biology; Computer Simulation; Crystallography,
	X-Ray; Humans; Kinetics; Ligands; Lymphocyte Specific Protein Tyrosine
	Kinase p56(lck); Models, Molecular; Models, Statistical; Peptides;
	Phosphotyrosine; Protein Binding; Protein Conformation; Thermodynamics;
	src Homology Domains},
  owner = {emilio},
  pii = {0409005102},
  pmid = {15867154},
  timestamp = {2010.04.21},
  url = {http://dx.doi.org/10.1073/pnas.0409005102}
}

@ARTICLE{Wood:Thompson:90,
  author = {Wood, R. H. and Thompson, P. T.},
  title = {Differences between pair and bulk hydrophobic interactions},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {1990},
  volume = {87},
  pages = {946-949},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Woods2003,
  author = {Woods, Christopher J. and Essex, Jonathan W. and King, Michael A.},
  title = {The Development of Replica-Exchange-Based Free-Energy Methods},
  journal = {J. Phys. Chem. B},
  year = {2003},
  volume = {107},
  pages = {13703--13710},
  number = {49},
  month = dec,
  abstract = {The calculation of relative free energies that involve large reorganizations
	of the environment is one of the great challenges of condensed-phase
	simulation. Such calculations are of particular importance in proteinligand
	free-energy calculations. To meet this challenge, we have developed
	new free-energy techniques that combine the advantages of the replica-exchange
	method with free-energy perturbation (FEP) and finite-difference
	thermodynamic integration (FDTI). These new techniques are tested
	and compared with FEP, FDTI, and the adaptive umbrella weighted histogram
	analysis method (AdUmWHAM) on the challenging calculation of the
	relative hydration free energy of methane and water. This calculation
	involves a large solvent configurational change. Through the use
	of replica-exchange moves along the lambda-coordinate, the configurations
	sampled along lambda are allowed to mix, which leads to dramatic
	improvements in solvent configurational sampling, an efficient reduction
	of random sampling error, and a reduction of general simulation error.
	This is achieved at effectively no extra computational cost, relative
	to standard FEP or FDTI.},
  comment = {doi: 10.1021/jp0356620},
  issn = {1520-6106},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2010.04.23},
  url = {http://dx.doi.org/10.1021/jp0356620}
}

@ARTICLE{Woods2003a,
  author = {Woods, Christopher J. and Essex, Jonathan W. and King, Michael A.},
  title = {Enhanced Configurational Sampling in Binding Free-Energy Calculations},
  journal = {J. Phys. Chem. B},
  year = {2003},
  volume = {107},
  pages = {13711--13718},
  number = {49},
  month = dec,
  abstract = {The newly developed method of replica-exchange thermodynamic integration
	(RETI) was tested and compared with finite-difference thermodynamic
	integration (FDTI) on the calculation of the relative binding free
	energies of halides to a calix[4]pyrrole derivative. The calculation
	was challenging, because the dimethylsulfoxide solvent was contaminated
	by small amounts of water. The λ-swap move of RETI enabled more-complete
	sampling of the solvents and produced relative binding free energies
	that included the effect of the fluoride's higher affinity for water.
	In addition, the λ-swap move increased the quality of the configurational
	sampling of the host, because the system was able to escape from
	local minima. The results demonstrate that the sampling of RETI is
	superior to that of FDTI, at no additional computational expense.},
  comment = {doi: 10.1021/jp036162+},
  issn = {1520-6106},
  owner = {emilio},
  publisher = {American Chemical Society},
  timestamp = {2010.09.17},
  url = {http://dx.doi.org/10.1021/jp036162+}
}

@ARTICLE{Wu2011,
  author = {Yujie Wu and Teng Lin and John C. Shelley and Woody Sherman},
  title = {Lambda hopping: An efficient replica exchange-based sampling method
	for relative free energy perturbation calculations},
  note = {In preparation},
  owner = {emilio},
  timestamp = {2010.10.07}
}

@ARTICLE{Wu:Narayan:Weinstock:Levy:Baum:2009,
  author = {Wu, {K.-P.} and Narayanan, C. and Weinstock, {D. S.} and Levy, {R.
	M.} and Baum, J.},
  title = {Acid-induced human alpha-synuclein is described in C-terminal compaction
	in parallel with exposed N-terminal and NAC regions},
  year = {2009},
  note = {Submitted for publication},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Wyman2010a,
  author = {Ian W Wyman and Donal H Macartney},
  title = {Host-guest complexations of local anaesthetics by cucurbit[7]uril
	in aqueous solution.},
  journal = {Org Biomol Chem},
  year = {2010},
  volume = {8},
  pages = {247--252},
  number = {1},
  month = {Jan},
  abstract = {The cucurbit[7]uril (CB[7]) host molecule forms very stable host-guest
	complexes with the local anaesthetics procaine (K(CB[7]) = (3.5 +/-
	0.7) x 10(4) dm(3) mol(-1)), tetracaine (K(CB[7]) = (1.5 +/- 0.4)
	x 10(4) dm(3) mol(-1)), procainamide (K(CB[7]) = (7.8 +/- 1.6) x
	10(4) dm(3) mol(-1)), dibucaine (K(CB[7]) = (1.8 +/- 0.4) x 10(5)
	dm(3) mol(-1)) and prilocaine (K(CB[7]) = (2.6 +/- 0.6) x 10(4) dm(3)
	mol(-1)) in aqueous solution (pD = 4.75). The stability constants
	are 2-3 orders of magnitude greater than the values reported for
	binding by the comparably sized beta-cyclodextrin host molecule.
	The inclusion by CB[7] raises the first pK(a) values of the anaesthetics
	by 0.5-1.9 pK units, as the protonated forms are bound more strongly
	in acidic solution. The complexation-induced chemical shift changes
	in the guest proton resonances provide an indication of the site(s)
	of binding and the effects of protonation on the location of the
	binding sites.},
  doi = {10.1039/b915694a},
  institution = {Department of Chemistry, Queen's University, 90 Bader Lane, Kingston,
	Ontario K7L 3N6, Canada.},
  keywords = {Anesthetics, Local, chemistry; Binding Sites; Bridged Compounds, chemistry;
	Imidazoles, chemistry; Magnetic Resonance Spectroscopy; Models, Molecular;
	Molecular Structure; Solutions; Spectrophotometry, Ultraviolet; Water,
	chemistry},
  language = {eng},
  medline-pst = {ppublish},
  owner = {emilio},
  pmid = {20024155},
  timestamp = {2011.10.15},
  url = {http://dx.doi.org/10.1039/b915694a}
}

@UNPUBLISHED{JunchaoXia:NanjieDeng:NMRinprep:2012,
  author = {Jun-chao Xia and Nanjie Deng and Ronald M. Levy},
  title = {Calculation of NMR Relaxation from Kinetic Network Model and Two-State
	Conformation Exchange Model of HIV-1 Protease},
  note = {In preparation.},
  owner = {emilio},
  timestamp = {2012.07.13}
}

