The consequences of scoring docked ligand conformations using free energy correlations.

[1]  F A Quiocho,et al.  Rates of ligand binding to periplasmic proteins involved in bacterial transport and chemotaxis. , 1983, The Journal of biological chemistry.

[2]  Florante A. Quiocho,et al.  Novel stereospecificity of the L-arabinose-binding protein , 1984, Nature.

[3]  J. Stürzebecher,et al.  Inhibition of bovine and human thrombins by derivatives of benzamidine. , 1984, Thrombosis research.

[4]  P. Goodford A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. , 1985, Journal of medicinal chemistry.

[5]  M G Rossmann,et al.  Structural analysis of a series of antiviral agents complexed with human rhinovirus 14. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[6]  M. N. Vyas,et al.  Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein. , 1988, Science.

[7]  A. Edmundson,et al.  Differences in crystal properties and ligand affinities of an antifluorescyl fab (4‐4‐20) in two solvent systems , 1988, Proteins.

[8]  M G Rossmann,et al.  Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses , 1990, Proteins.

[9]  D. Goodsell,et al.  Automated docking of substrates to proteins by simulated annealing , 1990, Proteins.

[10]  P. Taylor,et al.  Role of the peripheral anionic site on acetylcholinesterase: inhibition by substrates and coumarin derivatives. , 1991, Molecular pharmacology.

[11]  F A Quiocho,et al.  Sugar-binding and crystallographic studies of an arabinose-binding protein mutant (Met108Leu) that exhibits enhanced affinity and altered specificity. , 1991, Biochemistry.

[12]  S E Ealick,et al.  Application of crystallographic and modeling methods in the design of purine nucleoside phosphorylase inhibitors. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[13]  D. Turk,et al.  Geometry of binding of the N alpha-tosylated piperidides of m-amidino-, p-amidino- and p-guanidino phenylalanine to thrombin and trypsin. X-ray crystal structures of their trypsin complexes and modeling of their thrombin complexes. , 1991, FEBS letters.

[14]  J. Saurat,et al.  Expression of CRABP-I and -II in human epidermal cells. Alteration of relative protein amounts is linked to the state of differentiation. , 1992, The Biochemical journal.

[15]  H Brandstetter,et al.  Refined 2.3 A X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP and MQPA. A starting point for improving antithrombotics. , 1992, Journal of molecular biology.

[16]  Z. Xu,et al.  The adipocyte lipid-binding protein at 1.6-A resolution. Crystal structures of the apoprotein and with bound saturated and unsaturated fatty acids. , 1994, The Journal of biological chemistry.

[17]  Ruben Abagyan,et al.  ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation , 1994, J. Comput. Chem..

[18]  L. Banaszak,et al.  X-ray crystallographic structures of adipocyte lipid-binding protein complexed with palmitate and hexadecanesulfonic acid. Properties of cavity binding sites. , 1994, Biochemistry.

[19]  A. Edmundson,et al.  Local and transmitted conformational changes on complexation of an anti-sweetener Fab. , 1994, Journal of molecular biology.

[20]  A. Kleinfeld,et al.  Equilibrium constants for the binding of fatty acids with fatty acid-binding proteins from adipocyte, intestine, heart, and liver measured with the fluorescent probe ADIFAB. , 1994, The Journal of biological chemistry.

[21]  Hans-Joachim Böhm,et al.  The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure , 1994, J. Comput. Aided Mol. Des..

[22]  T. A. Jones,et al.  Crystal structures of cellular retinoic acid binding proteins I and II in complex with all-trans-retinoic acid and a synthetic retinoid. , 1995, Structure.

[23]  R. Glen,et al.  Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. , 1995, Journal of molecular biology.

[24]  T. Lybrand Ligand-protein docking and rational drug design. , 1995, Current Opinion in Structural Biology.

[25]  K. D. Hardman,et al.  1.85 A structure of anti-fluorescein 4-4-20 Fab. , 1995, Protein engineering.

[26]  Z. Derewenda,et al.  The occurrence of C-H...O hydrogen bonds in proteins. , 1995, Journal of molecular biology.

[27]  David S. Goodsell,et al.  Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4 , 1996, J. Comput. Aided Mol. Des..

[28]  Thomas Lengauer,et al.  A fast flexible docking method using an incremental construction algorithm. , 1996, Journal of molecular biology.

