Prediction of protein-protein interactions by docking methods.
暂无分享,去创建一个
[1] M. Sternberg,et al. Modelling Protein–Protein and Protein–DNA Docking , 2004 .
[2] Rebecca C Wade,et al. Biomolecular diffusional association. , 2002, Current opinion in structural biology.
[3] Thomas Lengauer,et al. Bioinformatics ‐ From Genomes to Drugs , 2001 .
[4] B Honig,et al. Electrostatic contributions to protein–protein interactions: Fast energetic filters for docking and their physical basis , 2001, Protein science : a publication of the Protein Society.
[5] L. Wyns,et al. Degenerate interfaces in antigen-antibody complexes. , 2001, Journal of molecular biology.
[6] Françoise Guerlesquin,et al. A novel approach for assesing macromolecular complexes combining soft‐docking calculations with NMR data , 2001, Protein science : a publication of the Protein Society.
[7] R. Ellis. Macromolecular crowding : obvious but underappreciated , 2022 .
[8] S. Vajda,et al. Protein docking along smooth association pathways , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[9] M. Sternberg,et al. Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. , 2001, Journal of molecular biology.
[10] I. Vakser,et al. How common is the funnel‐like energy landscape in protein‐protein interactions? , 2001, Protein science : a publication of the Protein Society.
[11] Eleanor J. Gardiner,et al. Protein docking using a genetic algorithm , 2001, Proteins.
[12] H. Wolfson,et al. Protein functional epitopes: hot spots, dynamics and combinatorial libraries. , 2001, Current opinion in structural biology.
[13] R Nussinov,et al. Automated multiple structure alignment and detection of a common substructural motif , 2001, Proteins.
[14] N. Ben-Tal,et al. Residue frequencies and pairing preferences at protein–protein interfaces , 2001, Proteins.
[15] Hans-Peter Lenhof,et al. Structure prediction of protein complexes by an NMR-based protein docking algorithm , 2001, Journal of biomolecular NMR.
[16] Todd J. A. Ewing,et al. DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases , 2001, J. Comput. Aided Mol. Des..
[17] Thomas Lengauer,et al. FlexE: efficient molecular docking considering protein structure variations. , 2001, Journal of molecular biology.
[18] D. Tobias,et al. Electrostatics calculations: recent methodological advances and applications to membranes. , 2001, Current opinion in structural biology.
[19] R C Wade,et al. Protein-protein association: investigation of factors influencing association rates by brownian dynamics simulations. , 2001, Journal of molecular biology.
[20] A. Elcock,et al. Computer Simulation of Protein−Protein Interactions , 2001 .
[21] S Vajda,et al. Dynamical view of the positions of key side chains in protein-protein recognition. , 2001, Biophysical journal.
[22] L. T. Ten Eyck,et al. Protein docking using continuum electrostatics and geometric fit. , 2001, Protein engineering.
[23] J A McCammon,et al. Calculation of weak protein-protein interactions: the pH dependence of the second virial coefficient. , 2001, Biophysical journal.
[24] S Vajda,et al. Discrimination of near‐native protein structures from misfolded models by empirical free energy functions , 2000, Proteins.
[25] R. M. Burnett,et al. DARWIN: A program for docking flexible molecules , 2000, Proteins.
[26] S. Vajda,et al. Scoring docked conformations generated by rigid‐body protein‐protein docking , 2000, Proteins.
[27] G M Clore,et al. Accurate and rapid docking of protein-protein complexes on the basis of intermolecular nuclear overhauser enhancement data and dipolar couplings by rigid body minimization. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[28] R. Nussinov,et al. Conservation of polar residues as hot spots at protein interfaces , 2000, Proteins.
[29] L. Krippahl,et al. BiGGER: A new (soft) docking algorithm for predicting protein interactions , 2000, Proteins.
[30] D. Ritchie,et al. Protein docking using spherical polar Fourier correlations , 2000, Proteins.
[31] M. Gerstein,et al. The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. , 2000, Nucleic acids research.
[32] Ernst Althaus,et al. A combinatorial approach to protein docking with flexible side-chains , 2000, RECOMB '00.
[33] R. Norel,et al. Electrostatic aspects of protein-protein interactions. , 2000, Current opinion in structural biology.
