Rescoring docking hit lists for model cavity sites: predictions and experimental testing.
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[1] S. Colowick,et al. Methods in Enzymology , Vol , 1966 .
[2] J. Gasteiger,et al. ITERATIVE PARTIAL EQUALIZATION OF ORBITAL ELECTRONEGATIVITY – A RAPID ACCESS TO ATOMIC CHARGES , 1980 .
[3] P. Kollman,et al. A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char , 1993 .
[4] M. M. Fitzgerald,et al. Small molecule binding to an artificially created cavity at the active site of cytochrome c peroxidase. , 1994, Biochemistry.
[5] Collaborative Computational,et al. The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.
[6] B. Matthews,et al. Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity. , 1995, Biochemistry.
[7] B. Matthews,et al. Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme. , 1995, Biochemistry.
[8] Donald G. Truhlar,et al. MODEL FOR AQUEOUS SOLVATION BASED ON CLASS IV ATOMIC CHARGES AND FIRST SOLVATION SHELL EFFECTS , 1996 .
[9] Z. Otwinowski,et al. Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.
[10] T. Satoh,et al. A computer screening approach to immunoglobulin superfamily structures and interactions: discovery of small non-peptidic CD4 inhibitors as novel immunotherapeutics. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[11] Donald G. Truhlar,et al. New Class IV Charge Model for Extracting Accurate Partial Charges from Wave Functions , 1998 .
[12] B. Shoichet,et al. Flexible ligand docking using conformational ensembles , 1998, Protein science : a publication of the Protein Society.
[13] Jörg Weiser,et al. Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO) , 1999, J. Comput. Chem..
[14] 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.
[15] D. Rognan,et al. Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. , 2000, Journal of medicinal chemistry.
[16] Araz Jakalian,et al. Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: I. Method , 2000 .
[17] Shaomeng Wang,et al. How Does Consensus Scoring Work for Virtual Library Screening? An Idealized Computer Experiment , 2001, J. Chem. Inf. Comput. Sci..
[18] Thomas Lengauer,et al. FlexE: efficient molecular docking considering protein structure variations. , 2001, Journal of molecular biology.
[19] G. Klebe,et al. Statistical potentials and scoring functions applied to protein-ligand binding. , 2001, Current opinion in structural biology.
[20] M Rarey,et al. Detailed analysis of scoring functions for virtual screening. , 2001, Journal of medicinal chemistry.
[21] R. Friesner,et al. Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides† , 2001 .
[22] Ronald M. Levy,et al. The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators , 2002, J. Comput. Chem..
[23] Christopher I. Bayly,et al. Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validation , 2002, J. Comput. Chem..
[24] W. Delano. The PyMOL Molecular Graphics System , 2002 .
[25] George A. Kaminski,et al. Force Field Validation Using Protein Side Chain Prediction , 2002 .
[26] G. Whitesides,et al. Combinatorial computational method gives new picomolar ligands for a known enzyme , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[27] Brian K Shoichet,et al. Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase. , 2002, Structure.
[28] Brian K. Shoichet,et al. Structure-Based Discovery of a Novel, Noncovalent Inhibitor of AmpC β-Lactamase , 2002 .
[29] D. Goodin,et al. Artificial protein cavities as specific ligand-binding templates: characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein. , 2002, Journal of molecular biology.
[30] B. Matthews,et al. A model binding site for testing scoring functions in molecular docking. , 2002, Journal of molecular biology.
[31] David S. Goodsell,et al. Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling , 2003, J. Comput. Aided Mol. Des..
[32] Stefan Boresch,et al. Absolute Binding Free Energies: A Quantitative Approach for Their Calculation , 2003 .
[33] D. Case,et al. Exploring protein native states and large‐scale conformational changes with a modified generalized born model , 2004, Proteins.
[34] Brian K Shoichet,et al. Testing a flexible-receptor docking algorithm in a model binding site. , 2004, Journal of molecular biology.
