Rotamer libraries and probabilities of transition between rotamers for the side chains in protein–protein binding
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Ilya A Vakser | Alexander V Tuzikov | Tatsiana Kirys | I. Vakser | A. M. Ruvinsky | T. Kirys | A. Tuzikov | Anatoly M Ruvinsky | Ilya A. Vakser | Tatsiana Kirys
[1] Z. Weng,et al. Protein–protein docking benchmark version 3.0 , 2008, Proteins.
[2] J. Janin,et al. Protein–protein interaction and quaternary structure , 2008, Quarterly Reviews of Biophysics.
[3] 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.
[4] Roland L. Dunbrack,et al. A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. , 2011, Structure.
[5] Ozlem Keskin,et al. Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations. , 2008, Biophysical journal.
[6] Julie C. Mitchell,et al. An automated decision‐tree approach to predicting protein interaction hot spots , 2007, Proteins.
[7] R. Nussinov,et al. Folding funnels and binding mechanisms. , 1999, Protein engineering.
[8] Roland L. Dunbrack,et al. Bayesian statistical analysis of protein side‐chain rotamer preferences , 1997, Protein science : a publication of the Protein Society.
[9] R. Nussinov,et al. Protein–protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[10] T. Bhat,et al. An analysis of side-chain conformation in proteins. , 2009, International journal of peptide and protein research.
[11] A. M. Ruvinsky,et al. Novel statistical‐thermodynamic methods to predict protein‐ligand binding positions using probability distribution functions , 2005, Proteins.
[12] E. Fischer. Einfluss der Configuration auf die Wirkung der Enzyme , 1894 .
[13] Feng Ding,et al. Rapid Flexible Docking Using a Stochastic Rotamer Library of Ligands , 2010, J. Chem. Inf. Model..
[14] 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.
[15] S. Vajda,et al. Anchor residues in protein-protein interactions. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[16] H. Scheraga,et al. Statistical and energetic analysis of side-chain conformations in oligopeptides. , 2009, International journal of peptide and protein research.
[17] Rafael Najmanovich,et al. Side‐chain flexibility in proteins upon ligand binding , 2000, Proteins.
[18] Ilya A Vakser,et al. Side-chain conformational changes upon Protein-Protein Association. , 2010, Journal of molecular biology.
[19] Dominique Douguet,et al. DOCKGROUND system of databases for protein recognition studies: Unbound structures for docking , 2007, Proteins.
[20] C. Chothia,et al. The atomic structure of protein-protein recognition sites. , 1999, Journal of molecular biology.
[21] A. Lesk,et al. Structural mechanisms for domain movements in proteins. , 1994, Biochemistry.
[22] Z. Xiang,et al. On the role of the crystal environment in determining protein side-chain conformations. , 2002, Journal of molecular biology.
[23] M. Sternberg,et al. Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. , 1987, Journal of molecular biology.
[24] Laurie J. Heyer,et al. Exploring expression data: identification and analysis of coexpressed genes. , 1999, Genome research.
[25] A J Olson,et al. Analysis of a data set of paired uncomplexed protein structures: New metrics for side‐chain flexibility and model evaluation , 2001, Proteins.
[26] J. Richardson,et al. The penultimate rotamer library , 2000, Proteins.
[27] Roland L. Dunbrack. Rotamer libraries in the 21st century. , 2002, Current opinion in structural biology.
[28] J. Janin,et al. Dissecting protein–protein recognition sites , 2002, Proteins.
[29] Roland L Dunbrack,et al. Minimal ensembles of side chain conformers for modeling protein–protein interactions , 2012, Proteins.
[30] Roland L. Dunbrack,et al. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. , 1993, Journal of molecular biology.
[31] J. Ponder,et al. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. , 1987, Journal of molecular biology.
[32] 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.
[33] M. Sternberg,et al. An analysis of conformational changes on protein-protein association: implications for predictive docking. , 1999, Protein engineering.
[34] R. Lavery,et al. A new approach to the rapid determination of protein side chain conformations. , 1991, Journal of biomolecular structure & dynamics.
[35] S Vajda,et al. Dynamical view of the positions of key side chains in protein-protein recognition. , 2001, Biophysical journal.
[36] 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.
[37] Joël Janin,et al. Side‐chain rotamer transitions at protein‐protein interfaces , 2010, Proteins.
[38] David S. Goodsell,et al. A semiempirical free energy force field with charge‐based desolvation , 2007, J. Comput. Chem..
[39] I Lasters,et al. All in one: a highly detailed rotamer library improves both accuracy and speed in the modelling of sidechains by dead-end elimination. , 1997, Folding & design.
[40] Franz Kummert,et al. Comparing bound and unbound protein structures using energy calculation and rotamer statistics , 2002, Silico Biol..
[41] M. Gerstein,et al. Conformational changes associated with protein-protein interactions. , 2004, Current opinion in structural biology.
[42] G. N. Ramachandran,et al. Studies on the conformation of amino acids. XI. Analysis of the observed side group conformation in proteins. , 2009, International journal of protein research.
[43] M. Levitt,et al. Conformation of amino acid side-chains in proteins. , 1978, Journal of molecular biology.
[44] I. Bahar,et al. Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[45] Hidetoschi Kono,et al. A new method for side-chain conformation prediction using a Hopfield network and reproduced rotamers , 1996, J. Comput. Chem..
[46] P. Argos,et al. Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins. , 1993, Journal of molecular biology.