TY - JOUR AU - Krüger, D. M. AU - Gohlke, H. PY - 2010 DA - 2010// TI - Drugscoreppi webserver: fast and accurate in silico alanine scanning for scoring protein–protein interactions JO - Nucleic Acids Res. VL - 38 ID - Krüger2010 ER - TY - JOUR AU - Bradshaw, R. T. AU - Patel, B. H. AU - Tate, E. W. AU - Leatherbarrow, R. J. AU - Gould, I. R. PY - 2011 DA - 2011// TI - Comparing experimental and computational alanine scanning techniques for probing a prototypical protein–protein interaction JO - Protein Eng Des Sel. VL - 24 ID - Bradshaw2011 ER - TY - JOUR AU - Aloy, P. AU - Russell, R. B. PY - 2004 DA - 2004// TI - Ten thousand interactions for the molecular biologist JO - Nat Biotechnol. VL - 22 ID - Aloy2004 ER - TY - JOUR AU - Porollo, A. AU - Meller, J. PY - 2012 DA - 2012// TI - Computational methods for prediction of protein-protein interaction sites. JO - Protein-Protein Interactions-Computational and Experimental Tools; W. Cai and H. Hong, Eds. InTech. VL - 472 ID - Porollo2012 ER - TY - JOUR AU - Jones, S. AU - Thornton, J. M. PY - 1997 DA - 1997// TI - Analysis of protein-protein interaction sites using surface patches JO - J Mol Biol. VL - 272 ID - Jones1997 ER - TY - JOUR AU - Jones, S. AU - Thornton, J. M. PY - 1997 DA - 1997// TI - Prediction of protein-protein interaction sites using patch analysis JO - J Mol Biol. VL - 272 ID - Jones1997 ER - TY - JOUR AU - Chen, C. -. T. AU - Peng, H. -. P. AU - Jian, J. -. W. AU - Tsai, K. -. C. AU - Chang, J. -. Y. AU - Yang, E. -. W. PY - 2012 DA - 2012// TI - Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces JO - PloS one. VL - 7 ID - Chen2012 ER - TY - JOUR AU - Šikić, M. AU - Tomić, S. AU - Vlahoviček, K. PY - 2009 DA - 2009// TI - Prediction of protein–protein interaction sites in sequences and 3d structures by random forests JO - PLoS Comput Biol. VL - 5 ID - Šikić2009 ER - TY - JOUR AU - Fiorucci, S. AU - Zacharias, M. PY - 2010 DA - 2010// TI - Prediction of protein-protein interaction sites using electrostatic desolvation profiles JO - Biophys J. VL - 98 ID - Fiorucci2010 ER - TY - JOUR AU - Dosztányi, Z. AU - Mészáros, B. AU - Simon, I. PY - 2009 DA - 2009// TI - Anchor: web server for predicting protein binding regions in disordered proteins JO - Bioinformatics. VL - 25 ID - Dosztányi2009 ER - TY - JOUR AU - Martin, J. AU - Lavery, R. PY - 2012 DA - 2012// TI - Arbitrary protein- protein docking targets biologically relevant interfaces JO - BMC Biophys. VL - 5 ID - Martin2012 ER - TY - JOUR AU - La, D. AU - Kihara, D. PY - 2012 DA - 2012// TI - A novel method for protein–protein interaction site prediction using phylogenetic substitution models JO - Proteins: Struct Funct Bioinform. VL - 80 ID - La2012 ER - TY - JOUR AU - Bradford, J. R. AU - Westhead, D. R. PY - 2005 DA - 2005// TI - Improved prediction of protein–protein binding sites using a support vector machines approach JO - Bioinformatics. VL - 21 ID - Bradford2005 ER - TY - JOUR AU - Chen, X. -. W. AU - Jeong, J. C. PY - 2009 DA - 2009// TI - Sequence-based prediction of protein interaction sites with an integrative method JO - Bioinformatics. VL - 25 ID - Chen2009 ER - TY - JOUR AU - Chung, J. -. L. AU - Wang, W. AU - Bourne, P. E. PY - 2006 DA - 2006// TI - Exploiting sequence and structure homologs to identify protein–protein binding sites JO - Proteins: Struct Funct Bioinform. VL - 62 ID - Chung2006 ER - TY - JOUR AU - Chen, H. AU - Zhou, H. -. X. PY - 2005 DA - 2005// TI - Prediction of interface residues in protein–protein complexes by a consensus neural network method: test against nmr data JO - Proteins: Struct Funct Bioinform. VL - 61 ID - Chen2005 ER - TY - JOUR AU - de Vries, S. J. AU - Bonvin, A. M. PY - 2011 DA - 2011// TI - Cport: a consensus interface predictor and its performance in prediction-driven docking with haddock JO - PLoS One. VL - 6 ID - de Vries2011 ER - TY - JOUR AU - Dong, Q. AU - Wang, X. AU - Lin, L. AU - Guan, Y. PY - 2007 DA - 2007// TI - Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins JO - BMC Bioinform. VL - 8 ID - Dong2007 ER - TY - JOUR AU - Fernández-Recio, J. AU - Totrov, M. AU - Abagyan, R. PY - 2004 DA - 2004// TI - Identification of protein–protein interaction sites from docking energy landscapes JO - J Mol Biol. VL - 335 ID - Fernández-Recio2004 ER - TY - JOUR AU - Xue, L. C. AU - Dobbs, D. AU - Honavar, V. PY - 2011 DA - 2011// TI - Homppi: a class of sequence homology based protein-protein interface prediction methods JO - BMC Bioinform. VL - 12 ID - Xue2011 ER - TY - JOUR AU - Shoemaker, B. A. AU - Zhang, D. AU - Thangudu, R. R. AU - Tyagi, M. AU - Fong, J. H. AU - Marchler-Bauer, A. PY - 2009 DA - 2009// TI - Inferred biomolecular interaction server—a web server to analyze and predict protein interacting partners and binding sites JO - Nucleic Acids Res. VL - 38 ID - Shoemaker2009 ER - TY - JOUR AU - Ofran, Y. AU - Rost, B. PY - 2007 DA - 2007// TI - Isis: interaction sites identified from sequence JO - Bioinformatics. VL - 23 ID - Ofran2007 ER - TY - JOUR AU - Engelen, S. AU - Trojan, L. A. AU - Sacquin-Mora, S. AU - Lavery, R. AU - Carbone, A. PY - 2009 DA - 2009// TI - Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling JO - PLoS Comput Biol. VL - 5 ID - Engelen2009 ER - TY - JOUR AU - Huang, B. AU - Schroeder, M. PY - 2008 DA - 2008// TI - Using protein binding site prediction to improve protein docking JO - Gene. VL - 422 ID - Huang2008 ER - TY - JOUR AU - Qin, S. AU - Zhou, H. -. X. PY - 2007 DA - 2007// TI - meta-ppisp: a meta web server for protein-protein interaction site prediction JO - Bioinformatics. VL - 23 ID - Qin2007 ER - TY - JOUR AU - Tjong, H. AU - Qin, S. AU - Zhou, H. -. X. PY - 2007 DA - 2007// TI - Pi2pe: protein interface/interior prediction engine JO - Nucleic Acids Res. VL - 35 ID - Tjong2007 ER - TY - JOUR AU - Kufareva, I. AU - Budagyan, L. AU - Raush, E. AU - Totrov, M. AU - Abagyan, R. PY - 2007 DA - 2007// TI - Pier: protein interface recognition for structural proteomics JO - Proteins: Struct Funct Bioinform. VL - 67 ID - Kufareva2007 ER - TY - JOUR AU - Liang, S. AU - Zhang, C. AU - Liu, S. AU - Zhou, Y. PY - 2006 DA - 2006// TI - Protein binding site prediction using an empirical scoring function JO - Nucleic Acids Res. VL - 34 ID - Liang2006 ER - TY - JOUR AU - Li, M. -. H. AU - Lin, L. AU - Wang, X. -. L. AU - Liu, T. PY - 2007 DA - 2007// TI - Protein–protein interaction site prediction based on conditional random fields JO - Bioinformatics. VL - 23 ID - Li2007 ER - TY - JOUR AU - Zhou, H. -. X. AU - Shan, Y. PY - 2001 DA - 2001// TI - Prediction of protein interaction sites from sequence profile and residue neighbor list JO - Proteins: Struct Funct Bioinform. VL - 44 ID - Zhou2001 ER - TY - JOUR AU - Zhang, Q. C. AU - Petrey, D. AU - Norel, R. AU - Honig, B. H. PY - 2010 DA - 2010// TI - Protein interface conservation across structure space JO - Proc Nat Acad Sci. VL - 107 ID - Zhang2010 ER - TY - STD TI - Zhang QC, Deng L, Fisher M, Guan J, Honig B, Petrey D. Predus: a web server for predicting protein interfaces using structural neighbors. Nucleic Acids Res. suppl 2; 39:283–7. ID - ref32 ER - TY - JOUR AU - Zellner, H. AU - Staudigel, M. AU - Trenner, T. AU - Bittkowski, M. AU - Wolowski, V. PY - 2012 DA - 2012// TI - Prescont: Predicting protein-protein interfaces utilizing four residue properties JO - Proteins: Struct Funct Bioinform. VL - 80 ID - Zellner2012 ER - TY - JOUR AU - Jordan, R. A. AU - Yasser, E. -. M. AU - Dobbs, D. AU - Honavar, V. PY - 2012 DA - 2012// TI - Predicting protein-protein interface residues using local surface structural similarity JO - BMC Bioinformatics. VL - 13 ID - Jordan2012 ER - TY - JOUR AU - Neuvirth, H. AU - Raz, R. AU - Schreiber, G. PY - 2004 DA - 2004// TI - Promate: a structure based prediction program to identify the location of protein–protein binding sites JO - J Mol Biol. VL - 338 ID - Neuvirth2004 ER - TY - JOUR AU - Murakami, Y. AU - Mizuguchi, K. PY - 2010 DA - 2010// TI - Applying the naïve bayes classifier with kernel density estimation to the prediction of protein–protein interaction sites JO - Bioinformatics. VL - 26 ID - Murakami2010 ER - TY - JOUR AU - Bendell, C. J. AU - Liu, S. AU - Aumentado-Armstrong, T. AU - Istrate, B. AU - Cernek, P. T. AU - Khan, S. PY - 2014 DA - 2014// TI - Transient protein-protein interface prediction: datasets, features, algorithms, and the rad-t predictor JO - BMC Bioinformatics. VL - 15 ID - Bendell2014 ER - TY - JOUR AU - Li, B. -. Q. AU - Feng, K. -. Y. AU - Chen, L. AU - Huang, T. AU - Cai, Y. -. D. PY - 2012 DA - 2012// TI - Prediction of protein-protein interaction sites by random forest algorithm with mrmr and ifs JO - PloS one. VL - 7 ID - Li2012 ER - TY - JOUR AU - Porollo, A. AU - Meller, J. PY - 2007 DA - 2007// TI - Prediction-based fingerprints of protein–protein interactions JO - PROTEINS: Structure Function Bioinform. VL - 66 ID - Porollo2007 ER - TY - JOUR AU - Segura, J. AU - Jones, P. F. AU - Fernandez-Fuentes, N. PY - 2011 DA - 2011// TI - Improving the prediction of protein binding sites by combining heterogeneous data and voronoi diagrams JO - BMC Bioinformatics. VL - 12 ID - Segura2011 ER - TY - JOUR AU - de Vries, S. J. AU - van Dijk, A. D. AU - Bonvin, A. M. PY - 2006 DA - 2006// TI - Whiscy: What information does surface conservation yield? application to data-driven docking JO - Proteins: Struct Funct Bioinform. VL - 63 ID - de Vries2006 ER - TY - JOUR AU - de Moraes, F. R. AU - Neshich, I. A. AU - Mazoni, I. AU - Yano, I. H. AU - Pereira, J. G. AU - Salim, J. A. PY - 2014 DA - 2014// TI - Improving predictions of protein-protein interfaces by combining amino acid-specific classifiers based on structural and physicochemical descriptors with their weighted neighbor averages JO - PloS One. VL - 9 ID - de Moraes2014 ER - TY - JOUR AU - Qiu, Z. AU - Wang, X. PY - 2012 DA - 2012// TI - Prediction of protein–protein interaction sites using patch-based residue characterization JO - J Theor Biol. VL - 293 ID - Qiu2012 ER - TY - STD TI - Janin J. Basic principles of protein–protein interaction. Computational protein–protein interactions, 2009:1–20. ID - ref44 ER - TY - STD TI - Alberts B, Johnson A, Raff M, Roberts K, Walter P. Molecular biology of the cell. 2008. ID - ref45 ER - TY - JOUR AU - Keskin, O. AU - Gursoy, A. AU - Ma, B. AU - Nussinov, R. PY - 2008 DA - 2008// TI - Principles of protein-protein interactions: what are the preferred ways for proteins to interact? JO - Chem Rev. VL - 108 ID - Keskin2008 ER - TY - BOOK PY - 2010 DA - 2010// TI - Computational Protein-protein Interactions PB - CRC Press CY - Boca Raton, FL, USA ID - ref47 ER - TY - JOUR AU - Nooren, I. AU - Thornton, J. M. PY - 2003 DA - 2003// TI - Diversity of protein–protein interactions JO - EMBO J. VL - 22 ID - Nooren2003 ER - TY - JOUR AU - Ozbabacan, S. E. A. AU - Engin, H. B. AU - Gursoy, A. AU - Keskin, O. PY - 2011 DA - 2011// TI - Transient protein–protein interactions JO - Protein Eng Des Sel. VL - 24 ID - Ozbabacan2011 ER - TY - STD TI - Amoutzias G, de Peer Y. Single-gene and whole-genome duplications and the evolution of protein-protein interaction networks. Evol Genomics