[29]  R. W. Harper,et al.  Dibasic benzo[b]thiophene derivatives as a novel class of active site-directed thrombin inhibitors. 1. Determination of the serine protease selectivity, structure-activity relationships, and binding orientation. , 1997, Journal of medicinal chemistry.

[30]  P Willett,et al.  Development and validation of a genetic algorithm for flexible docking. , 1997, Journal of molecular biology.

[31]  Colin McMartin,et al.  QXP: Powerful, rapid computer algorithms for structure-based drug design , 1997, J. Comput. Aided Mol. Des..

[32]  Irwin D. Kuntz,et al.  Automated flexible ligand docking method and its application for database search , 1997 .

[33]  David S. Goodsell,et al.  Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998 .

[34]  M Stahl,et al.  Development of filter functions for protein-ligand docking. , 1998, Journal of molecular graphics & modelling.

[35]  J L Sussman,et al.  Static Laue diffraction studies on acetylcholinesterase. , 1998, Acta crystallographica. Section D, Biological crystallography.

[36]  Mark A. Murcko,et al.  Virtual screening : an overview , 1998 .

[37]  David A. Agard,et al.  The Structural Basis of Estrogen Receptor/Coactivator Recognition and the Antagonism of This Interaction by Tamoxifen , 1998, Cell.

[38]  Thomas Lengauer,et al.  Evaluation of the FLEXX incremental construction algorithm for protein–ligand docking , 1999, Proteins.

[39]  I. Kuntz,et al.  Flexible ligand docking: A multistep strategy approach , 1999, Proteins.

[40]  M. Murcko,et al.  Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. , 1999, Journal of medicinal chemistry.

[41]  T Lengauer,et al.  Two-stage method for protein-ligand docking. , 1999, Journal of medicinal chemistry.

[42]  D. Rognan,et al.  Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. , 2000, Journal of medicinal chemistry.

[43]  Glen E. Kellogg,et al.  Hydrophobicity: is LogPo/w more than the sum of its parts? , 2000 .

[44]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[45]  Rubicelia Vargas,et al.  How Strong Is the Cα−H···OC Hydrogen Bond? , 2000 .

[46]  C. Sargent,et al.  Immunosuppressive and anti-inflammatory effects of cyclic AMP phosphodiesterase (PDE) type 4 inhibitors. , 2000, Immunopharmacology.

[47]  Ingo Muegge,et al.  Evaluation of docking/scoring approaches: A comparative study based on MMP3 inhibitors , 2000, J. Comput. Aided Mol. Des..

[48]  G E Kellogg,et al.  Computational methodology for estimating changes in free energies of biomolecular association upon mutation. The importance of bound water in dimer-tetramer assembly for beta 37 mutant hemoglobins. , 2000, Biochemistry.

[49]  M. Zhang,et al.  The crystal structures of human α‐thrombin complexed with active site‐directed diamino benzo[b] thiophene derivatives: A binding mode for a structurally novel class of inhibitors , 2008, Protein science : a publication of the Protein Society.

[50]  G. Klebe,et al.  Knowledge-based scoring function to predict protein-ligand interactions. , 2000, Journal of molecular biology.

[51]  A. Ortiz,et al.  Evaluation of docking functions for protein-ligand docking. , 2001, Journal of medicinal chemistry.

[52]  F. Jørgensen,et al.  A new concept for multidimensional selection of ligand conformations (MultiSelect) and multidimensional scoring (MultiScore) of protein-ligand binding affinities. , 2001, Journal of medicinal chemistry.

[53]  M Rarey,et al.  Detailed analysis of scoring functions for virtual screening. , 2001, Journal of medicinal chemistry.

[54]  G E Kellogg,et al.  Computationally accessible method for estimating free energy changes resulting from site‐specific mutations of biomolecules: Systematic model building and structural/hydropathic analysis of deoxy and oxy hemoglobins , 2001, Proteins.

[55]  Anna Marabotti,et al.  Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 1. Models without explicit constrained water. , 2002, Journal of medicinal chemistry.

[56]  Luhua Lai,et al.  Further development and validation of empirical scoring functions for structure-based binding affinity prediction , 2002, J. Comput. Aided Mol. Des..

[57]  R. Clark,et al.  Consensus scoring for ligand/protein interactions. , 2002, Journal of molecular graphics & modelling.