@ARTICLE{Yang:93,
  author = {Yang, A. S. and Gunner, M. and Sampogna, R. and Sharp, K. and Honig,
	B.},
  journal = {Proteins},
  year = {1993},
  volume = {15},
  pages = {252-265},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Yang:Sharp:Honig:92,
  author = {Yang, A.-S. and Sharp, K. A. and Honig, B.},
  title = {Analysis of the Heat Capacity Dependence of Protein Folding},
  journal = {J. Mol. Biol.},
  year = {1992},
  volume = {227},
  pages = {889-900},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Yang2009,
  author = {Chao-Yie Yang and Haiying Sun and Jianyong Chen and Zaneta Nikolovska-Coleska
	and Shaomeng Wang},
  title = {Importance of ligand reorganization free energy in protein-ligand
	binding-affinity prediction.},
  journal = {J. Am. Chem. Soc.},
  year = {2009},
  volume = {131},
  pages = {13709--13721},
  number = {38},
  month = {Sep},
  abstract = {Accurate prediction of the binding affinities of small-molecule ligands
	to their biological targets is fundamental for structure-based drug
	design but remains a very challenging task. In this paper, we have
	performed computational studies to predict the binding models of
	31 small-molecule Smac (the second mitochondria-derived activator
	of caspase) mimetics to their target, the XIAP (X-linked inhibitor
	of apoptosis) protein, and their binding affinities. Our results
	showed that computational docking was able to reliably predict the
	binding models, as confirmed by experimentally determined crystal
	structures of some Smac mimetics complexed with XIAP. However, all
	the computational methods we have tested, including an empirical
	scoring function, two knowledge-based scoring functions, and MM-GBSA
	(molecular mechanics and generalized Born surface area), yield poor
	to modest prediction for binding affinities. The linear correlation
	coefficient (r(2)) value between the predicted affinities and the
	experimentally determined affinities was found to be between 0.21
	and 0.36. Inclusion of ensemble protein-ligand conformations obtained
	from molecular dynamic simulations did not significantly improve
	the prediction. However, major improvement was achieved when the
	free-energy change for ligands between their free- and bound-states,
	or "ligand-reorganization free energy", was included in the MM-GBSA
	calculation, and the r(2) value increased from 0.36 to 0.66. The
	prediction was validated using 10 additional Smac mimetics designed
	and evaluated by an independent group. This study demonstrates that
	ligand reorganization free energy plays an important role in the
	overall binding free energy between Smac mimetics and XIAP. This
	term should be evaluated for other ligand-protein systems and included
	in the development of new scoring functions. To our best knowledge,
	this is the first computational study to demonstrate the importance
	of ligand reorganization free energy for the prediction of protein-ligand
	binding free energy.},
  comment = {Ligand reorganization},
  doi = {10.1021/ja9039373},
  institution = {Department of Internal Medicine, University of Michigan, 1500 East
	Medical Center Drive, Ann Arbor, Michigan 48109, USA.},
  keywords = {Amino Acid Sequence; Biomimetic Materials; Computational Biology;
	Intracellular Signaling Peptides and Proteins; Ligands; Mitochondrial
	Proteins; Molecular Sequence Data; Protein Binding; Protein Conformation;
	Thermodynamics; X-Linked Inhibitor of Apoptosis Protein},
  owner = {emilio},
  pmid = {19736924},
  timestamp = {2010.04.20},
  url = {http://dx.doi.org/10.1021/ja9039373}
}

@ARTICLE{Yang:96,
  author = {Yang, L. and Valdeavella, C. and Pettitt, B. M.},
  journal = {Biophys. J.},
  year = {1996},
  volume = {71},
  pages = {3022-3029},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@INCOLLECTION{Yang2010,
  author = {Yang, Wei and Cui, Qiang and Min, Donghong and Li, Hongzhi},
  title = {QM/MM Alchemical Free Energy Simulations: Challenges and Recent Developments},
  publisher = {Elsevier},
  year = {2010},
  editor = {Wheeler, Ralph A.},
  volume = {Volume 6},
  pages = {51--62},
  abstract = {The difference between free energy changes occurring at two chemical
	states can be rigorously estimated via alchemical free energy (AFE)
	simulations. Traditionally, most AFE simulations are carried out
	under the classical energy potential treatment; then, accuracy and
	applicability of AFE simulations are limited. Following the natural
	evolution, employing the quantum mechanical (QM)-based potentials,
	particularly the combined QM and molecular mechanical (QM/MM) potentials,
	in AFE simulations is a natural next step. To make such QM/MM AFE
	simulations routinely applicable and reliable to complex systems,
	several major challenges have to be met: (1) to ensure structural
	integrities for robust electronic structural calculations when unphysical
	states are simulated; (2) to accurately describe long-range electrostatic
	interactions; and (3) to efficiently sample the configuration space
	to guarantee free energy convergence when costly QM/MM potentials
	are applied. This review summarizes recent developments related to
	these challenges.},
  issn = {1574-1400},
  keywords = {alchemical free energy simulation, combined quantum mechanical/molecular
	mechanical potential, generalized ensemble simulation, conformational
	sampling, long-range electrostatic interaction},
  owner = {emilio},
  timestamp = {2011.01.13},
  url = {http://www.sciencedirect.com/science/article/B7RNN-50SG02W-8/2/67c5c503b65de62cb4096097d36711fa}
}

@ARTICLE{Yeh2008,
  author = {Yeh, In-Chul and Olson, Mark A. and Lee, Michael S. and Wallqvist,
	Anders},
  title = {Free-Energy Profiles of Membrane Insertion of the M2 Transmembrane
	Peptide from Influenza A Virus},
  journal = {Biophysical Journal},
  year = {2008},
  volume = {95},
  pages = {5021--5029},
  number = {11},
  month = dec,
  abstract = {The insertion of the M2 transmembrane peptide from influenza A virus
	into a membrane has been studied with molecular-dynamics simulations.
	This system is modeled by an atomically detailed peptide interacting
	with a continuum representation of a membrane bilayer in aqueous
	solution. We performed replica-exchange molecular-dynamics simulations
	with umbrella-sampling techniques to characterize the probability
	distribution and conformation preference of the peptide in the solution,
	at the membrane interface, and in the membrane. The minimum in the
	calculated free-energy surface of peptide insertion corresponds to
	a fully inserted, helical peptide spanning the membrane. The free-energy
	profile also shows that there is a significant barrier for the peptide
	to enter into this minimum in a nonhelical conformation. The sequence
	of the peptide is such that hydrophilic amino acid residues at the
	ends of the otherwise primarily hydrophobic peptide create a trapped,
	U-shaped conformation with the hydrophilic residues associated with
	the aqueous phase and the hydrophobic residues embedded in the membrane.
	Analysis of the free energy shows that the barrier to insertion is
	largely enthalpic in nature, whereas the membrane-spanning global
	minimum is favored by entropy.},
  issn = {0006-3495},
  owner = {emilio},
  timestamp = {2011.01.13},
  url = {http://www.sciencedirect.com/science/article/B94RW-4VB4W2T-4/2/af1247cbf04a01ae1b58b07a2a6fa0a8}
}

