Computational sampling of a cryptic drug binding site in a protein receptor: explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase.
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[1] R. Engh,et al. Structural aspects of protein kinase control-role of conformational flexibility. , 2002, Pharmacology & therapeutics.
[2] J Moult,et al. Analysis of the steric strain in the polypeptide backbone of protein molecules , 1991, Proteins.
[3] Valerie Daggett,et al. Molecular dynamics simulations of the protein unfolding/folding reaction. , 2002, Accounts of chemical research.
[4] Luping Liu,et al. Design and synthesis of potent, orally bioavailable dihydroquinazolinone inhibitors of p38 MAP kinase. , 2003, Bioorganic & medicinal chemistry letters.
[5] S. Nosé. A unified formulation of the constant temperature molecular dynamics methods , 1984 .
[6] J. Mongan,et al. Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. , 2004, The Journal of chemical physics.
[7] K. Tai. Conformational sampling for the impatient. , 2004, Biophysical chemistry.
[8] E. Goldsmith,et al. The structure of mitogen-activated protein kinase p38 at 2.1-A resolution. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[9] Viktor Hornak,et al. Development of softcore potential functions for overcoming steric barriers in molecular dynamics simulations. , 2004, Journal of molecular graphics & modelling.
[10] Malin M. Young,et al. Predicting conformational switches in proteins , 1999, Protein science : a publication of the Protein Society.
[11] I. Luque,et al. Structural stability of binding sites: Consequences for binding affinity and allosteric effects , 2000, Proteins.
[12] S. Teague. Implications of protein flexibility for drug discovery , 2003, Nature Reviews Drug Discovery.
[13] D. Jacobs,et al. Protein flexibility predictions using graph theory , 2001, Proteins.
[14] Martin Zacharias,et al. Rapid protein–ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: Binding of FK506 to FKBP , 2004, Proteins.
[15] V. Daggett. Molecular dynamics simulations of the protein unfolding/folding reaction. , 2002, Accounts of chemical research.
[16] L. Wodicka,et al. A small molecule–kinase interaction map for clinical kinase inhibitors , 2005, Nature Biotechnology.
[17] H. Berendsen,et al. Interaction Models for Water in Relation to Protein Hydration , 1981 .
[18] J. Boehm,et al. p38 MAP kinases: key signalling molecules as therapeutic targets for inflammatory diseases , 2003, Nature Reviews Drug Discovery.
[19] P. Kollman,et al. Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models , 1992 .
[20] J. Warmus,et al. Structures of human MAP kinase kinase 1 (MEK1) and MEK2 describe novel noncompetitive kinase inhibition , 2004, Nature Structural &Molecular Biology.
[21] E. Goldsmith,et al. Structural basis of inhibitor selectivity in MAP kinases. , 1998, Structure.
[22] D. van der Spoel,et al. GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .
[23] Janet M Thornton,et al. Ligand selectivity and competition between enzymes in silico , 2004, Nature Biotechnology.
[24] Natasja Brooijmans,et al. Molecular recognition and docking algorithms. , 2003, Annual review of biophysics and biomolecular structure.
[25] J. Wells,et al. Searching for new allosteric sites in enzymes. , 2004, Current opinion in structural biology.
[26] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[27] Haruki Nakamura,et al. A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor , 2004, J. Comput. Chem..
[28] Gang Liu,et al. Discovery of a potent, selective protein tyrosine phosphatase 1B inhibitor using a linked-fragment strategy. , 2003, Journal of the American Chemical Society.
[29] William J. Welsh,et al. Identification of a Minimal Subset of Receptor Conformations for Improved Multiple Conformation Docking and Two-Step Scoring. , 2004 .
[30] R A Sayle,et al. RASMOL: biomolecular graphics for all. , 1995, Trends in biochemical sciences.
[31] J. Thornton,et al. Searching for functional sites in protein structures. , 2004, Current opinion in chemical biology.
[32] David S. Goodsell,et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998, J. Comput. Chem..
[33] J. Thornton,et al. A revised set of potentials for beta-turn formation in proteins. , 1994, Protein science : a publication of the Protein Society.
[34] D. Sept,et al. Localization of the antimitotic peptide and depsipeptide binding site on beta-tubulin. , 2004, Biochemistry.
[35] Yuan-Ping Pang,et al. Prediction of the binding site of 1-benzyl-4-[(5,6-dimethoxy-1-indanon-2-yl)methyl]piperidine in acetylcholinesterase by docking studies with the SYSDOC program , 1994, J. Comput. Aided Mol. Des..
[36] L. Johnson,et al. Protein Kinase Inhibitors: Insights into Drug Design from Structure , 2004, Science.
[37] Michelle Browner,et al. Design and synthesis of 4-azaindoles as inhibitors of p38 MAP kinase. , 2003, Journal of medicinal chemistry.
[38] James R Horn,et al. Allosteric inhibition through core disruption. , 2004, Journal of molecular biology.
[39] L. Tong,et al. Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site , 2002, Nature Structural Biology.
[40] Viktor Hornak,et al. Improved conformational sampling through an efficient combination of mean-field simulation approaches , 2004 .
[41] S. J. Campbell,et al. Ligand binding: functional site location, similarity and docking. , 2003, Current opinion in structural biology.
[42] W. L. Jorgensen,et al. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .
[43] Hoover,et al. Canonical dynamics: Equilibrium phase-space distributions. , 1985, Physical review. A, General physics.
[44] G Vriend,et al. WHAT IF: a molecular modeling and drug design program. , 1990, Journal of molecular graphics.
[45] Berk Hess,et al. LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..
[46] W Patrick Walters,et al. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance , 2004, Proteins.
[47] Alexander D. MacKerell,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.
[48] Gerhard Klebe,et al. Probing flexibility and “induced‐fit” phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations , 2004, Proteins.
[49] E. Jaeger,et al. Docking: successes and challenges. , 2005, Current pharmaceutical design.
[50] J. Kuriyan,et al. The Conformational Plasticity of Protein Kinases , 2002, Cell.
[51] A. Elcock. Prediction of functionally important residues based solely on the computed energetics of protein structure. , 2001, Journal of molecular biology.
[52] Yuan-Ping Pang,et al. Prediction of the binding sites of huperzine A in acetylcholinesterase by docking studies , 1994, J. Comput. Aided Mol. Des..
[53] 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 .
[54] J. Thornton,et al. Conformational changes observed in enzyme crystal structures upon substrate binding. , 2005, Journal of molecular biology.
[55] F. Bushman,et al. Developing a dynamic pharmacophore model for HIV-1 integrase. , 2000, Journal of medicinal chemistry.
[56] Ruben Abagyan,et al. Comparative study of several algorithms for flexible ligand docking , 2003, J. Comput. Aided Mol. Des..
[57] Dino Moras,et al. Structural adaptability in the ligand-binding pocket of the ecdysone hormone receptor , 2003, Nature.
[58] Berk Hess,et al. GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .
[59] A. W. Schüttelkopf,et al. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. , 2004, Acta crystallographica. Section D, Biological crystallography.
[60] 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.
[61] C. Pargellis,et al. The kinetics of binding to p38MAP kinase by analogues of BIRB 796. , 2003, Bioorganic & medicinal chemistry letters.