Understanding the challenges of protein flexibility in drug design
暂无分享,去创建一个
[1] D. Koshland. Application of a Theory of Enzyme Specificity to Protein Synthesis. , 1958, Proceedings of the National Academy of Sciences of the United States of America.
[2] S. Kim,et al. "Soft docking": matching of molecular surface cubes. , 1991, Journal of molecular biology.
[3] Ruben Abagyan,et al. ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation , 1994, J. Comput. Chem..
[4] H J Berendsen,et al. Molecular dynamics simulation of the docking of substrates to proteins , 1994, Proteins.
[5] 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..
[6] A. Leach,et al. Ligand docking to proteins with discrete side-chain flexibility. , 1994, Journal of molecular biology.
[7] R. Glen,et al. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. , 1995, Journal of molecular biology.
[8] Pieter F. W. Stouten,et al. A molecular mechanics/grid method for evaluation of ligand–receptor interactions , 1995, J. Comput. Chem..
[9] I Lasters,et al. Computation of the binding of fully flexible peptides to proteins with flexible side chains , 1997, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[10] I. Kuntz,et al. Molecular docking to ensembles of protein structures. , 1997, Journal of molecular biology.
[11] Gennady M Verkhivker,et al. Predicting structural effects in HIV‐1 protease mutant complexes with flexible ligand docking and protein side‐chain optimization , 1998, Proteins.
[12] J. Tainer,et al. Screening a peptidyl database for potential ligands to proteins with side‐chain flexibility , 1998, Proteins.
[13] Amedeo Caflisch,et al. Docking small ligands in flexible binding sites , 1998, J. Comput. Chem..
[14] R Nussinov,et al. Flexible docking allowing induced fit in proteins: Insights from an open to closed conformational isomers , 1998, Proteins.
[15] A. di Nola,et al. Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation , 1999, Proteins.
[16] 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, J. Comput. Chem..
[17] István Kolossváry,et al. Low-mode conformational search elucidated: Application to C39H80 and flexible docking of 9-deazaguanine inhibitors into PNP , 1999, J. Comput. Chem..
[18] L. Kuhn,et al. Virtual screening with solvation and ligand-induced complementarity , 2000 .
[19] Rafael Najmanovich,et al. Side‐chain flexibility in proteins upon ligand binding , 2000, Proteins.
[20] HIV-1 Protease , 2000 .
[21] F. Bushman,et al. Developing a dynamic pharmacophore model for HIV-1 integrase. , 2000, Journal of medicinal chemistry.
[22] B. X. Carlson,et al. A single glycine residue at the entrance to the first membrane-spanning domain of the gamma-aminobutyric acid type A receptor beta(2) subunit affects allosteric sensitivity to GABA and anesthetics. , 2000, Molecular pharmacology.
[23] J A McCammon,et al. Accommodating protein flexibility in computational drug design. , 2000, Molecular pharmacology.
[24] R. Nussinov,et al. Protein Folding: Binding of Conformationally Fluctuating Building Blocks Via Population Selection , 2001, Critical reviews in biochemistry and molecular biology.
[25] Thomas Lengauer,et al. FlexE: efficient molecular docking considering protein structure variations. , 2001, Journal of molecular biology.
[26] H. Bosshard,et al. Molecular recognition by induced fit: how fit is the concept? , 2001, News in physiological sciences : an international journal of physiology produced jointly by the International Union of Physiological Sciences and the American Physiological Society.
[27] I Kolossváry,et al. Fully flexible low-mode docking: application to induced fit in HIV integrase. , 2001, Journal of the American Chemical Society.
[28] D. Goodsell,et al. Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock , 2002, Proteins.
[29] J. Mccammon,et al. Computational drug design accommodating receptor flexibility: the relaxed complex scheme. , 2002, Journal of the American Chemical Society.
[30] M L Teodoro,et al. Conformational flexibility models for the receptor in structure based drug design. , 2003, Current pharmaceutical design.
[31] Lydia E. Kavraki,et al. Understanding Protein Flexibility through Dimensionality Reduction , 2003, J. Comput. Biol..
[32] Diane Joseph-McCarthy,et al. Pharmacophore‐based molecular docking to account for ligand flexibility , 2003, Proteins.
[33] B. Shoichet,et al. Soft docking and multiple receptor conformations in virtual screening. , 2004, Journal of medicinal chemistry.