@ARTICLE{Yelle:Ichiye:97,
  author = {Yelle, R. B. and Ichiye, T.},
  journal = {J. Phys. Chem. B},
  year = {1997},
  volume = {101},
  pages = {4127-4135},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{York:93,
  author = {York, D. M. and Darden, T. A. and Pedersen, L. G.},
  journal = {J. Chem. Phys.},
  year = {1993},
  volume = {99},
  pages = {8345-8351},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Yoshida:Imai:Kovalenko:Hirata:2009,
  author = {Yoshida, N. and Imai, T. and Phongphanphanee, S. and Kovalenko, A.
	and Hirata, F.},
  title = {Molecular Recognition in Biomolecules Studied by Statistical-Mechanical
	Integral-Equation Theory of Liquids},
  journal = {J. Phys. Chem. B},
  year = {2009},
  volume = {113},
  pages = {873--886},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{You:Bashford:95,
  author = {You, T. J. and Bashford, D.},
  journal = {Biophys. J.},
  year = {1995},
  volume = {69},
  pages = {1721-1733},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Young2007,
  author = {Tom Young and Robert Abel and Byungchan Kim and Bruce J Berne and
	Richard A Friesner},
  title = {Motifs for molecular recognition exploiting hydrophobic enclosure
	in protein-ligand binding.},
  journal = {Proc Natl Acad Sci U S A},
  year = {2007},
  volume = {104},
  pages = {808--813},
  number = {3},
  month = {Jan},
  abstract = {The thermodynamic properties and phase behavior of water in confined
	regions can vary significantly from that observed in the bulk. This
	is particularly true for systems in which the confinement is on the
	molecular-length scale. In this study, we use molecular dynamics
	simulations and a powerful solvent analysis technique based on inhomogenous
	solvation theory to investigate the properties of water molecules
	that solvate the confined regions of protein active sites. Our simulations
	and analysis indicate that the solvation of protein active sites
	that are characterized by hydrophobic enclosure and correlated hydrogen
	bonds induce atypical entropic and enthalpic penalties of hydration.
	These penalties apparently stabilize the protein-ligand complex with
	respect to the independently solvated ligand and protein, which leads
	to enhanced binding affinities. Our analysis elucidates several challenging
	cases, including the super affinity of the streptavidin-biotin system.},
  doi = {10.1073/pnas.0610202104},
  institution = {Department of Chemistry, Columbia University, 3000 Broadway, New
	York, NY 10027, USA.},
  keywords = {Amino Acid Motifs; Antibodies; Binding Sites; Cyclooxygenase 2; HIV
	Protease; Hydrophobicity; Ligands; Models, Molecular; Protein Binding;
	Protein Structure, Tertiary; Proteins; Water},
  owner = {emilio},
  pii = {0610202104},
  pmid = {17204562},
  timestamp = {2010.09.17},
  url = {http://dx.doi.org/10.1073/pnas.0610202104}
}

@ARTICLE{Young2010,
  author = {Tom Young and Lan Hua and Xuhui Huang and Robert Abel and Richard
	Friesner and B. J. Berne},
  title = {Dewetting transitions in protein cavities.},
  journal = {Proteins},
  year = {2010},
  volume = {78},
  pages = {1856--1869},
  number = {8},
  month = {Jun},
  abstract = {In a previous analysis of the solvation of protein active sites, a
	drying transition was observed in the narrow hydrophobic binding
	cavity of Cox-2. With the use of a crude metric that often seems
	able to discriminate those protein cavities that dry from those that
	do not, we made an extensive search of the PDB, and identified five
	other proteins that, in molecular dynamics simulations, undergo drying
	transitions in their active sites. Because such cavities need not
	desolvate before binding hydrophobic ligands they often exhibit very
	large binding affinities. This article gives evidence that drying
	in protein cavities is not unique to Cox-2.},
  doi = {10.1002/prot.22699},
  institution = {Department of Chemistry, Columbia University, New York, NY 10027,
	USA. simpleliquid@gmail.com},
  keywords = {Animals; Binding Sites; Cattle; Databases, Protein; Humans; Hydrophobicity;
	Models, Molecular; Protein Structure, Secondary; Proteins; Serum
	Albumin; Surface Properties; Water},
  owner = {emilio},
  pmid = {20225258},
  timestamp = {2010.09.17},
  url = {http://dx.doi.org/10.1002/prot.22699}
}

@ARTICLE{Yu2010,
  author = {Hongtao Yu and Steven W Rick},
  title = {Free energy, entropy, and enthalpy of a water molecule in various
	protein environments.},
  journal = {J Phys Chem B},
  year = {2010},
  volume = {114},
  pages = {11552--11560},
  number = {35},
  month = {Sep},
  abstract = {To examine the wide variety of cavities available to water molecules
	inside proteins, a model of the protein cavities is developed with
	the local environment treated at atomic detail and the nonlocal environment
	treated approximately. The cavities are then changed to vary in size
	and in the number of hydrogen bonds available to a water molecule
	inside the cavity. The free energy, entropy, and enthalpy change
	for the transfer of a water molecule to the cavity from the bulk
	liquid is calculated from thermodynamic integration. The results
	of the model are close to those of similar cavities calculated using
	the full protein and solvent environment. As the number of hydrogen
	bonds resulting from the addition of the water molecule increases,
	the free energy decreases, as the enthalpic gain of making a hydrogen
	bond outweighs the entropic cost. Changing the volume of the cavity
	has a smaller effect on the thermodynamics. Once the hydrogen bond
	contribution is taken into account, the volume dependence on DeltaG,
	DeltaS, and DeltaH is small and roughly the same for a hydrophobic
	cavity as a hydrophilic cavity.},
  doi = {10.1021/jp104209w},
  institution = {Department of Chemistry, University of New Orleans, New Orleans,
	Louisiana 70148, USA.},
  owner = {emilio},
  pmid = {20704188},
  timestamp = {2010.09.17},
  url = {http://dx.doi.org/10.1021/jp104209w}
}

@ARTICLE{Yu2009,
  author = {Hongtao Yu and Steven W Rick},
  title = {Free energies and entropies of water molecules at the inhibitor-protein
	interface of DNA gyrase.},
  journal = {J Am Chem Soc},
  year = {2009},
  volume = {131},
  pages = {6608--6613},
  number = {18},
  month = {May},
  abstract = {Complexes of the antibiotics novobiocin and clorobiocin with DNA gyrase
	are illustrative of the importance of bound water to binding thermodynamics.
	Mutants resistant to novobiocin as well as those with a decreased
	affinity for novobiocin over clorobiocin both involve a less favorable
	entropy of binding, which more than compensates for a more favorable
	enthalpy, and additional water molecules at the protein-ligand interface.
	Free energy, enthalpy, and entropy for these water molecules were
	calculated by thermodynamic integration computer simulations. The
	calculations show that addition of the water molecules is entropically
	unfavorable, with values that are comparable to the measured entropy
	differences. The free energies and entropies correlate with the change
	in the number of hydrogen bonds due to the addition of water molecules.},
  doi = {10.1021/ja809696s},
  institution = {ew Orleans, New Orleans, Louisiana 70148, USA.},
  keywords = {Anti-Bacterial Agents; DNA Gyrase; Entropy; Hydrogen Bonding; Mutant
	Proteins; Novobiocin; Thermodynamics; Water},
  owner = {emilio},
  pmid = {19374378},
  timestamp = {2010.09.17},
  url = {http://dx.doi.org/10.1021/ja809696s}
}

