Burial Level Change Defines a High Energetic Relevance for Protein Binding Interfaces
暂无分享,去创建一个
Zhenhua Li | Jinyan Li | Ying He | Limsoon Wong | Jinyan Li | L. Wong | Zhenhua Li | Ying He
[1] C. Dominguez,et al. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. , 2003, Journal of the American Chemical Society.
[2] Michael Nilges,et al. Shelling the Voronoi interface of protein–protein complexes reveals patterns of residue conservation, dynamics, and composition , 2009, Proteins.
[3] L. Serrano,et al. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. , 2002, Journal of molecular biology.
[4] N. Ben-Tal,et al. Residue frequencies and pairing preferences at protein–protein interfaces , 2001, Proteins.
[5] Zhenhua Li,et al. DBAC: A simple prediction method for protein binding hot spots based on burial levels and deeply buried atomic contacts , 2011, BMC Systems Biology.
[6] J. Kirsch,et al. Energetic analysis of an antigen/antibody interface: Alanine scanning mutagenesis and double mutant cycles on the hyhel‐10/lysozyme interaction , 1999, Protein science : a publication of the Protein Society.
[7] Gerhard Hummer,et al. Interface-Resolved Network of Protein-Protein Interactions , 2013, PLoS Comput. Biol..
[8] Benjamin A. Shoemaker,et al. Correlated evolution of interacting proteins: looking behind the mirrortree. , 2009, Journal of molecular biology.
[9] H. Wolfson,et al. A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. , 1996, Journal of molecular biology.
[10] Huan‐Xiang Zhou,et al. Prediction of protein interaction sites from sequence profile and residue neighbor list , 2001, Proteins.
[11] T. Clackson,et al. A hot spot of binding energy in a hormone-receptor interface , 1995, Science.
[12] David L. Robertson,et al. Specificity in protein interactions and its relationship with sequence diversity and coevolution , 2007, Proceedings of the National Academy of Sciences.
[13] Z. Weng,et al. Protein–protein docking benchmark version 3.0 , 2008, Proteins.
[14] Haruki Nakamura,et al. Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: an exhaustive structural classification study. , 2010, Journal of molecular biology.
[15] F. Wilcoxon. Individual Comparisons by Ranking Methods , 1945 .
[16] Ozlem Keskin,et al. Similar binding sites and different partners: implications to shared proteins in cellular pathways. , 2007, Structure.
[17] M. Uhlén,et al. Mutational analysis of the interaction between staphylococcal protein A and human IgG1. , 1993, Protein engineering.
[18] J. Janin,et al. Dissecting protein–protein recognition sites , 2002, Proteins.
[19] B. Rost,et al. Analysing six types of protein-protein interfaces. , 2003, Journal of molecular biology.
[20] Tanja Kortemme,et al. Design of Multi-Specificity in Protein Interfaces , 2007, PLoS Comput. Biol..
[21] A. Bogan,et al. Anatomy of hot spots in protein interfaces. , 1998, Journal of molecular biology.
[22] A. Valencia,et al. Correlated mutations contain information about protein-protein interaction. , 1997, Journal of molecular biology.
[23] Huan-Xiang Zhou,et al. Prediction of interface residues in protein–protein complexes by a consensus neural network method: Test against NMR data , 2005, Proteins.
[24] Sarah A. Teichmann,et al. Principles of protein-protein interactions , 2002, ECCB.
[25] W. C. Still,et al. Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .
[26] Daniel R. Caffrey,et al. Are protein–protein interfaces more conserved in sequence than the rest of the protein surface? , 2004, Protein science : a publication of the Protein Society.
[27] Ozlem Keskin,et al. HotPoint: hot spot prediction server for protein interfaces , 2010, Nucleic Acids Res..
[28] T. Clackson,et al. Structural and functional analysis of the 1:1 growth hormone:receptor complex reveals the molecular basis for receptor affinity. , 1998, Journal of molecular biology.
[29] Jinyan Li,et al. Geometrically centered region: A “wet” model of protein binding hot spots not excluding water molecules , 2010, Proteins.