[34] Brian K Shoichet,et al. Testing a flexible-receptor docking algorithm in a model binding site. , 2004, Journal of molecular biology.
[35] Claudio N. Cavasotto,et al. Protein flexibility in ligand docking and virtual screening to protein kinases. , 2004, Journal of molecular biology.
[36] William J. Welsh,et al. Identification of a Minimal Subset of Receptor Conformations for Improved Multiple Conformation Docking and Two-Step Scoring , 2004, J. Chem. Inf. Model..
[37] 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.
[38] Conrad C. Huang,et al. UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..
[39] M. Nilges,et al. Complementarity of structure ensembles in protein-protein binding. , 2004, Structure.
[40] Claudio N. Cavasotto,et al. Representing receptor flexibility in ligand docking through relevant normal modes. , 2005, Journal of the American Chemical Society.
[41] Claudio N. Cavasotto,et al. Conformational Sampling of Protein Flexibility in Generalized Coordinates: Application to Ligand Docking , 2005 .
[42] X. Barril,et al. Unveiling the full potential of flexible receptor docking using multiple crystallographic structures. , 2005, Journal of medicinal chemistry.
[43] Akiko Itai,et al. Effective handling of induced‐fit motion in flexible docking , 2006, Proteins.
[44] Jens Meiler,et al. ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility , 2006, Proteins.
[45] X. Barril,et al. Incorporating protein flexibility into docking and structure-based drug design , 2006, Expert opinion on drug discovery.
[46] R. Friesner,et al. Novel procedure for modeling ligand/receptor induced fit effects. , 2006, Journal of medicinal chemistry.
[47] J. G. Park,et al. FlexE ensemble docking approach to virtual screening for CDK2 inhibitors , 2007 .
[48] Jonathan Kadmon,et al. Molecular dynamics simulations of palmitate entry into the hydrophobic pocket of the fatty acid binding protein , 2007, FEBS letters.
[49] Heather A Carlson,et al. Exploring experimental sources of multiple protein conformations in structure-based drug design. , 2007, Journal of the American Chemical Society.
[50] X. Zou,et al. Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking , 2006, Proteins.
[51] Markus Wagener,et al. A flexible approach to induced fit docking. , 2007, Journal of medicinal chemistry.
[52] Xiaoqin Zou,et al. Efficient molecular docking of NMR structures: Application to HIV‐1 protease , 2006, Protein science : a publication of the Protein Society.
[53] Christopher R. Corbeil,et al. Docking Ligands into Flexible and Solvated Macromolecules, 1. Development and Validation of FITTED 1.0 , 2007, J. Chem. Inf. Model..
[54] Rommie E. Amaro,et al. An improved relaxed complex scheme for receptor flexibility in computer-aided drug design , 2008, J. Comput. Aided Mol. Des..
[55] Christopher R. Corbeil,et al. Docking Ligands into Flexible and Solvated Macromolecules. 2. Development and Application of Fitted 1.5 to the Virtual Screening of Potential HCV Polymerase Inhibitors , 2008, J. Chem. Inf. Model..
[56] Chung F Wong,et al. Flexible protein–flexible ligand docking with disrupted velocity simulated annealing , 2008, Proteins.
[57] David Baker,et al. Macromolecular modeling with rosetta. , 2008, Annual review of biochemistry.
[58] M. Zacharias,et al. Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking. , 2008, Journal of medicinal chemistry.
[59] Nurit Haspel,et al. Electrostatic contributions drive the interaction between Staphylococcus aureus protein Efb‐C and its complement target C3d , 2008, Protein science : a publication of the Protein Society.
[60] L. Kavraki,et al. Multiscale characterization of protein conformational ensembles , 2009, Proteins.
[61] Christopher R. Corbeil,et al. Docking Ligands into Flexible and Solvated Macromolecules. 3. Impact of Input Ligand Conformation, Protein Flexibility, and Water Molecules on the Accuracy of Docking Programs , 2009, J. Chem. Inf. Model..
[62] Ruben Abagyan,et al. Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes , 2009, J. Chem. Inf. Model..
[63] B. Zagrovic,et al. Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin , 2009, Proceedings of the National Academy of Sciences.
[64] Roger S Armen,et al. An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics. , 2009, Journal of chemical theory and computation.
[65] Ruben Abagyan,et al. Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. , 2009, Journal of medicinal chemistry.
[66] Erin S. Bolstad,et al. In pursuit of virtual lead optimization: Pruning ensembles of receptor structures for increased efficiency and accuracy during docking , 2009, Proteins.