@ARTICLE{Yu:Karplus:88,
  author = {Yu, H.-A. and Karplus, M.},
  journal = {J. Chem. Phys.},
  year = {1988},
  volume = {89},
  pages = {2366},
  number = {4},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@BOOK{Yu:Mittra:2006,
  title = {Parallel Finite-Difference Time-Domain Method},
  publisher = {Artech House Publishers},
  year = {2006},
  author = {Yu, W. and Mittra, R. and Su, T. and Liu, Y. and Yang, X.},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Yu:Jacobson:Friesner:2004,
  author = {Yu, Z. and Jacobson, {M. P.} and Josovitz, J. and Rapp, {C. S.} and
	Friesner, {R. A.}},
  title = {First-Shell Solvation of Ion Pairs: Correction of Systematic Errors
	in Implicit Solvent Models},
  journal = {J. Phys. Chem. B},
  year = {2004},
  volume = {108},
  pages = {6643--6654},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Zacharias:2003,
  author = {Zacharias, M.},
  title = {Continuum Solvent Modeling of Nonpolar Solvation: Improvement by
	Separating Surface Area Dependent Cavity and Dispersion Contributions.},
  journal = {J. Phys. Chem. A},
  year = {2003},
  volume = {107},
  pages = {3000--3004},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Zauhar:Morgan:85,
  author = {Zauhar, R. J. and Morgan, R. S.},
  title = {A New Method for Computing the Macromolecular Electric Potential},
  journal = {J. Mol. Biol.},
  year = {1985},
  volume = {186},
  pages = {815-820},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Zeng:Hush:Reimers:93,
  author = {Zeng, J. and Hush, N. S. and Reimers, J. R.},
  title = {Enthalpy of Hydration and Partial Molar Specific Volume as Criteria
	for Evaluation of Intermolecular Potentials. NPT-ensemble Monte Carlo
	Calculations for Dilute Neon in Water},
  journal = {Chem. Phys. Lett.},
  year = {1993},
  volume = {206},
  pages = {318},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Zhang2010,
  author = {Cheng Zhang and Jianpeng Ma},
  title = {Enhanced sampling and applications in protein folding in explicit
	solvent.},
  journal = {J Chem Phys},
  year = {2010},
  volume = {132},
  pages = {244101},
  number = {24},
  month = {Jun},
  abstract = {We report a single-copy tempering method for simulating large complex
	systems. In a generalized ensemble, the method uses runtime estimate
	of the thermal average energy computed from a novel integral identity
	to guide a continuous temperature-space random walk. We first validated
	the method in a two-dimensional Ising model and a Lennard-Jones liquid
	system. It was then applied to folding of three small proteins, trpzip2,
	trp-cage, and villin headpiece in explicit solvent. Within 0.5-1
	microsecond, all three systems were reversibly folded into atomic
	accuracy: the alpha carbon root mean square deviations of the best
	folded conformations from the native states were 0.2, 0.4, and 0.4
	A, for trpzip2, trp-cage, and villin headpiece, respectively.},
  doi = {10.1063/1.3435332},
  institution = {Department of Bioengineering and Applied Physics Program, Rice University
	Houston, Texas 77005, USA.},
  keywords = {Amino Acid Sequence; Microfilament Proteins; Models, Molecular; Molecular
	Sequence Data; Peptides; Protein Conformation; Protein Folding; Proteins;
	Solvents; Temperature; Thermodynamics},
  owner = {emilio},
  pmid = {20590175},
  timestamp = {2010.11.01},
  url = {http://dx.doi.org/10.1063/1.3435332}
}

@ARTICLE{Zhang2009,
  author = {Cheng Zhang and Jianpeng Ma},
  title = {Enhanced sampling in generalized ensemble with large gap of sampling
	parameter: case study in temperature space random walk.},
  journal = {J Chem Phys},
  year = {2009},
  volume = {130},
  pages = {194112},
  number = {19},
  month = {May},
  abstract = {We present an efficient sampling method for computing a partition
	function and accelerating configuration sampling. The method performs
	a random walk in the lambda space, with lambda being any thermodynamic
	variable that characterizes a canonical ensemble such as the reciprocal
	temperature beta or any variable that the Hamiltonian depends on.
	The partition function is determined by minimizing the difference
	of the thermal conjugates of lambda (the energy in the case of lambda
	= beta), defined as the difference between the value from the dynamically
	updated derivatives of the partition function and the value directly
	measured from simulation. Higher-order derivatives of the partition
	function are included to enhance the Brownian motion in the lambda
	space. The method is much less sensitive to the system size, and
	to the size of lambda window than other methods. On the two dimensional
	Ising model, it is shown that the method asymptotically converges
	the partition function, and the error of the logarithm of the partition
	function is much smaller than the algorithm using the Wang-Landau
	recursive scheme. The method is also applied to off-lattice model
	proteins, the AB models, in which cases many low energy states are
	found in different models.},
  doi = {10.1063/1.3139192},
  institution = {Department of Bioengineering, Rice University, Houston, Texas 77005,
	USA.},
  keywords = {Computer Simulation; Models, Molecular; Motion; Protein Folding; Proteins;
	Stochastic Processes; Temperature; Thermodynamics},
  owner = {emilio},
  pmid = {19466826},
  timestamp = {2010.11.01},
  url = {http://dx.doi.org/10.1063/1.3139192}
}

@ARTICLE{Zhang2008,
  author = {Cheng Zhang and Jianpeng Ma},
  title = {Comparison of sampling efficiency between simulated tempering and
	replica exchange.},
  journal = {J Chem Phys},
  year = {2008},
  volume = {129},
  pages = {134112},
  number = {13},
  month = {Oct},
  abstract = {We compared the sampling efficiency of simulated tempering and replica
	exchange. Our results indicate that simulated tempering is superior
	to replica exchange if the parameters for temperature transition
	in simulated tempering are adjusted to be proportional to the partition
	function. It is shown that, in simulated tempering, the rate of traversing
	energy space of different temperatures is much higher than that in
	replica exchange, especially in the case of low tempering frequency
	and/or larger temperature separations.},
  doi = {10.1063/1.2988339},
  institution = {Department of Bioengineering, Rice University, Houston, Texas 77005,
	USA.},
  keywords = {Algorithms; Monte Carlo Method; Transition Temperature},
  owner = {emilio},
  pmid = {19045083},
  timestamp = {2010.11.01},
  url = {http://dx.doi.org/10.1063/1.2988339}
}

@ARTICLE{Zhang:Gallicchio:Friesner:Levy:2001,
  author = {Zhang, L. and Gallicchio, E. and Friesner, R. A. and Levy, R. M.},
  title = {Solvent Models for Protein-Ligand Binding: Comparison of Implicit
	Solvent Poisson and Surface Generalized Born Models with Explicit
	Solvent Simulations},
  journal = {J. Comp. Chem.},
  year = {2001},
  volume = {22},
  pages = {591-607},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@INPROCEEDINGS{Zhang:Gallicchio:Levy:99,
  author = {Zhang, L. and Gallicchio, E. and Levy, R. M.},
  title = {Implicit Solvent Models for Protein-Ligand Binding: Insights Based
	on Explicit Solvent Simulations},
  booktitle = {AIP Conference Proceedings (Simulation and Theory of Electrostatic
	Interactions in Solutions)},
  year = {1999},
  volume = {492},
  pages = {451-472},
  address = {Melville, NY},
  publisher = {AIP Publishing Center},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@INPROCEEDINGS{1690613,
  author = {Li Zhang and Parashar, M. and Gallicchio, E. and Levy, R.M.},
  title = {Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular
	Dynamics Applications},
  booktitle = {Parallel Processing, 2006. ICPP 2006. International Conference on},
  year = {2006},
  pages = {127 -134},
  month = aug.,
  abstract = {This paper presents Salsa, a novel, decentralized and asynchronous
	realization of the "replica exchange" algorithm for simulating the
	structure, function, folding, and dynamics of proteins. Salsa provides
	a scalable communication and interaction substrate that presents
	a virtual shared space abstraction and enables the dynamic and asynchronous
	interactions required by the simulations to be simply and efficiently
	implemented. The design, implementation and experimental evaluation
	of Salsa and replica exchange-based simulations using Salsa are presented},
  doi = {10.1109/ICPP.2006.63},
  issn = {0190-3918},
  keywords = {Salsa;parallel molecular dynamics application;replica exchange algorithm;scalable
	asynchronous replica exchange;virtual shared space abstraction;chemistry
	computing;molecular dynamics method;parallel processing;proteins;},
  owner = {emilio},
  timestamp = {2011.02.03}
}