Syst Biol. 2010:413–29. ID - ref50 ER - TY - JOUR AU - Perkins, J. R. AU - Diboun, I. AU - Dessailly, B. H. AU - Lees, J. G. AU - Orengo, C. PY - 2010 DA - 2010// TI - Transient protein-protein interactions: structural, functional, and network properties JO - Structure. VL - 18 ID - Perkins2010 ER - TY - JOUR AU - La, D. AU - Kong, M. AU - Hoffman, W. AU - Choi, Y. I. AU - Kihara, D. PY - 2013 DA - 2013// TI - Predicting permanent and transient protein–protein interfaces JO - Proteins: Struct Funct Bioinform. VL - 81 ID - La2013 ER - TY - JOUR AU - Fernandez-Recio, J. AU - Totrov, M. AU - Skorodumov, C. AU - Abagyan, R. PY - 2005 DA - 2005// TI - Optimal docking area: a new method for predicting protein–protein interaction sites JO - PROTEINS: Struct Funct Bioinform. VL - 58 ID - Fernandez-Recio2005 ER - TY - JOUR AU - Liu, R. AU - Jiang, W. AU - Zhou, Y. PY - 2010 DA - 2010// TI - Identifying protein–protein interaction sites in transient complexes with temperature factor, sequence profile and accessible surface area JO - Amino Acids. VL - 38 ID - Liu2010 ER - TY - JOUR AU - Choi, Y. S. AU - Yang, J. -. S. AU - Choi, Y. AU - Ryu, S. H. AU - Kim, S. PY - 2009 DA - 2009// TI - Evolutionary conservation in multiple faces of protein interaction JO - Proteins: Struct Funct Bioinform. VL - 77 ID - Choi2009 ER - TY - JOUR AU - Phizicky, E. M. AU - Fields, S. PY - 1995 DA - 1995// TI - Protein-protein interactions: methods for detection and analysis JO - Microbiol Rev. VL - 59 ID - Phizicky1995 ER - TY - JOUR AU - Chichili, V. AU - Kumar, V. AU - Sivaraman, J. PY - 2013 DA - 2013// TI - A method to trap transient and weak interacting protein complexes for structural studies JO - Intrinsically Disordered. VL - 1 ID - Chichili2013 ER - TY - JOUR AU - Tuncbag, N. AU - Gursoy, A. AU - Keskin, O. PY - 2011 DA - 2011// TI - Prediction of protein–protein interactions: unifying evolution and structure at protein interfaces JO - Phys Biol. VL - 8 ID - Tuncbag2011 ER - TY - JOUR AU - Sprinzak, E. AU - Altuvia, Y. AU - Margalit, H. PY - 2006 DA - 2006// TI - Characterization and prediction of protein–protein interactions within and between complexes JO - Proc Nat Acad Sci. VL - 103 ID - Sprinzak2006 ER - TY - JOUR AU - Mintseris, J. AU - Weng, Z. PY - 2005 DA - 2005// TI - Structure, function, and evolution of transient and obligate protein–protein interactions JO - Proc Nat Acad Sci USA. VL - 102 ID - Mintseris2005 ER - TY - JOUR AU - Brown, K. R. AU - Jurisica, I. PY - 2007 DA - 2007// TI - Unequal evolutionary conservation of human protein interactions in interologous networks JO - Genome Biol. VL - 8 ID - Brown2007 ER - TY - JOUR AU - Mihalek, I. AU - Reš, I. AU - Lichtarge, O. PY - 2007 DA - 2007// TI - On itinerant water molecules and detectability of protein–protein interfaces through comparative analysis of homologues JO - J Mol Biol. VL - 369 ID - Mihalek2007 ER - TY - JOUR AU - Levy, Y. AU - Onuchic, J. N. PY - 2006 DA - 2006// TI - Water mediation in protein folding and molecular recognition JO - Annu Rev Biophys Biomol Struct. VL - 35 ID - Levy2006 ER - TY - JOUR AU - Conte, L. L. AU - Chothia, C. AU - Janin, J. PY - 1999 DA - 1999// TI - The atomic structure of protein-protein recognition sites JO - J Mol Biol. VL - 285 ID - Conte1999 ER - TY - JOUR AU - Nooren, I. AU - Thornton, J. M. PY - 2003 DA - 2003// TI - Structural characterisation and functional significance of transient protein–protein interactions JO - J Mol Biol. VL - 325 ID - Nooren2003 ER - TY - JOUR AU - Carl, N. AU - Konc, J. AU - Janezic, D. PY - 2008 DA - 2008// TI - Protein surface conservation in binding sites JO - J Chem Inform Model. VL - 48 ID - Carl2008 ER - TY - JOUR AU - Zhu, H. AU - Domingues, F. S. AU - Sommer, I. AU - Lengauer, T. PY - 2006 DA - 2006// TI - Noxclass: prediction of protein-protein interaction types JO - BMC Bioinformatics. VL - 7 ID - Zhu2006 ER - TY - JOUR AU - Aziz, M. AU - Maleki, M. AU - Rueda, L. AU - Raza, M. AU - Banerjee, S. PY - 2011 DA - 2011// TI - Prediction of biological protein–protein interactions using atom-type and amino acid properties JO - Proteomics. VL - 11 ID - Aziz2011 ER - TY - JOUR AU - Maleki, M. AU - Vasudev, G. AU - Rueda, L. PY - 2013 DA - 2013// TI - The role of electrostatic energy in prediction of obligate protein-protein interactions JO - Proteome Sci. VL - 11 ID - Maleki2013 ER - TY - JOUR AU - Guharoy, M. AU - Chakrabarti, P. PY - 2005 DA - 2005// TI - Conservation and relative importance of residues across protein-protein interfaces JO - Proc Nat Acad Sci USA. VL - 102 ID - Guharoy2005 ER - TY - JOUR AU - Larsen, T. A. AU - Olson, A. J. AU - Goodsell, D. S. PY - 1998 DA - 1998// TI - Morphology of protein–protein interfaces JO - Structure. VL - 6 ID - Larsen1998 ER - TY - JOUR AU - Chakrabarti, P. AU - Janin, J. PY - 2002 DA - 2002// TI - Dissecting protein–protein recognition sites JO - Proteins: Struct Funct Bioinform. VL - 47 ID - Chakrabarti2002 ER - TY - JOUR AU - Karanicolas, J. AU - Corn, J. E. AU - Chen, I. AU - Joachimiak, L. A. AU - Dym, O. AU - Peck, S. H. PY - 2011 DA - 2011// TI - A de novo protein binding pair by computational design and directed evolution JO - Molecular cell. VL - 42 ID - Karanicolas2011 ER - TY - JOUR AU - Truong, K. AU - Ikura, M. PY - 2001 DA - 2001// TI - The use of fret imaging microscopy to detect protein–protein interactions and protein conformational changes in vivo JO - Current Opin Struct Biol. VL - 11 ID - Truong2001 ER - TY - JOUR AU - Ezkurdia, I. AU - Bartoli, L. AU - Fariselli, P. AU - Casadio, R. AU - Valencia, A. AU - Tress, M. L. PY - 2009 DA - 2009// TI - Progress and challenges in predicting protein–protein interaction sites JO - Brief Bioinformatics. VL - 30 ID - Ezkurdia2009 ER - TY - JOUR AU - Janin, J. AU - Bahadur, R. P. AU - Chakrabarti, P. PY - 2008 DA - 2008// TI - Protein–protein interaction and quaternary structure JO - Q Rev Biophys. VL - 41 ID - Janin2008 ER - TY - JOUR AU - Hwang, H. AU - Pierce, B. AU - Mintseris, J. AU - Janin, J. AU - Weng, Z. PY - 2008 DA - 2008// TI - Protein–protein docking benchmark version 3.0 JO - Proteins: Struct Funct Bioinform. VL - 73 ID - Hwang2008 ER - TY - JOUR AU - Janin, J. AU - Wodak, S. PY - 2007 DA - 2007// TI - The third capri assessment meeting toronto, canada, april 20–21, 2007 JO - Structure. VL - 15 ID - Janin2007 ER - TY - JOUR AU - Bernstein, F. C. AU - Koetzle, T. F. AU - Williams, G. J. AU - Meyer EF, J. r. AU - Brice, M. D. AU - Rodgers, J. R. PY - 1978 DA - 1978// TI - The protein data bank: a computer-based archival file for macromolecular structures JO - Arch Biochem Biophys. VL - 185 ID - Bernstein1978 ER - TY - JOUR AU - Ofran, Y. AU - Rost, B. PY - 2003 DA - 2003// TI - Analysing six types of protein–protein interfaces JO - J Mol Biol. VL - 325 ID - Ofran2003 ER - TY - JOUR AU - Henrick, K. AU - Thornton, J. M. PY - 1998 DA - 1998// TI - Pqs: a protein quaternary structure file server JO - Trends Biochem Sci. VL - 23 ID - Henrick1998 ER - TY - JOUR AU - Krissinel, E. AU - Henrick, K. PY - 2007 DA - 2007// TI - Inference of macromolecular assemblies from crystalline state JO - J Mol Biol. VL - 372 ID - Krissinel2007 ER - TY - JOUR AU - Krissinel, E. PY - 2010 DA - 2010// TI - Crystal contacts as nature’s docking solutions JO - J Comput Chem. VL - 31 ID - Krissinel2010 ER - TY - JOUR AU - Altschul, S. F. AU - Gish, W. AU - Miller, W. AU - Myers, E. W. AU - Lipman, D. J. PY - 1990 DA - 1990// TI - Basic local alignment search tool JO - J Mol Biol. VL - 215 ID - Altschul1990 ER - TY - JOUR AU - Wang, G. AU - Dunbrack, R. L. PY - 2003 DA - 2003// TI - Pisces: a protein sequence culling server JO - Bioinformatics. VL - 19 ID - Wang2003 ER - TY - JOUR AU - Wang, G. AU - Dunbrack, R. L. PY - 2005 DA - 2005// TI - Pisces: recent improvements to a pdb sequence culling server JO - Nucleic Acids Res. VL - 33 ID - Wang2005 ER - TY - JOUR AU - Li, W. AU - Godzik, A. PY - 2006 DA - 2006// TI - Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences JO - Bioinformatics. VL - 22 ID - Li2006 ER - TY - JOUR AU - Huang, Y. AU - Niu, B. AU - Gao, Y. AU - Fu, L. AU - Li, W. PY - 2010 DA - 2010// TI - Cd-hit suite: a web server for clustering and comparing biological sequences JO - Bioinformatics. VL - 26 ID - Huang2010 ER - TY - JOUR AU - Murzin, A. G. AU - Brenner, S. E. AU - Hubbard, T. AU - Chothia, C. PY - 1995 DA - 1995// TI - Scop: a structural classification of proteins database for the investigation of sequences and structures JO - J Mol Biol. VL - 247 ID - Murzin1995 ER - TY - JOUR AU - Andreeva, A. AU - Howorth, D. AU - Brenner, S. E. AU - Hubbard, T. J. AU - Chothia, C. AU - Murzin, A. G. PY - 2004 DA - 2004// TI - Scop database in 2004: refinements integrate structure and sequence family data JO - Nucleic Acids Res. VL - 32 ID - Andreeva2004 ER - TY - STD TI - Jordan R, Wu F, Dobbs D, Honavar V. Protindb: A database of protein-protein interface residues. Iowa State University (In Preparation) ID - ref91 ER - TY - JOUR AU - Bickerton, G. R. AU - Higueruelo, A. P. AU - Blundell, T. L. PY - 2011 DA - 2011// TI - Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the piccolo database JO - BMC Bioinformatics. VL - 12 ID - Bickerton2011 ER - TY - JOUR AU - Smialowski, P. AU - Pagel, P. AU - Wong, P. AU - Brauner, B. AU - Dunger, I. AU - Fobo, G. PY - 2010 DA - 2010// TI - The negatome database: a reference set of non-interacting protein pairs JO - Nucleic Acids Res. VL - 38 ID - Smialowski2010 ER - TY - JOUR AU - Finn, R. D. AU - Marshall, M. AU - Bateman, A. PY - 2005 DA - 2005// TI - ipfam: visualization of protein–protein interactions in pdb at domain and amino acid resolutions JO - Bioinformatics. VL - 21 ID - Finn2005 ER - TY - JOUR AU - Finn, R. D. AU - Miller, B. L. AU - Clements, J. AU - Bateman, A. PY - 2014 DA - 2014// TI - ipfam: a database of protein family and domain interactions found in the protein data bank JO - Nucleic Acids Res. VL - 42 ID - Finn2014 ER - TY - JOUR AU - Stein, A. AU - Russell, R. B. AU - Aloy, P. PY - 2005 DA - 2005// TI - 3did: interacting protein domains of known three-dimensional structure JO - Nucleic Acids Res. VL - 33 ID - Stein2005 ER - TY - JOUR AU - Consortium, U. PY - 2013 DA - 2013// TI - Update on activities at the universal protein resource (uniprot) in 2013 JO - Nucleic Acids Res. VL - 41 ID - Consortium2013 ER - TY - JOUR AU - Martin, A. C. PY - 2005 DA - 2005// TI - Mapping pdb chains to uniprotkb entries JO - Bioinformatics. VL - 21 ID - Martin2005 ER - TY - JOUR AU - Schneider, M. AU - Fu, X. AU - Keating, A. E. PY - 2009 DA - 2009// TI - X-ray vs. nmr structures as templates for computational protein design JO - Proteins: Struct Funct Bioinform. VL - 77 ID - Schneider2009 ER - TY - JOUR AU - Fan, H. AU - Mark, A. E. PY - 2003 DA - 2003// TI - Relative stability of protein structures determined by x-ray crystallography or nmr spectroscopy: A molecular dynamics simulation study JO - PROTEINS: Struct Funct Bioinform. VL - 53 ID - Fan2003 ER - TY - JOUR AU - Lee, M. R. AU - Kollman, P. A. PY - 2001 DA - 2001// TI - Free-energy calculations highlight differences in accuracy between x-ray and nmr structures