[67] Ian W. Davis,et al. RosettaLigand docking with full ligand and receptor flexibility. , 2009, Journal of molecular biology.
[68] David S. Goodsell,et al. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility , 2009, J. Comput. Chem..
[69] Somesh D. Sharma,et al. Managing protein flexibility in docking and its applications. , 2009, Drug discovery today.
[70] Christopher R. Corbeil,et al. Modeling Reality for Optimal Docking of Small Molecules to Biological Targets , 2009 .
[71] Xavier Barril,et al. Ensemble Docking from Homology Models. , 2010, Journal of chemical theory and computation.
[72] Ana T. Winck,et al. Mining flexible-receptor docking experiments to select promising protein receptor snapshots , 2010, BMC Genomics.
[73] Y. Li,et al. Studies of benzothiadiazine derivatives as hepatitis C virus NS5B polymerase inhibitors using 3D-QSAR, molecular docking and molecular dynamics. , 2010, Current medicinal chemistry.
[74] Feng Ding,et al. Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands , 2010, J. Chem. Inf. Model..
[75] Olivier Sperandio,et al. How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis , 2010, European Biophysics Journal.
[76] Huan‐Xiang Zhou. From induced fit to conformational selection: a continuum of binding mechanism controlled by the timescale of conformational transitions. , 2010, Biophysical journal.
[77] Jonathan W. Essex,et al. Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments , 2010, J. Chem. Inf. Model..
[78] Iris Antes,et al. DynaDock: A new molecular dynamics‐based algorithm for protein–peptide docking including receptor flexibility , 2010, Proteins: Structure, Function, and Bioinformatics.
[79] Victor Guallar,et al. Exploring hierarchical refinement techniques for induced fit docking with protein and ligand flexibility , 2009, J. Comput. Chem..
[80] Thierry Siméon,et al. Simulating ligand-induced conformational changes in proteins using a mechanical disassembly method. , 2010, Physical chemistry chemical physics : PCCP.
[81] R. Nussinov,et al. Induced Fit, Conformational Selection and Independent Dynamic Segments: an Extended View of Binding Events Opinion , 2022 .
[82] R. Nussinov,et al. Allostery and population shift in drug discovery. , 2010, Current opinion in pharmacology.
[83] Bert L. de Groot,et al. Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations , 2010, PLoS Comput. Biol..
[84] L. Kavraki,et al. Multi‐scale characterization of the energy landscape of proteins with application to the C3D/Efb‐C complex , 2010, Proteins.
[85] J. D. Figueroa-Villar,et al. Design, docking studies and molecular dynamics of new potential selective inhibitors of Plasmodium falciparum serine hydroxymethyltransferase , 2010 .
[86] Ian T. Crosby,et al. Homology Modeling and Docking Evaluation of Aminergic G Protein-Coupled Receptors , 2010, J. Chem. Inf. Model..
[87] Zhiwei Yang,et al. Synergistic effects in the designs of neuraminidase ligands: analysis from docking and molecular dynamics studies. , 2010, Journal of theoretical biology.
[88] Ruben Abagyan,et al. Recipes for the Selection of Experimental Protein Conformations for Virtual Screening , 2010, J. Chem. Inf. Model..
[89] Martin Zacharias,et al. Tackling the challenges posed by target flexibility in drug design , 2010, Expert opinion on drug discovery.
[90] Ruben Abagyan,et al. Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles , 2010, J. Comput. Aided Mol. Des..
[91] Arthur J. Olson,et al. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading , 2009, J. Comput. Chem..
[92] Christine Humblet,et al. Chemical space sampling by different scoring functions and crystal structures , 2010, J. Comput. Aided Mol. Des..
[93] Mengang Xu,et al. Significant Enhancement of Docking Sensitivity Using Implicit Ligand Sampling , 2011, J. Chem. Inf. Model..
[94] R. Abagyan,et al. Systematic Exploitation of Multiple Receptor Conformations for Virtual Ligand Screening , 2011, PloS one.
[95] Masahiko Ito,et al. A new method for induced fit docking (GENIUS) and its application to virtual screening of novel HCV NS3-4A protease inhibitors. , 2011, Bioorganic & Medicinal Chemistry.
[96] K. Whalen,et al. Hybrid Steered Molecular Dynamics‐Docking: An Efficient Solution to the Problem of Ranking Inhibitor Affinities Against a Flexible Drug Target. , 2011, Molecular informatics.