@INPROCEEDINGS{Zhang:Parashar:Gallicchio:Levy:2006,
  author = {Zhang, L. and Parashar, M. and Gallicchio, E. and Levy, {R. M.}},
  title = {Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular
	Dynamics Applications},
  booktitle = {ICPP '06: Proceedings of the 2006 International Conference on Parallel
	Processing},
  year = {2006},
  pages = {127--134},
  address = {Washington, DC, USA},
  publisher = {IEEE Computer Society},
  doi = {http://dx.doi.org/10.1109/ICPP.2006.63},
  isbn = {0-7695-2636-5},
  owner = {emilio},
  timestamp = {2010.10.28}
}

@INCOLLECTION{Zhang2010a,
  author = {Zhang, Rui and Lev, Bogdan and Cuervo, Javier Eduardo and Noskov,
	Sergei Yu and Salahub, Dennis R.},
  title = {A Guide to QM/MM Methodology and Applications},
  booktitle = {Combining Quantum Mechanics and Molecular Mechanics. Some Recent
	Progresses in QM/MM Methods},
  publisher = {Academic Press},
  year = {2010},
  editor = {Sabin, John R. and Br�ndas, Erkki},
  volume = {Volume 59},
  pages = {353--400},
  abstract = {This review provides a general introduction to quantum mechanical/molecular
	mechanical (QM)/(MM) methodology and techniques. It starts with the
	description of the effective QM/MM Hamiltonian and partitioning of
	the system, followed by geometry optimization and transition state
	search techniques. Subsequently, QM/MM sampling approaches are brought
	in for free energy calculations including thermodynamic integration,
	free energy perturbation, umbrella sampling, and the path integral
	method to account for nuclear quantum effects. Lastly, QM/MM studies
	of DNA polymerases are reviewed as a state-of-the-art application
	to the study of enzymatic catalysis.},
  issn = {0065-3276},
  owner = {emilio},
  timestamp = {2011.01.13},
  url = {http://www.sciencedirect.com/science/article/B7CSN-4YVNF05-H/2/3d74a964712a9752ea59c759a9261007}
}

@ARTICLE{Zhang2009a,
  author = {Yang Zhang},
  title = {Protein structure prediction: when is it useful?},
  journal = {Curr. Opin. Struct. Biol.},
  year = {2009},
  volume = {19},
  pages = {145--155},
  number = {2},
  month = {Apr},
  abstract = {Computationally predicted three-dimensional structure of protein molecules
	has demonstrated the usefulness in many areas of biomedicine, ranging
	from approximate family assignments to precise drug screening. For
	nearly 40 years, however, the accuracy of the predicted models has
	been dictated by the availability of close structural templates.
	Progress has recently been achieved in refining low-resolution models
	closer to the native ones; this has been made possible by combining
	knowledge-based information from multiple sources of structural templates
	as well as by improving the energy funnel of physics-based force
	fields. Unfortunately, there has been no essential progress in the
	development of techniques for detecting remotely homologous templates
	and for predicting novel protein structures.},
  doi = {10.1016/j.sbi.2009.02.005},
  institution = {Center for Bioinformatics and Department of Molecular Biosciences,
	University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA.
	yzhang@ku.edu},
  keywords = {Algorithms; Computational Biology; Computer Simulation; Databases,
	Protein; Humans; Models, Molecular; Protein Conformation; Proteins;
	Structure-Activity Relationship},
  owner = {emilio},
  pii = {S0959-440X(09)00025-6},
  pmid = {19327982},
  timestamp = {2010.04.22},
  url = {http://dx.doi.org/10.1016/j.sbi.2009.02.005}
}

@ARTICLE{Zheng2008a,
  author = {Zheng, Lianqing and Chen, Mengen and Yang, Wei},
  title = {Random walk in orthogonal space to achieve efficient free-energy
	simulation of complex systems},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2008},
  volume = {105},
  pages = {20227--20232},
  number = {51},
  abstract = {In the past few decades, many ingenious efforts have been made in
	the development of free-energy simulation methods. Because complex
	systems often undergo nontrivial structural transition during state
	switching, achieving efficient free-energy calculation can be challenging.
	As identified earlier, the “Hamiltonian” lagging, which reveals the
	fact that necessary structural relaxation falls behind the order
	parameter move, has been a primary problem for generally low free-energy
	simulation efficiency. Here, we propose an algorithm by achieving
	a random walk in both the order parameter space and its generalized
	force space; thereby, the order parameter move and the required conformational
	relaxation can be efficiently synchronized. As demonstrated in both
	the alchemical transition and the conformational transition, a leapfrog
	improvement in free-energy simulation efficiency can be obtained;
	for instance, (i) it allows us to solve a notoriously challenging
	problem: accurately predicting the pKa value of a buried titratable
	residue, Asp-66, in the interior of the V66E staphylococcal nuclease
	mutant, and (ii) it allows us to gain superior efficiency over the
	metadynamics algorithm.},
  date = {December 23, 2008},
  doi = {10.1073/pnas.0810631106},
  owner = {emilio},
  timestamp = {2012.06.21},
  url = {http://www.pnas.org/content/105/51/20227.abstract}
}

@ARTICLE{Zheng2009,
  author = {Weihua Zheng and Michael Andrec and Emilio Gallicchio and Ronald
	M Levy},
  title = {Recovering kinetics from a simplified protein folding model using
	replica exchange simulations: a kinetic network and effective stochastic
	dynamics.},
  journal = {J Phys Chem B},
  year = {2009},
  volume = {113},
  pages = {11702--11709},
  number = {34},
  month = {Aug},
  abstract = {We present an approach to recover kinetics from a simplified protein
	folding model at different temperatures using the combined power
	of replica exchange (RE), a kinetic network, and effective stochastic
	dynamics. While RE simulations generate a large set of discrete states
	with the correct thermodynamics, kinetic information is lost due
	to the random exchange of temperatures. We show how we can recover
	the kinetics of a 2D continuous potential with an entropic barrier
	by using RE-generated discrete states as nodes of a kinetic network.
	By choosing the neighbors and the microscopic rates between the neighbors
	appropriately, the correct kinetics of the system can be recovered
	by running a kinetic simulation on the network. We fine-tune the
	parameters of the network by comparison with the effective drift
	velocities and diffusion coefficients of the system determined from
	short-time stochastic trajectories. One of the advantages of the
	kinetic network model is that the network can be built on a high-dimensional
	discretized state space, which can consist of multiple paths not
	consistent with a single reaction coordinate.},
  doi = {10.1021/jp900445t},
  institution = {Department of Physics and Astronomy, Rutgers, The State University
	of New Jersey, 136 Frelinghuysen Road, Piscataway, New Jersey 08854,
	USA.},
  keywords = {Computer Simulation; Kinetics; Models, Chemical; Protein Folding;
	Proteins; Thermodynamics},
  owner = {emilio},
  pmid = {19655770},
  timestamp = {2010.07.14},
  url = {http://dx.doi.org/10.1021/jp900445t}
}