[30] H. Wolfson,et al. A new, structurally nonredundant, diverse data set of protein–protein interfaces and its implications , 2004, Protein science : a publication of the Protein Society.
[31] David E. Kim,et al. Computational Alanine Scanning of Protein-Protein Interfaces , 2004, Science's STKE.
[32] B. L. de Groot,et al. Predicting free energy changes using structural ensembles. , 2009, Nature methods.
[33] R. Nussinov,et al. Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues. , 2005, Journal of molecular biology.
[34] Oliviero Carugo,et al. Atom depth as a descriptor of the protein interior. , 2003, Biophysical journal.
[35] P. Bourne,et al. Exploiting sequence and structure homologs to identify protein–protein binding sites , 2005, Proteins.
[36] T. N. Bhat,et al. The Protein Data Bank , 2000, Nucleic Acids Res..
[37] Kurt S. Thorn,et al. ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions , 2001, Bioinform..
[38] Zoran Obradovic,et al. Statistical analysis of interface similarity in crystals of homologous proteins. , 2008, Journal of molecular biology.
[39] Doheon Lee,et al. A feature-based approach to modeling protein–protein interaction hot spots , 2009, Nucleic acids research.
[40] Michael Schroeder,et al. The Many Faces of Protein–Protein Interactions: A Compendium of Interface Geometry , 2006, PLoS Comput. Biol..
[41] GusfieldDan. Introduction to the IEEE/ACM Transactions on Computational Biology and Bioinformatics , 2004 .
[42] E. Levy. A simple definition of structural regions in proteins and its use in analyzing interface evolution. , 2010, Journal of molecular biology.
[43] J. Wells,et al. Comparison of a structural and a functional epitope. , 1993, Journal of molecular biology.
[44] R. Raz,et al. ProMate: a structure based prediction program to identify the location of protein-protein binding sites. , 2004, Journal of molecular biology.
[45] Carles Pons,et al. pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring , 2013, Bioinform..
[46] Stefan Günther,et al. Structural features and evolution of protein-protein interactions. , 2010, Genome informatics. International Conference on Genome Informatics.
[47] Alexandre M J J Bonvin,et al. Flexible protein-protein docking. , 2006, Current opinion in structural biology.
[48] Zhiping Weng,et al. Protein–protein docking benchmark version 4.0 , 2010, Proteins.
[49] Julie C. Mitchell,et al. KFC2: A knowledge‐based hot spot prediction method based on interface solvation, atomic density, and plasticity features , 2011, Proteins.
[50] Kei Yura,et al. The interwinding nature of protein–protein interfaces and its implication for protein complex formation , 2009, Bioinform..
[51] C. Chothia,et al. The atomic structure of protein-protein recognition sites. , 1999, Journal of molecular biology.
[52] G Schreiber,et al. Energetics of protein-protein interactions: analysis of the barnase-barstar interface by single mutations and double mutant cycles. , 1995, Journal of molecular biology.
[53] A. Kortt,et al. Effects of substitutions in the binding surface of an antibody on antigen affinity. , 1998, Protein engineering.
[54] Xing-Ming Zhao,et al. APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility , 2010, BMC Bioinformatics.
[55] Iain H. Moal,et al. Protein-protein binding affinity prediction on a diverse set of structures , 2011, Bioinform..
[56] Z. Weng,et al. Structure, function, and evolution of transient and obligate protein-protein interactions. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[57] H W Hellinga,et al. Dissection of the protein G B1 domain binding site for human IgG Fc fragment , 1999, Protein science : a publication of the Protein Society.
[58] Huan-Xiang Zhou,et al. Interaction-site prediction for protein complexes: a critical assessment , 2007, Bioinform..
[59] Julie C. Mitchell,et al. An automated decision‐tree approach to predicting protein interaction hot spots , 2007, Proteins.
[60] D. Baker,et al. A simple physical model for binding energy hot spots in protein–protein complexes , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[61] Oliviero Carugo,et al. DPX: for the analysis of the protein core , 2003, Bioinform..
[62] Ozlem Keskin,et al. Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy , 2009, Bioinform..