[97] Nir London,et al. Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors , 2011, PloS one.
[98] Harrison J. Hocker,et al. Novel Allosteric Sites on Ras for Lead Generation , 2011, PloS one.
[99] Wolfgang Wenzel,et al. Receptor flexibility in small‐molecule docking calculations , 2011 .
[100] P. Sokkar,et al. Computational modeling on the recognition of the HRE motif by HIF-1: molecular docking and molecular dynamics studies , 2012, Journal of Molecular Modeling.
[101] J. Changeux,et al. Conformational selection or induced fit? 50 years of debate resolved , 2011, F1000 biology reports.
[102] Martin Zacharias,et al. Efficient inclusion of receptor flexibility in grid‐based protein–ligand docking* , 2011, J. Comput. Chem..
[103] Claudio N. Cavasotto,et al. Docking-based virtual screening for ligands of G protein-coupled receptors: not only crystal structures but also in silico models. , 2011, Journal of molecular graphics & modelling.
[104] Yan Li,et al. Discovery of Novel Checkpoint Kinase 1 Inhibitors by Virtual Screening Based on Multiple Crystal Structures , 2011, J. Chem. Inf. Model..
[105] Patrick McCabe,et al. The Ensemble Performance Index: An Improved Measure for Assessing Ensemble Pose Prediction Performance , 2011, J. Chem. Inf. Model..
[106] James Andrew McCammon,et al. Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening , 2011, J. Chem. Inf. Model..
[107] M. Lill. Efficient incorporation of protein flexibility and dynamics into molecular docking simulations. , 2011, Biochemistry.
[108] Riccardo Baron,et al. Computational Drug Discovery and Design , 2012, Methods in Molecular Biology.
[109] Joseph Audie,et al. Recent work in the development and application of protein-peptide docking. , 2012, Future medicinal chemistry.
[110] Isabel C F R Ferreira,et al. Selective Flexibility of Side‐Chain Residues Improves VEGFR‐2 Docking Score using AutoDock Vina , 2012, Chemical biology & drug design.
[111] Xavier Barril,et al. Physico-Chemical and Computational Approaches to Drug Discovery , 2012 .
[112] Matteo Masetti,et al. Chapter 11:Enhanced Sampling Methods in Drug Design , 2012 .
[113] Wolfgang Wenzel,et al. Modeling loop backbone flexibility in receptor‐ligand docking simulations , 2012, J. Comput. Chem..
[114] Ruben Abagyan,et al. ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather than a Single Leader , 2012, J. Chem. Inf. Model..
[115] Lydia E Kavraki,et al. Computational models of protein kinematics and dynamics: beyond simulation. , 2012, Annual review of analytical chemistry.
[116] Lydia E. Kavraki,et al. Modeling Structures and Motions of Loops in Protein Molecules , 2012, Entropy.
[117] Thomas Lengauer,et al. On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking , 2012, J. Chem. Inf. Model..
[118] Modesto Orozco,et al. Application of Drug-Perturbed Essential Dynamics/Molecular Dynamics (ED/MD) to Virtual Screening and Rational Drug Design. , 2012, Journal of chemical theory and computation.
[119] Jens Meiler,et al. Rosetta Ligand docking with flexible XML protocols. , 2012, Methods in molecular biology.
[120] G. Bowman,et al. Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites , 2012, Proceedings of the National Academy of Sciences.
[121] Lydia E. Kavraki,et al. Protein–Ligand Interactions: Computational Docking , 2012 .
[122] Vishwesh Venkatraman,et al. Flexible protein docking refinement using pose‐dependent normal mode analysis , 2012, Proteins.
[123] Chaok Seok,et al. GalaxyDock: Protein-Ligand Docking with Flexible Protein Side-chains , 2012, J. Chem. Inf. Model..
[124] Katrina W Lexa,et al. Protein flexibility in docking and surface mapping , 2012, Quarterly Reviews of Biophysics.
[125] M. Rosales-Hernández,et al. Docking and DFT Studies to explore the Topoisomerase II ATP Pocket employing 3-Substituted 2,6-Piperazindiones for drug design , 2012 .
[126] Mengang Xu,et al. Utilizing Experimental Data for Reducing Ensemble Size in Flexible-Protein Docking , 2012, J. Chem. Inf. Model..