and add value to protein structure prediction JO - Structure. VL - 9 ID - Lee2001 ER - TY - JOUR AU - Jones, S. AU - Thornton, J. M. PY - 1996 DA - 1996// TI - Principles of protein-protein interactions JO - Proc Nat Acad Sci. VL - 93 ID - Jones1996 ER - TY - JOUR AU - Martin, J. PY - 2014 DA - 2014// TI - Benchmarking protein–protein interface predictions: Why you should care about protein size JO - Proteins: Struct Funct Bioinform. VL - 82 ID - Martin2014 ER - TY - JOUR AU - Tuncbag, N. AU - Kar, G. AU - Keskin, O. AU - Gursoy, A. AU - Nussinov, R. PY - 2009 DA - 2009// TI - A survey of available tools and web servers for analysis of protein–protein interactions and interfaces JO - Briefings Bioinform. VL - 10 ID - Tuncbag2009 ER - TY - JOUR AU - Fernández-Recio, J. PY - 2011 DA - 2011// TI - Prediction of protein binding sites and hot spots JO - Wiley Interdiscip Rev Comput Mol Sci. VL - 1 ID - Fernández-Recio2011 ER - TY - JOUR AU - Chen, R. AU - Mintseris, J. AU - Janin, J. AU - Weng, Z. PY - 2003 DA - 2003// TI - A protein–protein docking benchmark JO - Proteins: Struct Funct Bioinform. VL - 52 ID - Chen2003 ER - TY - JOUR AU - Mintseris, J. AU - Wiehe, K. AU - Pierce, B. AU - Anderson, R. AU - Chen, R. AU - Janin, J. PY - 2005 DA - 2005// TI - Protein–protein docking benchmark 2.0: an update JO - Proteins: Struct Funct Bioinform. VL - 60 ID - Mintseris2005 ER - TY - JOUR AU - Hwang, H. AU - Vreven, T. AU - Janin, J. AU - Weng, Z. PY - 2010 DA - 2010// TI - Protein–protein docking benchmark version 4.0 JO - Proteins: Struct Funct Bioinform. VL - 78 ID - Hwang2010 ER - TY - JOUR AU - Zhou, H. -. X. AU - Qin, S. PY - 2007 DA - 2007// TI - Interaction-site prediction for protein complexes: a critical assessment JO - Bioinformatics. VL - 23 ID - Zhou2007 ER - TY - JOUR AU - Mintz, S. AU - Shulman-Peleg, A. AU - Wolfson, H. J. AU - Nussinov, R. PY - 2005 DA - 2005// TI - Generation and analysis of a protein–protein interface data set with similar chemical and spatial patterns of interactions JO - Proteins: Struct Funct Bioinform. VL - 61 ID - Mintz2005 ER - TY - JOUR AU - Lensink, M. F. AU - Wodak, S. J. PY - 2010 DA - 2010// TI - Blind predictions of protein interfaces by docking calculations in capri JO - Proteins: Struct Funct Bioinform. VL - 78 ID - Lensink2010 ER - TY - JOUR AU - Stein, A. AU - Céol, A. AU - Aloy, P. PY - 2011 DA - 2011// TI - 3did: identification and classification of domain-based interactions of known three-dimensional structure JO - Nucleic Acids Res. VL - 39 ID - Stein2011 ER - TY - JOUR AU - Mészáros, B. AU - Simon, I. AU - Dosztányi, Z. PY - 2009 DA - 2009// TI - Prediction of protein binding regions in disordered proteins JO - PLoS Comput Biol. VL - 5 ID - Mészáros2009 ER - TY - JOUR AU - Kawashima, S. AU - Kanehisa, M. PY - 2000 DA - 2000// TI - Aaindex: amino acid index database JO - Nucleic Acids Res. VL - 28 ID - Kawashima2000 ER - TY - JOUR AU - Kawashima, S. AU - Pokarowski, P. AU - Pokarowska, M. AU - Kolinski, A. AU - Katayama, T. AU - Kanehisa, M. PY - 2008 DA - 2008// TI - Aaindex: amino acid index database, progress report 2008 JO - Nucleic Acids Res. VL - 36 ID - Kawashima2008 ER - TY - JOUR AU - Neshich, G. AU - Mazoni, I. AU - Oliveira, S. AU - Yamagishi, M. AU - Kuser-Falcão, P. AU - Borro, L. PY - 2005 DA - 2005// TI - The star sting server: a multiplatform environment for protein structure analysis JO - Genet Mol Res GMR. VL - 5 ID - Neshich2005 ER - TY - JOUR AU - Mihel, J. AU - Šikić, M. AU - Tomić, S. AU - Jeren, B. AU - Vlahoviček, K. PY - 2008 DA - 2008// TI - Psaia–protein structure and interaction analyzer JO - BMC Struct Biol. VL - 8 ID - Mihel2008 ER - TY - JOUR AU - Tsodikov, O. V. AU - Record, M. T. AU - Sergeev, Y. V. PY - 2002 DA - 2002// TI - Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature JO - J Comput Chem. VL - 23 ID - Tsodikov2002 ER - TY - JOUR AU - Kabsch, W. AU - Sander, C. PY - 1983 DA - 1983// TI - Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features JO - Biopolymers. VL - 22 ID - Kabsch1983 ER - TY - STD TI - Hubbard SJ, Thornton JM. Naccess. Computer Program, Department of Biochemistry and Molecular Biology, University College London. 