@ARTICLE{Zheng2008,
  author = {Weihua Zheng and Michael Andrec and Emilio Gallicchio and Ronald
	M Levy},
  title = {Simple continuous and discrete models for simulating replica exchange
	simulations of protein folding.},
  journal = {J. Phys. Chem. B},
  year = {2008},
  volume = {112},
  pages = {6083--6093},
  number = {19},
  month = {May},
  abstract = {The efficiency of temperature replica exchange (RE) simulations hinge
	on their ability to enhance conformational sampling at physiological
	temperatures by taking advantage of more rapid conformational interconversions
	at higher temperatures. While temperature RE is a parallel simulation
	technique that is relatively straightforward to implement, kinetics
	in the RE ensemble is complicated, and there is much to learn about
	how best to employ RE simulations in computational biophysics. Protein
	folding rates often slow down above a certain temperature due to
	entropic bottlenecks. This "anti-Arrhenius" behavior represents a
	challenge for RE. However, it is far from straightforward to systematically
	explore the impact of this on RE by brute force molecular simulations,
	since RE simulations of protein folding are very difficult to converge.
	To understand some of the basic mechanisms that determine the efficiency
	of RE, it is useful to study simplified low dimensionality systems
	that share some of the key characteristics of molecular systems.
	Results are presented concerning the efficiency of temperature RE
	on a continuous two-dimensional potential that contains an entropic
	bottleneck. Optimal efficiency was obtained when the temperatures
	of the replicas did not exceed the temperature at which the harmonic
	mean of the folding and unfolding rates is maximized. This confirms
	a result we previously obtained using a discrete network model of
	RE. Comparison of the efficiencies obtained using the continuous
	and discrete models makes it possible to identify non-Markovian effects,
	which slow down equilibration of the RE ensemble on the more complex
	continuous potential. In particular, the rate of temperature diffusion
	and also the efficiency of RE is limited by the time scale of conformational
	rearrangements within free energy basins.},
  doi = {10.1021/jp076377+},
  institution = {Department of Physics and Astronomy, Rutgers, the State University
	of New Jersey, 136 Frelinghuysen Road, Piscataway, New Jersey 08854,
	USA.},
  keywords = {Computer Simulation; Kinetics; Models, Biological; Probability; Protein
	Folding; Proteins; Temperature; Thermodynamics},
  owner = {emilio},
  pmid = {18251533},
  timestamp = {2010.07.14},
  url = {http://dx.doi.org/10.1021/jp076377+}
}

@ARTICLE{Zheng2007,
  author = {Weihua Zheng and Michael Andrec and Emilio Gallicchio and Ronald
	M Levy},
  title = {Simulating replica exchange simulations of protein folding with a
	kinetic network model.},
  journal = {Proc Natl Acad Sci U S A},
  year = {2007},
  volume = {104},
  pages = {15340--15345},
  number = {39},
  month = {Sep},
  abstract = {Replica exchange (RE) is a generalized ensemble simulation method
	for accelerating the exploration of free-energy landscapes, which
	define many challenging problems in computational biophysics, including
	protein folding and binding. Although temperature RE (T-RE) is a
	parallel simulation technique whose implementation is relatively
	straightforward, kinetics and the approach to equilibrium in the
	T-RE ensemble are very complicated; there is much to learn about
	how to best employ T-RE to protein folding and binding problems.
	We have constructed a kinetic network model for RE studies of protein
	folding and used this reduced model to carry out "simulations of
	simulations" to analyze how the underlying temperature dependence
	of the conformational kinetics and the basic parameters of RE (e.g.,
	the number of replicas, the RE rate, and the temperature spacing)
	all interact to affect the number of folding transitions observed.
	When protein folding follows anti-Arrhenius kinetics, we observe
	a speed limit for the number of folding transitions observed at the
	low temperature of interest, which depends on the maximum of the
	harmonic mean of the folding and unfolding transition rates at high
	temperature. The results shown here for the network RE model suggest
	ways to improve atomic-level RE simulations such as the use of "training"
	simulations to explore some aspects of the temperature dependence
	for folding of the atomic-level models before performing RE studies.},
  doi = {10.1073/pnas.0704418104},
  institution = {Department of Physics and Astronomy, Rutgers, The State University
	of New Jersey, 136 Frelinghuysen Road, Piscataway, NJ 08854, USA.},
  keywords = {Biochemistry; Computer Simulation; Kinetics; Markov Chains; Models,
	Chemical; Models, Molecular; Models, Statistical; Molecular Conformation;
	Protein Conformation; Protein Denaturation; Protein Folding; Protein
	Structure, Secondary; Temperature; Thermodynamics},
  owner = {emilio},
  pii = {0704418104},
  pmid = {17878309},
  timestamp = {2010.07.14},
  url = {http://dx.doi.org/10.1073/pnas.0704418104}
}

@ARTICLE{Zheng2010,
  author = {Zheng, W. and Gallicchio, E. and Deng, N. and Andrec, M. and Levy,
	R.M.},
  title = {Kinetic Network Study of the Diversity and Temperature Dependence
	of TRP-Cage Folding Pathways: Combining Transition Path Theory with
	Stochastic Simulations},
  journal = {J. Phys. Chem. B},
  year = {2010},
  pages = {In press},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Zheng2011,
  author = {Zheng, Weihua and Gallicchio, Emilio and Deng, Nanjie and Andrec,
	Michael and Levy, Ronald M.},
  title = {Kinetic Network Study of the Diversity and Temperature Dependence
	of Trp-Cage Folding Pathways: Combining Transition Path Theory with
	Stochastic Simulations},
  journal = {J. Phys. Chem. B},
  year = {2011},
  volume = {115},
  pages = {1512--1523},
  number = {6},
  month = feb,
  abstract = {null},
  comment = {doi: 10.1021/jp1089596},
  issn = {1520-6106},
  owner = {mauro},
  publisher = {American Chemical Society},
  timestamp = {2011.08.16},
  url = {http://dx.doi.org/10.1021/jp1089596}
}