[127] R. Nussinov,et al. Expanding the conformational selection paradigm in protein-ligand docking. , 2012, Methods in molecular biology.
[128] Oliver Korb,et al. Potential and Limitations of Ensemble Docking , 2012, J. Chem. Inf. Model..
[129] António J. M. Ribeiro,et al. Protein-ligand docking in the new millennium--a retrospective of 10 years in the field. , 2013, Current medicinal chemistry.
[130] L. Kavraki,et al. DINC: A new AutoDock-based protocol for docking large ligands , 2013, BMC Structural Biology.
[131] Marcel Schumann,et al. Systematic and efficient side chain optimization for molecular docking using a cheapest‐path procedure , 2013, J. Comput. Chem..
[132] Olivier Sperandio,et al. One hundred thousand mouse clicks down the road: selected online resources supporting drug discovery collected over a decade. , 2013, Drug discovery today.
[133] J. Correa-Basurto,et al. Automated docking for novel drug discovery , 2013, Expert opinion on drug discovery.
[134] L. Kavraki,et al. SIMS: A Hybrid Method for Rapid Conformational Analysis , 2013, PloS one.
[135] Marcin Hoffmann,et al. The MM2QM tool for combining docking, molecular dynamics, molecular mechanics, and quantum mechanics † , 2013, J. Comput. Chem..
[136] J. Mccammon,et al. Accounting for Receptor Flexibility and Enhanced Sampling Methods in Computer‐Aided Drug Design , 2013, Chemical biology & drug design.
[137] Elizabeth Yuriev,et al. Latest developments in molecular docking: 2010–2011 in review , 2013, Journal of molecular recognition : JMR.
[138] Arthur J. Olson,et al. Automated Docking with Protein Flexibility in the Design of Femtomolar "Click Chemistry" Inhibitors of Acetylcholinesterase , 2013, J. Chem. Inf. Model..
[139] L. Dardenne,et al. Receptor–ligand molecular docking , 2013, Biophysical Reviews.
[140] Andrzej Kolinski,et al. CABS-fold: server for the de novo and consensus-based prediction of protein structure , 2013, Nucleic Acids Res..
[141] Martin Smiesko. DOLINA - Docking Based on a Local Induced-Fit Algorithm: Application toward Small-Molecule Binding to Nuclear Receptors , 2013, J. Chem. Inf. Model..
[142] M. Rosales-Hernández,et al. o-Alkylselenenylated benzoic acid accesses several sites in serum albumin according to fluorescence studies, Raman spectroscopy and theoretical simulations. , 2013, Protein and peptide letters.
[143] Valérie Campagna-Slater,et al. Methods for docking small molecules to macromolecules: a user's perspective. 2. Applications. , 2014, Current pharmaceutical design.
[144] J. Mccammon,et al. Exploring the role of receptor flexibility in structure-based drug discovery. , 2014, Biophysical chemistry.
[145] Haiou Li,et al. PaFlexPepDock: Parallel Ab-Initio Docking of Peptides onto Their Receptors with Full Flexibility Based on Rosetta , 2014, PloS one.
[146] Xiaoqin Zou,et al. Challenges, Applications, and Recent Advances of Protein-Ligand Docking in Structure-Based Drug Design , 2014, Molecules.
[147] Matthias Rarey,et al. Benchmark Data Sets for Structure-Based Computational Target Prediction , 2014, J. Chem. Inf. Model..
[148] Vincent Zoete,et al. Toward On-The-Fly Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: Development and Benchmark of a Scoring Function , 2014, J. Chem. Inf. Model..
[149] Valérie Campagna-Slater,et al. Methods for docking small molecules to macromolecules: a user's perspective. 1. The theory. , 2014, Current pharmaceutical design.
[150] Hasup Lee,et al. GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization , 2015, Nucleic Acids Res..
[151] Jessica Holien,et al. Improvements, trends, and new ideas in molecular docking: 2012–2013 in review , 2015, Journal of molecular recognition : JMR.
[152] Mateusz Kurcinski,et al. Coarse-Grained Modeling of Peptide Docking Associated with Large Conformation Transitions of the Binding Protein: Troponin I Fragment–Troponin C System , 2015, Molecules.
[153] Bernhard Y. Renard,et al. Docking small peptides remains a great challenge: an assessment using AutoDock Vina , 2015, Briefings Bioinform..
[154] Matteo Masetti,et al. Protein Flexibility in Drug Discovery: From Theory to Computation , 2015, ChemMedChem.