1993;2(1). ID - ref120 ER - TY - JOUR AU - Hildebrandt, A. AU - Dehof, A. K. AU - Rurainski, A. AU - Bertsch, A. AU - Schumann, M. AU - Toussaint, N. C. PY - 2010 DA - 2010// TI - Ball-biochemical algorithms library 1.3 JO - BMC Bioinformatics. VL - 11 ID - Hildebrandt2010 ER - TY - JOUR AU - Cheng, J. AU - Randall, A. Z. AU - Sweredoski, M. J. AU - Baldi, P. PY - 2005 DA - 2005// TI - Scratch: a protein structure and structural feature prediction server JO - Nucleic Acids Res. VL - 33 ID - Cheng2005 ER - TY - JOUR AU - Sanner, M. F. AU - Olson, A. J. AU - Spehner, J. -. C. PY - 1996 DA - 1996// TI - Reduced surface: an efficient way to compute molecular surfaces JO - Biopolymers. VL - 38 ID - Sanner1996 ER - TY - JOUR AU - Hoskins, J. AU - Lovell, S. AU - Blundell, T. L. PY - 2006 DA - 2006// TI - An algorithm for predicting protein–protein interaction sites: abnormally exposed amino acid residues and secondary structure elements JO - Protein Sci. VL - 15 ID - Hoskins2006 ER - TY - JOUR AU - Sander, C. AU - Schneider, R. PY - 1991 DA - 1991// TI - Database of homology-derived protein structures and the structural meaning of sequence alignment JO - Proteins: Struct Funct Bioinform. VL - 9 ID - Sander1991 ER - TY - JOUR AU - Dodge, C. AU - Schneider, R. AU - Sander, C. PY - 1998 DA - 1998// TI - The hssp database of protein structure—sequence alignments and family profiles JO - Nucleic Acids Res. VL - 26 ID - Dodge1998 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schäffer, A. A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. PY - 1997 DA - 1997// TI - Gapped blast and psi-blast: a new generation of protein database search programs JO - Nucleic Acids Res. VL - 25 ID - Altschul1997 ER - TY - JOUR AU - Valdar, W. S. PY - 2002 DA - 2002// TI - Scoring residue conservation JO - Proteins: Struct Funct Bioinform. VL - 48 ID - Valdar2002 ER - TY - JOUR AU - Pupko, T. AU - Bell, R. E. AU - Mayrose, I. AU - Glaser, F. AU - Ben-Tal, N. PY - 2002 DA - 2002// TI - Rate4site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues JO - Bioinformatics. VL - 18 ID - Pupko2002 ER - TY - JOUR AU - Pei, J. AU - Grishin, N. V. PY - 2001 DA - 2001// TI - Al2co: calculation of positional conservation in a protein sequence alignment JO - Bioinformatics. VL - 17 ID - Pei2001 ER - TY - JOUR AU - Pintar, A. AU - Carugo, O. AU - Pongor, S. PY - 2003 DA - 2003// TI - Dpx: for the analysis of the protein core JO - Bioinformatics. VL - 19 ID - Pintar2003 ER - TY - JOUR AU - Pintar, A. AU - Carugo, O. AU - Pongor, S. PY - 2002 DA - 2002// TI - Cx, an algorithm that identifies protruding atoms in proteins JO - Bioinformatics. VL - 18 ID - Pintar2002 ER - TY - JOUR AU - Lijnzaad, P. AU - Berendsen, H. J. AU - Argos, P. PY - 1996 DA - 1996// TI - A method for detecting hydrophobic patches on protein surfaces JO - Proteins: Struct Funct Bioinform. VL - 26 ID - Lijnzaad1996 ER - TY - JOUR AU - Fauchere, J. AU - Pliska, V. PY - 1983 DA - 1983// TI - Hydrophobic parameters-pi of amino-acid side-chains from the partitioning of n-acetyl-amino-acid amides JO - Eur J Med Chem. VL - 18 ID - Fauchere1983 ER - TY - JOUR AU - Crowley, P. B. AU - Golovin, A. PY - 2005 DA - 2005// TI - Cation– π interactions in protein–protein interfaces JO - