Modified AutoDock for accurate docking of protein kinase inhibitors
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[1] Kevan M. Shokat,et al. Chemical genetic analysis of the budding-yeast p21-activated kinase Cla4p , 2000, Nature Cell Biology.
[2] Yi Liu,et al. Generation of Monospecific Nanomolar Tyrosine Kinase Inhibitors via a Chemical Genetic Approach , 1999 .
[3] S Vajda,et al. Continuum electrostatic analysis of preferred solvation sites around proteins in solution , 2000, Proteins.
[4] M R Lee,et al. Use of MM‐PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece , 2000, Proteins.
[5] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[6] Robert M. Sweet,et al. Structure of an Enzyme Required for Aminoglycoside Antibiotic Resistance Reveals Homology to Eukaryotic Protein Kinases , 1997, Cell.
[7] Norman L. Allinger,et al. Molecular mechanics. The MM3 force field for hydrocarbons. 1 , 1989 .
[8] Peter A. Kollman,et al. FREE ENERGY CALCULATIONS : APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA , 1993 .
[9] R. Glen,et al. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. , 1995, Journal of molecular biology.
[10] Anthony C. Bishop,et al. Unnatural ligands for engineered proteins: new tools for chemical genetics. , 2000, Annual review of biophysics and biomolecular structure.
[11] I. Kuntz,et al. Docking flexible ligands to macromolecular receptors by molecular shape. , 1986, Journal of medicinal chemistry.
[12] R. Huber,et al. Substrate specificity determinants of human macrophage elastase (MMP-12) based on the 1.1 A crystal structure. , 2001, Journal of molecular biology.
[13] J M Blaney,et al. A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.
[14] J. Gao,et al. A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations. , 1992, Science.
[15] D. Case,et al. Generalized born models of macromolecular solvation effects. , 2000, Annual review of physical chemistry.
[16] Garland R. Marshall,et al. Van der Waals volume fragmental constants , 1985 .
[17] Anton J. Hopfinger,et al. Prediction of Ligand-Receptor Binding Thermodynamics by Free Energy Force Field (FEFF) 3D-QSAR Analysis: Application to a Set of Peptidometic Renin Inhibitors , 1997, J. Chem. Inf. Comput. Sci..
[18] M. Morgan,et al. Targeting the Ras signaling pathway: a rational, mechanism-based treatment for hematologic malignancies? , 2000 .
[19] C. Sander,et al. An effective solvation term based on atomic occupancies for use in protein simulations , 1993 .
[20] A. Saltiel,et al. Signaling pathways in insulin action: molecular targets of insulin resistance. , 2000, The Journal of clinical investigation.
[21] S Suhai,et al. QM/MM study of the active site of free papain and of the NMA-papain complex. , 1999, Journal of biomolecular structure & dynamics.
[22] K. Shokat,et al. Engineering of the Myosin-Iβ Nucleotide-binding Pocket to Create Selective Sensitivity to N 6-modified ADP Analogs* , 1999, The Journal of Biological Chemistry.
[23] Michael J. Eck,et al. Three-dimensional structure of the tyrosine kinase c-Src , 1997, Nature.
[24] John Mendelsohn,et al. Type I Receptor Tyrosine Kinases as Targets for Therapy in Breast Cancer , 2004, Journal of Mammary Gland Biology and Neoplasia.
[25] J. S. Johnson,et al. 1-Phenyl-5-pyrazolyl ureas: potent and selective p38 kinase inhibitors. , 2000, Bioorganic & medicinal chemistry letters.
[26] John Kuriyan,et al. Crystal structure of the Src family tyrosine kinase Hck , 1997, Nature.
[27] Paul R. Caron,et al. Crystal Structure of p38 Mitogen-activated Protein Kinase* , 1996, The Journal of Biological Chemistry.
[28] J. Kuriyan,et al. Crystal structure of Hck in complex with a Src family-selective tyrosine kinase inhibitor. , 1999, Molecular cell.
[29] T. Pakkanen,et al. Quantum mechanical model assembly study on the energetics of binding of arabinose, fucose, and galactose to L‐arabinose‐binding protein , 1994, Proteins.
[30] Peter G. Schultz,et al. A chemical switch for inhibitor-sensitive alleles of any protein kinase , 2000, Nature.
[31] K. Shokat,et al. Acquisition of inhibitor-sensitive protein kinases through protein design. , 1999, Pharmacology & therapeutics.
[32] R. Somwar,et al. Activation of p38 mitogen-activated protein kinase alpha and beta by insulin and contraction in rat skeletal muscle: potential role in the stimulation of glucose transport. , 2000, Diabetes.
[33] G Klebe,et al. Energetic and entropic factors determining binding affinity in protein-ligand complexes. , 1997, Journal of receptor and signal transduction research.
[34] P. Kollman,et al. An all atom force field for simulations of proteins and nucleic acids , 1986, Journal of computational chemistry.
[35] P Willett,et al. Development and validation of a genetic algorithm for flexible docking. , 1997, Journal of molecular biology.
[36] S. Harrison,et al. Crystal structures of c-Src reveal features of its autoinhibitory mechanism. , 1999, Molecular cell.
[37] P. Cohen,et al. Specificity and mechanism of action of some commonly used protein kinase inhibitors , 2000 .
[38] S. Kim,et al. High-resolution crystal structures of human cyclin-dependent kinase 2 with and without ATP: bound waters and natural ligand as guides for inhibitor design. , 1996, Journal of medicinal chemistry.
[39] Ajay,et al. Computational methods to predict binding free energy in ligand-receptor complexes. , 1995, Journal of medicinal chemistry.
[40] Harold A. Scheraga,et al. Free energies of hydration of solute molecules. 1. Improvement of the hydration shell model by exact computations of overlapping volumes , 1987 .
[41] Y. Liu,et al. Catalytic activation of mitogen-activated protein (MAP) kinase phosphatase-1 by binding to p38 MAP kinase: critical role of the p38 C-terminal domain in its negative regulation. , 2000, The Biochemical journal.
[42] K. Shokat,et al. Engineering Src family protein kinases with unnatural nucleotide specificity. , 1998, Chemistry & biology.
[43] 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..
[44] David S. Goodsell,et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998 .
[45] Tim D. J. Perkins,et al. New Approach to Molecular Docking and Its Application to Virtual Screening of Chemical Databases , 2000, J. Chem. Inf. Comput. Sci..
[46] A. D. McLachlan,et al. Solvation energy in protein folding and binding , 1986, Nature.
[47] R A Friesner,et al. Quantum mechanical calculations on biological systems. , 1998, Current opinion in structural biology.