[58]  Hwa-Young Kim,et al.  Three-dimensional structures of PDE4D in complex with roliprams and implication on inhibitor selectivity. , 2003, Structure.

[59]  Wladek Minor,et al.  Measurement errors and their consequences in protein crystallography. , 2003, Acta crystallographica. Section D, Biological crystallography.

[60]  Martin Stahl,et al.  Binding site characteristics in structure-based virtual screening: evaluation of current docking tools , 2003, Journal of molecular modeling.

[61]  Renxiao Wang,et al.  Comparative evaluation of 11 scoring functions for molecular docking. , 2003, Journal of medicinal chemistry.

[62]  Richard D. Taylor,et al.  Improved protein–ligand docking using GOLD , 2003, Proteins.

[63]  Pietro Cozzini,et al.  Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 2. Computational titration and pH effects in molecular models of neuraminidase-inhibitor complexes. , 2003, Journal of medicinal chemistry.

[64]  Ruben Abagyan,et al.  Comparative study of several algorithms for flexible ligand docking , 2003, J. Comput. Aided Mol. Des..

[65]  Gerard J Kleywegt,et al.  Application and limitations of X-ray crystallographic data in structure-based ligand and drug design. , 2003, Angewandte Chemie.

[66]  M. Mor,et al.  Synthesis, pharmacological evaluation, and structure-activity relationships of benzopyran derivatives with potent SERM activity. , 2004, Bioorganic & medicinal chemistry.

[67]  Pietro Cozzini,et al.  Simple, intuitive calculations of free energy of binding for protein-ligand complexes. 3. The free energy contribution of structural water molecules in HIV-1 protease complexes. , 2004, Journal of medicinal chemistry.

[68]  Li Xing,et al.  Evaluation and application of multiple scoring functions for a virtual screening experiment , 2004, J. Comput. Aided Mol. Des..

[69]  Maria Kontoyianni,et al.  Evaluation of docking performance: comparative data on docking algorithms. , 2004, Journal of medicinal chemistry.

[70]  D. J. Price,et al.  Assessing scoring functions for protein-ligand interactions. , 2004, Journal of medicinal chemistry.

[71]  Anna Marabotti,et al.  Free energy of ligand binding to protein: evaluation of the contribution of water molecules by computational methods. , 2004, Current medicinal chemistry.

[72]  Anna Vulpetti,et al.  Assessment of Docking Poses: Interactions-Based Accuracy Classification (IBAC) versus Crystal Structure Deviations , 2004, J. Chem. Inf. Model..

[73]  W. Patrick Walters,et al.  Filtering databases and chemical libraries , 2004, Molecular Diversity.

[74]  W Patrick Walters,et al.  A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance , 2004, Proteins.

[75]  M. Tota,et al.  Crystal structure of human phosphodiesterase 3B: atomic basis for substrate and inhibitor specificity. , 2004, Biochemistry.

[76]  Shaomeng Wang,et al.  An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein-Ligand Complexes , 2004, J. Chem. Inf. Model..

[77]  Matthew P. Repasky,et al.  Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. , 2004, Journal of medicinal chemistry.

[78]  Didier Rognan,et al.  Comparative evaluation of eight docking tools for docking and virtual screening accuracy , 2004, Proteins.

[79]  Kam Y. J. Zhang,et al.  A family of phosphodiesterase inhibitors discovered by cocrystallography and scaffold-based drug design , 2005, Nature Biotechnology.

[80]  Robin Taylor,et al.  Comparing protein–ligand docking programs is difficult , 2005, Proteins.

[81]  M. Fornabaio,et al.  Paramyxovirus Receptor-Binding Molecules: Engagement of One Site on the Hemagglutinin-Neuraminidase Protein Modulates Activity at the Second Site , 2006, Journal of Virology.

[82]  Pietro Cozzini,et al.  Mapping the energetics of water-protein and water-ligand interactions with the "natural" HINT forcefield: predictive tools for characterizing the roles of water in biomolecules. , 2006, Journal of molecular biology.

[83]  Jin Li,et al.  On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors , 2006, J. Chem. Inf. Model..

[84]  C. E. Peishoff,et al.  A critical assessment of docking programs and scoring functions. , 2006, Journal of medicinal chemistry.