Accounting for global protein deformability during protein-protein and protein-ligand docking.
暂无分享,去创建一个
[1] Martin Zacharias,et al. Refinement of protein cores and protein-peptide interfaces using a potential scaling approach. , 2005, Protein engineering, design & selection : PEDS.
[2] M. Sternberg,et al. The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. , 2005, Journal of molecular biology.
[3] C. Prigent,et al. The Protein Kinase Resource: everything you always wanted to know about protein kinases but were afraid to ask , 2005, Biology of the cell.
[4] 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..
[5] Susan S. Taylor,et al. Regulation of protein kinases; controlling activity through activation segment conformation. , 2004, Molecular cell.
[6] M. Noble,et al. The role of structure in kinase-targeted inhibitor design. , 2004, Current opinion in drug discovery & development.
[7] Claudio N. Cavasotto,et al. Protein flexibility in ligand docking and virtual screening to protein kinases. , 2004, Journal of molecular biology.
[8] Susan S. Taylor,et al. PKA: a portrait of protein kinase dynamics. , 2004, Biochimica et biophysica acta.
[9] 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.
[10] Richard Lavery,et al. Docking macromolecules with flexible segments , 2003, J. Comput. Chem..
[11] J Andrew McCammon,et al. Protein flexibility and computer-aided drug design. , 2003, Annual review of pharmacology and toxicology.
[12] Natasja Brooijmans,et al. Molecular recognition and docking algorithms. , 2003, Annual review of biophysics and biomolecular structure.
[13] S. Teague. Implications of protein flexibility for drug discovery , 2003, Nature Reviews Drug Discovery.
[14] Martin Zacharias,et al. Protein–protein docking with a reduced protein model accounting for side‐chain flexibility , 2003, Protein science : a publication of the Protein Society.
[15] E. Sausville,et al. Issues and progress with protein kinase inhibitors for cancer treatment , 2003, Nature Reviews Drug Discovery.
[16] Susan S. Taylor,et al. Dynamic features of cAMP-dependent protein kinase revealed by apoenzyme crystal structure. , 2003, Journal of molecular biology.
[17] Ruth Nussinov,et al. Principles of docking: An overview of search algorithms and a guide to scoring functions , 2002, Proteins.
[18] J. Mccammon,et al. Computational drug design accommodating receptor flexibility: the relaxed complex scheme. , 2002, Journal of the American Chemical Society.
[19] Jonathan W. Essex,et al. A review of protein-small molecule docking methods , 2002, J. Comput. Aided Mol. Des..
[20] D. Goodsell,et al. Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock , 2002, Proteins.
[21] I Kolossváry,et al. Fully flexible low-mode docking: application to induced fit in HIV integrase. , 2001, Journal of the American Chemical Society.
[22] R Abagyan,et al. High-throughput docking for lead generation. , 2001, Current opinion in chemical biology.
[23] Thomas Lengauer,et al. FlexE: efficient molecular docking considering protein structure variations. , 2001, Journal of molecular biology.
[24] Y. Sanejouand,et al. Conformational change of proteins arising from normal mode calculations. , 2001, Protein engineering.
[25] A. Sali,et al. Comparative protein structure modeling of genes and genomes. , 2000, Annual review of biophysics and biomolecular structure.
[26] Gennady Verkhivker,et al. Deciphering common failures in molecular docking of ligand-protein complexes , 2000, J. Comput. Aided Mol. Des..
[27] Rafael Najmanovich,et al. Side‐chain flexibility in proteins upon ligand binding , 2000, Proteins.
[28] J A McCammon,et al. Accommodating protein flexibility in computational drug design. , 2000, Molecular pharmacology.
[29] Youngshang Pak,et al. Application of a Molecular Dynamics Simulation Method with a Generalized Effective Potential to the Flexible Molecular Docking Problems , 2000 .
[30] Christopher W. Murray,et al. The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase , 1999, J. Comput. Aided Mol. Des..
[31] J. Andrew McCammon,et al. Method for Including the Dynamic Fluctuations of a Protein in Computer-Aided Drug Design , 1999 .
[32] A. di Nola,et al. Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation , 1999, Proteins.
[33] A. Davis,et al. Hydrogen Bonding, Hydrophobic Interactions, and Failure of the Rigid Receptor Hypothesis. , 1999, Angewandte Chemie.
[34] Heinz Sklenar,et al. Harmonic modes as variables to approximately account for receptor flexibility in ligand–receptor docking simulations: Application to DNA minor groove ligand complex , 1999 .
[35] K. Hinsen. Analysis of domain motions by approximate normal mode calculations , 1998, Proteins.
[36] R Nussinov,et al. Flexible docking allowing induced fit in proteins: Insights from an open to closed conformational isomers , 1998, Proteins.
[37] Amedeo Caflisch,et al. Docking small ligands in flexible binding sites , 1998, J. Comput. Chem..
[38] Ruth Nussinov,et al. A Method for Biomolecular Structural Recognition and Docking Allowing Conformational Flexibility , 1998, J. Comput. Biol..
[39] R. Huber,et al. Staurosporine-induced conformational changes of cAMP-dependent protein kinase catalytic subunit explain inhibitory potential. , 1997, Structure.
[40] A. Atilgan,et al. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. , 1997, Folding & design.
[41] I. Kuntz,et al. Molecular docking to ensembles of protein structures. , 1997, Journal of molecular biology.
[42] J Deisenhofer,et al. Mechanism of ribonuclease inhibition by ribonuclease inhibitor protein based on the crystal structure of its complex with ribonuclease A. , 1996, Journal of molecular biology.
[43] Thomas Lengauer,et al. A fast flexible docking method using an incremental construction algorithm. , 1996, Journal of molecular biology.
[44] G. Vriend,et al. Molecular docking using surface complementarity , 1996, Proteins.
[45] K. Schulten,et al. Principal Component Analysis and Long Time Protein Dynamics , 1996 .
[46] M. Murcko,et al. Comparative X-ray structures of the major binding protein for the immunosuppressant FK506 (tacrolimus) in unliganded form and in complex with FK506 and rapamycin. , 1995, Acta crystallographica. Section D, Biological crystallography.
[47] A. Leach,et al. Ligand docking to proteins with discrete side-chain flexibility. , 1994, Journal of molecular biology.
[48] H. Berendsen,et al. Essential dynamics of proteins , 1993, Proteins.
[49] Bostjan Kobe,et al. Crystal structure of porcine ribonuclease inhibitor, a protein with leucine-rich repeats , 1993, Nature.
[50] R F Standaert,et al. Atomic structure of FKBP-FK506, an immunophilin-immunosuppressant complex , 1991, Science.
[51] M Karplus,et al. Solution structure of FKBP, a rotamase enzyme and receptor for FK506 and rapamycin , 1991, Science.
[52] J M Blaney,et al. A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.