[35] B. Honig,et al. A hierarchical approach to all‐atom protein loop prediction , 2004, Proteins.
[36] J. Wendoloski,et al. Identification of compounds with nanomolar binding affinity for checkpoint kinase-1 using knowledge-based virtual screening. , 2004, Journal of medicinal chemistry.
[37] Junmei Wang,et al. Development and testing of a general amber force field , 2004, J. Comput. Chem..
[38] Kevin Cowtan,et al. research papers Acta Crystallographica Section D Biological , 2005 .
[39] M. Gilson,et al. Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm. , 2004, Journal of the American Chemical Society.
[40] G. Klebe,et al. Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model. , 2004, Journal of medicinal chemistry.
[41] Alexander D. MacKerell,et al. Identification of non-phosphate-containing small molecular weight inhibitors of the tyrosine kinase p56 Lck SH2 domain via in silico screening against the pY + 3 binding site. , 2004, Journal of medicinal chemistry.
[42] A. W. Schüttelkopf,et al. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. , 2004, Acta crystallographica. Section D, Biological crystallography.
[43] Brian K. Shoichet,et al. ZINC - A Free Database of Commercially Available Compounds for Virtual Screening , 2005, J. Chem. Inf. Model..
[44] I. Kuntz,et al. Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA. , 2005, Journal of medicinal chemistry.
[45] Marta Bueno,et al. Design of Ligand Binding to an Engineered Protein Cavity Using Virtual Screening and Thermal Up-shift Evaluation , 2005, J. Comput. Aided Mol. Des..
[46] Renxiao Wang,et al. A low-molecular-weight compound discovered through virtual database screening inhibits Stat3 function in breast cancer cells. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[47] B. Shoichet,et al. Decoys for docking. , 2005, Journal of medicinal chemistry.
[48] Richard A. Friesner,et al. Integrated Modeling Program, Applied Chemical Theory (IMPACT) , 2005, J. Comput. Chem..
[49] M. Jacobson,et al. Virtual screening against highly charged active sites: identifying substrates of alpha-beta barrel enzymes. , 2005, Biochemistry.
[50] Nadine H. Elowe,et al. Experimental Screening of Dihydrofolate Reductase Yields a “Test Set” of 50,000 Small Molecules for a Computational Data-Mining and Docking Competition , 2005, Journal of biomolecular screening.
[51] Brian K Shoichet,et al. Prediction of protein-ligand interactions. Docking and scoring: successes and gaps. , 2006, Journal of medicinal chemistry.
[52] P. Kollman,et al. Automatic atom type and bond type perception in molecular mechanical calculations. , 2006, Journal of molecular graphics & modelling.
[53] 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..
[54] 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.
[55] E. Perola. Minimizing false positives in kinase virtual screens , 2006, Proteins.
[56] Benoît Roux,et al. Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant. , 2006, Journal of chemical theory and computation.
[57] 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.
[58] Claudio N Cavasotto,et al. In silico identification of novel EGFR inhibitors with antiproliferative activity against cancer cells. , 2006, Bioorganic & medicinal chemistry letters.
[59] B. Shoichet,et al. Probing molecular docking in a charged model binding site. , 2006, Journal of molecular biology.
[60] K. Dill,et al. Predicting absolute ligand binding free energies to a simple model site. , 2007, Journal of molecular biology.
[61] Kai Zhu,et al. Multiscale Optimization of a Truncated Newton Minimization Algorithm and Application to Proteins and Protein-Ligand Complexes. , 2007, Journal of chemical theory and computation.
[62] Heidi J. Imker,et al. Prediction and assignment of function for a divergent N-succinyl amino acid racemase. , 2007, Nature chemical biology.
[63] David L Mobley,et al. The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change. , 2007, Journal of chemical theory and computation.
[64] Yaxiong Sun,et al. Improving Docking Accuracy through Molecular Mechanics Generalized Born Optimization and Scoring. , 2007, Journal of chemical theory and computation.