Using Protein Homology Models for Structure-Based Studies: Approaches to Model Refinement
暂无分享,去创建一个
[1] J. Åqvist,et al. Computational prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active site. , 2004, Biochemistry.
[2] Ceslovas Venclovas,et al. Progress over the first decade of CASP experiments , 2005, Proteins.
[3] Ruben Abagyan,et al. Discovery of diverse thyroid hormone receptor antagonists by high-throughput docking , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[4] Richard D. Taylor,et al. Improved protein–ligand docking using GOLD , 2003, Proteins.
[5] Prashant V Desai,et al. Probing the structure of falcipain‐3, a cysteine protease from Plasmodium falciparum: Comparative protein modeling and docking studies , 2003, Protein science : a publication of the Protein Society.
[6] J. Bajorath,et al. Docking and scoring in virtual screening for drug discovery: methods and applications , 2004, Nature Reviews Drug Discovery.
[7] S. Diekmann,et al. Molecular Basis of the Interaction Specificity between the Human Glucocorticoid Receptor and Its Endogenous Steroid Ligand Cortisol , 2005, Chembiochem : a European journal of chemical biology.
[8] Andreas Evers,et al. Virtual screening of biogenic amine-binding G-protein coupled receptors: comparative evaluation of protein- and ligand-based virtual screening protocols. , 2005, Journal of medicinal chemistry.
[9] O. Wiest,et al. Inhibition studies with rationally designed inhibitors of the human low molecular weight protein tyrosine phosphatase. , 2004, Bioorganic & medicinal chemistry.
[10] Y. Martin,et al. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. , 1999, Journal of medicinal chemistry.
[11] R Abagyan,et al. High-throughput docking for lead generation. , 2001, Current opinion in chemical biology.
[12] Mark Whittaker,et al. The selection and design of GPCR ligands: from concept to the clinic. , 2004, Combinatorial chemistry & high throughput screening.
[13] Margaret A. Johnson,et al. A novel modeling protocol for protein receptors guided by bound-ligand conformation. , 2003, Biochemistry.
[14] E. Jaeger,et al. Docking: successes and challenges. , 2005, Current pharmaceutical design.
[15] S. Tanuma,et al. Structure basis for the inhibitory mechanism of a novel DNase γ-specific inhibitor, DR396 , 2006 .
[16] 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.
[17] Johan Schultz,et al. Structure-based screening and design in drug discovery. , 2002, Drug discovery today.
[18] G Klebe,et al. Docking ligands onto binding site representations derived from proteins built by homology modelling. , 2001, Journal of molecular biology.
[19] Didier Rognan,et al. Protein‐based virtual screening of chemical databases. II. Are homology models of g‐protein coupled receptors suitable targets? , 2002, Proteins.
[20] Thomas Meyer,et al. Identification of cylin-dependent kinase 1 inhibitors of a new chemical type by structure-based design and database searching , 2001, J. Comput. Aided Mol. Des..
[21] M. Pusch,et al. Molecular modeling of p-chlorophenoxyacetic acid binding to the CLC-0 channel. , 2003, Biochemistry.
[22] T. Bishop,et al. Homology modeling using multiple molecular dynamics simulations and docking studies of the human androgen receptor ligand binding domain bound to testosterone and nonsteroidal ligands. , 2001, Journal of medicinal chemistry.
[23] Michael K. Gilson,et al. Screening Drug-Like Compounds by Docking to Homology Models: A Systematic Study , 2006, J. Chem. Inf. Model..
[24] Laurence Miguet,et al. Comparison of a homology model and the crystallographic structure of human 11β-hydroxysteroid dehydrogenase type 1 (11βHSD1) in a structure-based identification of inhibitors , 2006, J. Comput. Aided Mol. Des..
[25] Alexander Hillisch,et al. Dissecting Physiological Roles of Estrogen Receptor α and β with Potent Selective Ligands from Structure-Based Design , 2004 .
[26] M. Inagaki,et al. Design and synthesis of Rho kinase inhibitors (I). , 2004, Bioorganic & medicinal chemistry.
[27] J. Mccammon,et al. Accommodating Protein Flexibility in Computational Drug Design 1 , 2 , 2000 .
[28] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[29] Cheng Luo,et al. A 3D model of SARS_CoV 3CL proteinase and its inhibitors design by virtual screening. , 2003, Acta pharmacologica Sinica.
[30] E. Bradley,et al. Performance of 3D-database molecular docking studies into homology models. , 2004, Journal of medicinal chemistry.
[31] Ruben Abagyan,et al. Nuclear hormone receptor targeted virtual screening. , 2003, Journal of medicinal chemistry.
[32] B. Honig,et al. Structural genomics: Computational methods for structure analysis , 2003, Protein science : a publication of the Protein Society.
[33] O. Wiest,et al. Toward selective histone deacetylase inhibitor design: homology modeling, docking studies, and molecular dynamics simulations of human class I histone deacetylases. , 2005, Journal of medicinal chemistry.
