Small Molecule Docking

[1]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[2]  C. Rommel,et al.  Furan-2-ylmethylene thiazolidinediones as novel, potent, and selective inhibitors of phosphoinositide 3-kinase gamma. , 2006, Journal of medicinal chemistry.

[3]  Julian Tirado-Rives,et al.  Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding. , 2006, Journal of medicinal chemistry.

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

[5]  Niu Huang,et al.  Physics-Based Scoring of Protein-Ligand Complexes: Enrichment of Known Inhibitors in Large-Scale Virtual Screening , 2006, J. Chem. Inf. Model..

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

[7]  Thomas Lengauer,et al.  FlexE: efficient molecular docking considering protein structure variations. , 2001, Journal of molecular biology.

[8]  Michael G. Lerner,et al.  Binding MOAD (Mother Of All Databases) , 2005, Proteins.

[9]  H. Carlson.  Protein flexibility and drug design: how to hit a moving target. , 2002, Current opinion in chemical biology.

[10]  Robert Abel,et al.  Motifs for molecular recognition exploiting hydrophobic enclosure in protein–ligand binding , 2007, Proceedings of the National Academy of Sciences.

[11]  R Abagyan,et al.  Flexible protein–ligand docking by global energy optimization in internal coordinates , 1997, Proteins.

[12]  D A Agard,et al.  Binding mode prediction for a flexible ligand in a flexible pocket using multi-conformation simulated annealing pseudo crystallographic refinement. , 2001, Journal of molecular biology.

[13]  Aniko Simon,et al.  eHiTS: a new fast, exhaustive flexible ligand docking system. , 2007, Journal of molecular graphics & modelling.

[14]  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.

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

[16]  György M. Keserü,et al.  Ensemble Docking into Flexible Active Sites. Critical Evaluation of FlexE against JNK-3 and beta-Secretase , 2006, J. Chem. Inf. Model..

[17]  Ajay N. Jain.  Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search , 2007, J. Comput. Aided Mol. Des..

[18]  Matthew P. Repasky,et al.  Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. , 2006, Journal of medicinal chemistry.

[19]  J Andrew McCammon,et al.  Studying the roles of W86, E202, and Y337 in binding of acetylcholine to acetylcholinesterase using a combined molecular dynamics and multiple docking approach , 2003, Protein science : a publication of the Protein Society.

[20]  J M Blaney,et al.  A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.

[21]  J Andrew McCammon,et al.  Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach. , 2002, Journal of the American Chemical Society.

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

[23]  J. Bajorath,et al.  Docking and scoring in virtual screening for drug discovery: methods and applications , 2004, Nature Reviews Drug Discovery.

[24]  D. Goodsell,et al.  Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock , 2002, Proteins.

[25]  Paul D Lyne,et al.  Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring. , 2006, Journal of medicinal chemistry.

[26]  Ajay N. Jain.  Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. , 2003, Journal of medicinal chemistry.

[27]  Woody Sherman,et al.  Use of an Induced Fit Receptor Structure in Virtual Screening , 2006, Chemical biology & drug design.

[28]  Stephen Hanessian,et al.  A method for induced-fit docking, scoring, and ranking of flexible ligands. Application to peptidic and pseudopeptidic beta-secretase (BACE 1) inhibitors. , 2006, Journal of medicinal chemistry.

[29]  H. Broughton,et al.  A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening. , 2000, Journal of molecular graphics & modelling.

[30]  A. Ghose,et al.  1,2,3-Thiadiazole substituted pyrazolones as potent KDR/VEGFR-2 kinase inhibitors. , 2007, Bioorganic & medicinal chemistry letters.

[31]  G. V. Paolini,et al.  Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes , 1997, J. Comput. Aided Mol. Des..

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

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

[34]  B. Shoichet,et al.  Soft docking and multiple receptor conformations in virtual screening. , 2004, Journal of medicinal chemistry.