[34] Peter Willett,et al. Graph-Theoretic Techniques for Macromolecular Docking , 2000, J. Chem. Inf. Comput. Sci..
[35] S Vajda,et al. Kinetics of desolvation-mediated protein-protein binding. , 2000, Biophysical journal.
[36] Colin Kleanthous,et al. Protein-protein recognition , 2000 .
[37] Brian B. Goldman,et al. QSD quadratic shape descriptors. 2. Molecular docking using quadratic shape descriptors (QSDock) , 2000, Proteins.
[38] R M Jackson,et al. Comparison of protein–protein interactions in serine protease‐inhibitor and antibody‐antigen complexes: Implications for the protein docking problem , 2008, Protein science : a publication of the Protein Society.
[39] David J. Diller,et al. A critical evaluation of several global optimization algorithms for the purpose of molecular docking , 1999, J. Comput. Chem..
[40] J. Ben Rosen,et al. Comparing search strategies for finding global optima on energy landscapes , 1999, J. Comput. Chem..
[41] H. Wolfson,et al. Examination of shape complementarity in docking of Unbound proteins , 1999, Proteins.
[42] I. Vakser,et al. A systematic study of low-resolution recognition in protein--protein complexes. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[43] Jill E. Gready,et al. Simple method for locating possible ligand binding sites on protein surfaces , 1999, J. Comput. Chem..
[44] M J Sternberg,et al. Use of pair potentials across protein interfaces in screening predicted docked complexes , 1999, Proteins.
[45] M. Sternberg,et al. An analysis of conformational changes on protein-protein association: implications for predictive docking. , 1999, Protein engineering.
[46] S Vajda,et al. Free energy landscapes of encounter complexes in protein-protein association. , 1999, Biophysical journal.
[47] Y. Martin,et al. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. , 1999, Journal of medicinal chemistry.
[48] C. Chothia,et al. The atomic structure of protein-protein recognition sites. , 1999, Journal of molecular biology.
[49] Charles DeLisi,et al. Protein‐protein recognition: exploring the energy funnels near the binding sites , 1999, Proteins.
[50] R. Nussinov,et al. Folding funnels, binding funnels, and protein function , 1999, Protein science : a publication of the Protein Society.
[51] J. Janin,et al. Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition. , 1999, Structure.
[52] M. Sternberg,et al. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. , 1998, Journal of molecular biology.
[53] Ruth Nussinov,et al. A Method for Biomolecular Structural Recognition and Docking Allowing Conformational Flexibility , 1998, J. Comput. Biol..
[54] M. Sternberg,et al. Modelling protein docking using shape complementarity, electrostatics and biochemical information. , 1997, Journal of molecular biology.
[55] J. Janin. The kinetics of protein‐protein recognition , 1997, Proteins.
[56] P Willett,et al. Development and validation of a genetic algorithm for flexible docking. , 1997, Journal of molecular biology.
[57] C. DeLisi,et al. Determination of atomic desolvation energies from the structures of crystallized proteins. , 1997, Journal of molecular biology.
[58] A. Fersht,et al. Rapid, electrostatically assisted association of proteins , 1996, Nature Structural Biology.
[59] J. Cherfils,et al. Molecular docking programs successfully predict the binding of a β-lactamase inhibitory protein to TEM-1 β-lactamase , 1996, Nature Structural Biology.
[60] M. Sanner,et al. Reduced surface: an efficient way to compute molecular surfaces. , 1996, Biopolymers.
[61] S. Jones,et al. Principles of protein-protein interactions. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[62] R Abagyan,et al. Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. , 1996, Nature structural biology.
[63] M J Sternberg,et al. A continuum model for protein-protein interactions: application to the docking problem. , 1995, Journal of molecular biology.
[64] I. Vakser. Protein docking for low-resolution structures. , 1995, Protein engineering.
[65] R. Nussinov,et al. A geometry-based suite of molecular docking processes. , 1995, Journal of molecular biology.
[66] L. C. Andrews,et al. The Fourier-Green's function and the rapid evaluation of molecular potentials. , 1994, Protein engineering.
[67] E. Katchalski‐Katzir,et al. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[68] M. L. Connolly. Analytical molecular surface calculation , 1983 .
[69] D. Ermak,et al. Brownian dynamics with hydrodynamic interactions , 1978 .