[34] M. Zacharias,et al. Molecular determinants for high-affinity block of human EAG potassium channels by antiarrhythmic agents. , 2004, Molecular pharmacology.
[35] P. Kollman,et al. Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding , 2000 .
[36] I. Muegge,et al. Virtual screening for kinase targets. , 2004, Current medicinal chemistry.
[37] Jiri Gut,et al. Identification of novel parasitic cysteine protease inhibitors using virtual screening. 1. The ChemBridge database. , 2004, Journal of medicinal chemistry.
[38] Renxiao Wang,et al. Comparative evaluation of 11 scoring functions for molecular docking. , 2003, Journal of medicinal chemistry.
[39] Hans-Dieter Höltje,et al. Molecular design of two sterol 14α-demethylase homology models and their interactions with the azole antifungals ketoconazole and bifonazole , 2005, J. Comput. Aided Mol. Des..
[40] B. Shoichet,et al. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. , 2003, Journal of medicinal chemistry.
[41] D. Diller,et al. Kinases, homology models, and high throughput docking. , 2003, Journal of medicinal chemistry.
[42] J A McCammon,et al. Accommodating protein flexibility in computational drug design. , 2000, Molecular pharmacology.
[43] Prashant Desai,et al. Homology Modeling of Falcipain-2: Validation, De Novo Ligand Design and Synthesis of Novel Inhibitors , 2002, Journal of biomolecular structure & dynamics.
[44] Thomas Lengauer,et al. Evaluation of the FLEXX incremental construction algorithm for protein–ligand docking , 1999, Proteins.
[45] Gordon C K Roberts,et al. Validation of model of cytochrome P450 2D6: an in silico tool for predicting metabolism and inhibition. , 2004, Journal of medicinal chemistry.
[46] Irina D. Pogozheva,et al. Homology modeling of opioid receptor-ligand complexes using experimental constraints , 2005, The AAPS Journal.
[47] Daniel Fischer,et al. Servers for protein structure prediction. , 2006, Current opinion in structural biology.
[48] Berk Hess,et al. GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .
[49] A. Elcock,et al. Rapid computational identification of the targets of protein kinase inhibitors. , 2005, Journal of medicinal chemistry.
[50] Christian Drosten,et al. Cinanserin Is an Inhibitor of the 3C-Like Proteinase of Severe Acute Respiratory Syndrome Coronavirus and Strongly Reduces Virus Replication In Vitro , 2005, Journal of Virology.
[51] G. Klebe,et al. Ligand-supported homology modelling of protein binding-sites using knowledge-based potentials. , 2003, Journal of molecular biology.
[52] Nikhil V. Shirahatti,et al. A Conserved Glutamate Residue in Transmembrane Helix 10 Influences Substrate Specificity of Rabbit OCT2 (SLC22A2)* , 2005, Journal of Biological Chemistry.
[53] Didier Rognan,et al. High-Throughput Modeling of Human G-Protein Coupled Receptors: Amino Acid Sequence Alignment, Three-Dimensional Model Building, and Receptor Library Screening , 2004, J. Chem. Inf. Model..
[54] D. Warhurst,et al. Resistance to Antifolates in Plasmodium Falciparum, the Causative Agent of Tropical Malaria , 2002, Science progress.
[55] M. Waterman,et al. Sterol 14α-demethylase, an abundant and essential mixed-function oxidase , 2005 .
[56] T. Klabunde,et al. Structure-based drug discovery using GPCR homology modeling: successful virtual screening for antagonists of the alpha1A adrenergic receptor. , 2005, Journal of medicinal chemistry.
[57] Thomas Lengauer,et al. FlexE: efficient molecular docking considering protein structure variations. , 2001, Journal of molecular biology.
[58] O. Moran,et al. Binding site of activators of the cystic fibrosis transmembrane conductance regulator in the nucleotide binding domains , 2005, Cellular and Molecular Life Sciences CMLS.
[59] L. Karlsson,et al. Checkpoint kinase inhibitors: SAR and radioprotective properties of a series of 2-arylbenzimidazoles. , 2005, Journal of medicinal chemistry.
[60] Ruth Nussinov,et al. Principles of docking: An overview of search algorithms and a guide to scoring functions , 2002, Proteins.
[61] K. Ginalski. Comparative modeling for protein structure prediction. , 2006, Current opinion in structural biology.
[62] S. Sine,et al. Toward atomic-scale understanding of ligand recognition in the muscle nicotinic receptor. , 2004, Current medicinal chemistry.
[63] John B. O. Mitchell,et al. Predicting protein-ligand binding affinities: a low scoring game? , 2004, Organic & biomolecular chemistry.
[64] Ceslovas Venclovas,et al. Comparative modeling in CASP5: Progress is evident, but alignment errors remain a significant hindrance , 2003, Proteins.
[65] Roland L. Dunbrack,et al. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. , 1997, Journal of molecular biology.