[35]  J. Aqvist,et al.  A new method for predicting binding affinity in computer-aided drug design. , 1994, Protein engineering.

[36]  G. Klebe.  Virtual ligand screening: strategies, perspectives and limitations , 2006, Drug Discovery Today.

[37]  W. Guida,et al.  Selective chemical probe inhibitor of Stat3, identified through structure-based virtual screening, induces antitumor activity , 2007, Proceedings of the National Academy of Sciences.

[38]  Hege S. Beard,et al.  Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. , 2004, Journal of medicinal chemistry.

[39]  Thomas M Frimurer,et al.  Ligand-induced conformational changes: improved predictions of ligand binding conformations and affinities. , 2003, Biophysical journal.

[40]  Robin Taylor,et al.  A new test set for validating predictions of protein–ligand interaction , 2002, Proteins.

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

[42]  J A McCammon,et al.  Accommodating protein flexibility in computational drug design. , 2000, Molecular pharmacology.

[43]  Victor Guallar,et al.  Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical (QM/MM) approach , 2005, J. Comput. Chem..

[44]  G. Hummer,et al.  Water conduction through the hydrophobic channel of a carbon nanotube , 2001, Nature.

[45]  C. Venkatachalam,et al.  LigScore: a novel scoring function for predicting binding affinities. , 2005, Journal of molecular graphics & modelling.

[46]  Victor A Kenyon,et al.  Novel human lipoxygenase inhibitors discovered using virtual screening with homology models. , 2006, Journal of medicinal chemistry.

[47]  S. Kim,et al.  "Soft docking": matching of molecular surface cubes. , 1991, Journal of molecular biology.

[48]  B. Kuhn,et al.  Validation and use of the MM-PBSA approach for drug discovery. , 2005, Journal of medicinal chemistry.

[49]  B. Berne,et al.  Drying and hydrophobic collapse of paraffin plates. , 2005, The journal of physical chemistry. B.

[50]  B. Berne,et al.  Effect of ions on the hydrophobic interaction between two plates. , 2007, Journal of the American Chemical Society.

[51]  J. Andrew McCammon,et al.  The structure of liquid water at an extended hydrophobic surface , 1984 .

[52]  I. Kuntz,et al.  Molecular docking to ensembles of protein structures. , 1997, Journal of molecular biology.

[53]  Hans-Joachim Böhm,et al.  Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs , 1998, J. Comput. Aided Mol. Des..

[54]  X. Zou,et al.  Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking , 2006, Proteins.

[55]  Todd J. A. Ewing,et al.  DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases , 2001, J. Comput. Aided Mol. Des..

[56]  R. Friesner,et al.  Novel procedure for modeling ligand/receptor induced fit effects. , 2006, Journal of medicinal chemistry.

[57]  P. Kollman,et al.  Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. , 2000, Journal of medicinal chemistry.

[58]  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..

[59]  Alpeshkumar K. Malde,et al.  Comparative residue interaction analysis (CoRIA): a 3D-QSAR approach to explore the binding contributions of active site residues with ligands , 2006, J. Comput. Aided Mol. Des..

[60]  Claudio N. Cavasotto,et al.  Protein flexibility in ligand docking and virtual screening to protein kinases. , 2004, Journal of molecular biology.

[61]  Gennady M Verkhivker,et al.  Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming. , 1995, Chemistry & biology.

[62]  Richard A. Friesner,et al.  Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets , 2007, J. Chem. Inf. Model..

[63]  Christopher I. Bayly,et al.  Evaluating Virtual Screening Methods: Good and Bad Metrics for the "Early Recognition" Problem , 2007, J. Chem. Inf. Model..

[64]  R M Stroud,et al.  Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking. , 2001, Chemistry & biology.

[65]  J. Irwin,et al.  Benchmarking sets for molecular docking. , 2006, Journal of medicinal chemistry.

[66]  C. Venkatachalam,et al.  LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. , 2003, Journal of molecular graphics & modelling.