@ARTICLE{Zhou:Szabo:95,
  author = {Zhou, H. X. and Szabo, A.},
  journal = {J. Chem. Phys.},
  year = {1995},
  volume = {103},
  pages = {3481-3494},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Zhou2010,
  author = {Huan-Xiang Zhou},
  title = {From induced fit to conformational selection: a continuum of binding
	mechanism controlled by the timescale of conformational transitions.},
  journal = {Biophys J},
  year = {2010},
  volume = {98},
  pages = {L15--L17},
  number = {6},
  month = {Mar},
  abstract = {In receptor-ligand binding, a question that generated considerable
	interest is whether the mechanism is induced fit or conformational
	selection. This question is addressed here by a solvable model, in
	which a receptor undergoes transitions between active and inactive
	forms. The inactive form is favored while unbound but the active
	form is favored while a ligand is loosely bound. As the active-inactive
	transition rates increase, the binding mechanism gradually shifts
	from conformational selection to induced fit. The timescale of conformational
	transitions thus plays a crucial role in controlling binding mechanisms.},
  doi = {10.1016/j.bpj.2009.11.029},
  institution = {Department of Physics and Institute of Molecular Biophysics, Florida
	State University, Tallahassee, Florida, USA. hzhou4@fsu.edu},
  keywords = {Binding Sites; Computer Simulation; Ligands; Models, Chemical; Models,
	Molecular; Protein Binding; Protein Conformation; Receptors, Cell
	Surface},
  owner = {emilio},
  pii = {S0006-3495(09)01758-5},
  pmid = {20303846},
  timestamp = {2011.01.18},
  url = {http://dx.doi.org/10.1016/j.bpj.2009.11.029}
}

@ARTICLE{Zhou2009,
  author = {Huan-Xiang Zhou and Michael K Gilson},
  title = {Theory of free energy and entropy in noncovalent binding.},
  journal = {Chem. Rev.},
  year = {2009},
  volume = {109},
  pages = {4092--4107},
  number = {9},
  month = {Sep},
  doi = {10.1021/cr800551w},
  institution = {Department of Physics and Institute of Molecular Biophysics, Florida
	State University, Tallahassee, Florida 32306, USA. hzhou4@fsu.edu},
  keywords = {Entropy; Protein Binding},
  owner = {emilio},
  pmid = {19588959},
  timestamp = {2010.04.21},
  url = {http://dx.doi.org/10.1021/cr800551w}
}

@ARTICLE{Zhou:2003,
  author = {Zhou, R.},
  title = {Trp-cage: Folding free energy landscape in explicit water},
  journal = {Proc. Natl. Acad. Sci. USA},
  year = {2003},
  volume = {100},
  pages = {13280-13285},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Zhou:Berne:Germain:2001,
  author = {Zhou, R. and Berne, B. J. and Germain, R.},
  title = {Free energy landscape of a beta-hairpin folding in explicit water},
  journal = {Proc. Natl. Acad. Sci.},
  year = {2001},
  volume = {98},
  pages = {14931--14936},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Zhou:Berne:2002,
  author = {Zhou, R. and Berne, {B. J.}},
  title = {Can a continuum solvent model reproduce the free energy landscape
	of a beta-hairpin folding in water?},
  journal = {Proc. Natl. Acad. Sci.},
  year = {2002},
  volume = {99},
  pages = {12777--12782},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Zhou:Berne:97,
  author = {Zhou, R. and Berne, {B. J.}},
  title = {Smart walking: A new method for Boltzmann sampling of protein conformations},
  journal = {J. Chem. Phys.},
  year = {1997},
  volume = {107},
  pages = {9185--9196},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Zhou:Friesner:Levy:2001,
  author = {Zhou, R. and Friesner, R. A. and Ghosh, A. and Rizzo, R. C. and Jorgensen,
	W. L. and Levy, R. M.},
  title = {New Linear Interaction Method For Binding Affinity Calculations Using
	a Continuum Solvent Model},
  journal = {J. Phys. Chem.},
  year = {2001},
  volume = {105},
  pages = {10388-10397},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Zhou:Huang:Margulis:Berne:2004,
  author = {Zhou, R. and Huang, X. and Margulis, C. and Berne, {B. J.}},
  title = {Hydrophobic Collapse in Multi-domain Protein Folding},
  journal = {Science},
  year = {2004},
  volume = {305},
  pages = {1605--1609},
  owner = {emilio},
  timestamp = {2011.01.18}
}

@ARTICLE{Zhou2007,
  author = {Zhiyong Zhou and Anthony K Felts and Richard A Friesner and Ronald
	M Levy},
  title = {Comparative performance of several flexible docking programs and
	scoring functions: enrichment studies for a diverse set of pharmaceutically
	relevant targets.},
  journal = {J. Chem. Inf. Model.},
  year = {2007},
  volume = {47},
  pages = {1599--1608},
  number = {4},
  abstract = {Virtual screening by molecular docking has become a widely used approach
	to lead discovery in the pharmaceutical industry when a high-resolution
	structure of the biological target of interest is available. The
	performance of three widely used docking programs (Glide, GOLD, and
	DOCK) for virtual database screening is studied when they are applied
	to the same protein target and ligand set. Comparisons of the docking
	programs and scoring functions using a large and diverse data set
	of pharmaceutically interesting targets and active compounds are
	carried out. We focus on the problem of docking and scoring flexible
	compounds which are sterically capable of docking into a rigid conformation
	of the receptor. The Glide XP methodology is shown to consistently
	yield enrichments superior to the two alternative methods, while
	GOLD outperforms DOCK on average. The study also shows that docking
	into multiple receptor structures can decrease the docking error
	in screening a diverse set of active compounds.},
  doi = {10.1021/ci7000346},
  institution = {BioMaPS Institute for Quantitative Biology, Department of Chemistry
	and Chemical Biology, Rutgers, The State University of New Jersey,
	Piscataway, New Jersey 08854, USA.},
  keywords = {Crystallography; Ligands; Models, Molecular; Pharmaceutical Preparations;
	Proteins},
  owner = {emilio},
  pmid = {17585856},
  timestamp = {2010.04.21},
  url = {http://dx.doi.org/10.1021/ci7000346}
}

@ARTICLE{Zhu2011,
  author = {Zhu, Fangqiang and Hummer, Gerhard},
  title = {Convergence and error estimation in free energy calculations using
	the weighted histogram analysis method},
  journal = {J. Comput. Chem.},
  year = {2011},
  pages = {In press},
  abstract = {The weighted histogram analysis method (WHAM) has become the standard
	technique for the analysis of umbrella sampling simulations. In this
	article, we address the challenges (1) of obtaining fast and accurate
	solutions of the coupled nonlinear WHAM equations, (2) of quantifying
	the statistical errors of the resulting free energies, (3) of diagnosing
	possible systematic errors, and (4) of optimally allocating of the
	computational resources. Traditionally, the WHAM equations are solved
	by a fixed-point direct iteration method, despite poor convergence
	and possible numerical inaccuracies in the solutions. Here, we instead
	solve the mathematically equivalent problem of maximizing a target
	likelihood function, by using superlinear numerical optimization
	algorithms with a significantly faster convergence rate. To estimate
	the statistical errors in one-dimensional free energy profiles obtained
	from WHAM, we note that for densely spaced umbrella windows with
	harmonic biasing potentials, the WHAM free energy profile can be
	approximated by a coarse-grained free energy obtained by integrating
	the mean restraining forces. The statistical errors of the coarse-grained
	free energies can be estimated straightforwardly and then used for
	the WHAM results. A generalization to multidimensional WHAM is described.
	We also propose two simple statistical criteria to test the consistency
	between the histograms of adjacent umbrella windows, which help identify
	inadequate sampling and hysteresis in the degrees of freedom orthogonal
	to the reaction coordinate. Together, the estimates of the statistical
	errors and the diagnostics of inconsistencies in the potentials of
	mean force provide a basis for the efficient allocation of computational
	resources in free energy simulations. © 2011 Wiley Periodicals, Inc.
	J Comput Chem, 2011},
  issn = {1096-987X},
  keywords = {free energy, potential of mean force, weighted histogram analysis
	method, statistical error, systematic error, optimization algorithm,
	convergence rate, block average, molecular dynamics, Monte Carlo},
  owner = {emilio},
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  journal = {J. Phys. Chem. B},
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  volume = {109},
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  journal = {J. Chem. Theor. Comput.},
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  pages = {2108--2119},
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  timestamp = {2011.01.18}
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@ARTICLE{Zichi:Rossky:86,
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  volume = {84},
  pages = {2814-2822},
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@BOOK{Reddy:Erion:2001,
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@article{hansmann1999new,
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  volume={9},
  number={2},
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  author={Pogorelov, Taras V and Luthey-Schulten, Zaida},
  journal={Biophysical journal},
  volume={87},
  number={1},
  pages={207--214},
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  publisher={Elsevier}
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@ARTICLE{ssi-cise,
author={Crouch, S. and Hong, N.C. and Hettrick, S. and Jackson, M. and Pawlik, A. and Sufi, S. and Carr, L. and De Roure, D. and Goble, C. and Parsons, M.},
journal={Computing in Science Engineering},
title={The Software Sustainability Institute: Changing Research Software Attitudes and Practices},
year={2013},
month={Nov},
volume={15},
number={6},
pages={74-80},
keywords={research and development;software engineering;Software Sustainability Institute;research software attitudes;research software practices;Domain engineering;Programming;Scientific computing;Software development;Software engineering;Software reliability;Training;domain engineering;maintainability;reliability;scientific computing;software engineering},
doi={10.1109/MCSE.2013.133},
ISSN={1521-9615},}

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 URL = "\url{http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=06691695 [ieeexplore.ieee.org]}",
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@misc{DavidSalomon.2011,
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@Manual{rcoreteam,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2017},
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@Article{Schulze2012,
author="Schulze, Stefan K.
and Kanwar, Rahul
and G{\"o}lzenleuchter, Meike
and Therneau, Terry M.
and Beutler, Andreas S.",
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journal="BMC Genomics",
year="2012",
volume="13",
number="1",
pages="524",
issn="1471-2164",
doi="10.1186/1471-2164-13-524",
url="http://dx.doi.org/10.1186/1471-2164-13-524"
}

@Article{Gentleman2004,
author="Gentleman, Robert C.
and Carey, Vincent J.
and Bates, Douglas M.
and Bolstad, Ben
and Dettling, Marcel
and Dudoit, Sandrine
and Ellis, Byron
and Gautier, Laurent
and Ge, Yongchao
and Gentry, Jeff
and Hornik, Kurt
and Hothorn, Torsten
and Huber, Wolfgang
and Iacus, Stefano
and Irizarry, Rafael
and Leisch, Friedrich
and Li, Cheng
and Maechler, Martin
and Rossini, Anthony J.
and Sawitzki, Gunther
and Smith, Colin
and Smyth, Gordon
and Tierney, Luke
and Yang, Jean YH
and Zhang, Jianhua",
title="Bioconductor: open software development for computational biology and bioinformatics",
journal="Genome Biology",
year="2004",
volume="5",
number="10",
pages="R80",
issn="1474-760X",
doi="10.1186/gb-2004-5-10-r80",
url="http://dx.doi.org/10.1186/gb-2004-5-10-r80"
}

@Article{Anders2010,
author="Anders, Simon and Huber, Wolfgang",
title="Differential expression analysis for sequence count data",
journal="Genome Biology",
year="2010",
volume="11",
number="10",
pages="R106",
issn="1474-760X",
doi="10.1186/gb-2010-11-10-r106",
url="http://dx.doi.org/10.1186/gb-2010-11-10-r106"
}

@Article{Love2014,
author="Love, Michael I. and Huber, Wolfgang and Anders, Simon",
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year="2014",
volume="15",
number="12",
pages="550",
issn="1474-760X",
doi="10.1186/s13059-014-0550-8",
url="http://dx.doi.org/10.1186/s13059-014-0550-8"
}

@article{cook1977,
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@article{BH1995,
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}

@article{BY2001,
 ISSN = {00905364},
 URL = {http://www.jstor.org/stable/2674075},
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@article{robinson2010,
author = {Robinson, Mark and McCarthy, Davis and Smyth, Gordon},
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@article{dillies2013,
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eprint = {/oup/backfile/content_public/journal/bib/14/6/10.1093/bib/bbs046/2/bbs046.pdf}
}

@article{robinson2008,
author = {Robinson, Mark and Smyth, Gordon},
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year = {2008},
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eprint = {/oup/backfile/content_public/journal/biostatistics/9/2/10.1093/biostatistics/kxm030/2/kxm030.pdf}
}

@article{robinson2007,
author = {Robinson, Mark and Smyth, Gordon},
title = {Moderated statistical tests for assessing differences in tag abundance},
journal = {Bioinformatics},
volume = {23},
number = {21},
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year = {2007},
doi = {10.1093/bioinformatics/btm453},
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eprint = {/oup/backfile/content_public/journal/bioinformatics/23/21/10.1093_bioinformatics_btm453/2/btm453.pdf}
}

@article{wu2013,
author = {Wu, Hao and Wang, Chi and Wu, Zhijin},
title = {A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data},
journal = {Biostatistics},
volume = {14},
number = {2},
pages = {232},
year = {2013},
doi = {10.1093/biostatistics/kxs033},
URL = {http://dx.doi.org/10.1093/biostatistics/kxs033},
eprint = {/oup/backfile/content_public/journal/biostatistics/14/2/10.1093/biostatistics/kxs033/2/kxs033.pdf}
}

@article{mccarthy2012,
author = {McCarthy, Davis and Chen, Yunshun and Smyth, Gordon},
title = {Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation},
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volume = {40},
number = {10},
pages = {4288},
year = {2012},
doi = {10.1093/nar/gks042},
URL = {http://dx.doi.org/10.1093/nar/gks042},
eprint = {/oup/backfile/content_public/journal/nar/40/10/10.1093_nar_gks042/2/gks042.pdf}
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@book{Friedman:2008:EPL:1378240,
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 title = {Essentials of Programming Languages, 3rd Edition},
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@InProceedings{nPersonGames,
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    title = {An Algorithmic Solution of N-Person Games},
    year = {1986},
    month = {8},
    publisher = {AAAI Press},
    booktitle = {
        Proceedings of the Fifth AAAI National Conference on Artificial
        Intelligence, Lecture Notes in Computer Science
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    pages = {158-–162},
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    series = {AAAI'86},
    doi = {10.5555/2887770.2887795},
    volume = {2883},
    url = {https://www.aaai.org/Papers/AAAI/1986/AAAI86-025.pdf}
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@InProceedings{compMultiPlGames,
    author = {Sturtevant, Nathan},
    editor = {Schaeffer, Jonathan and Müller, Martin and Björnsson, Yngvi},
    title = {A Comparison of Algorithms for Multi-player Games},
    booktitle = {Computers and Games},
    year = {2003},
    publisher = {Springer Berlin Heidelberg},
    address = {Berlin, Heidelberg},
    pages = {108--122},
    isbn = {978-3-540-20545-6},
    doi = {10.1007/978-3-540-40031-8\_8}
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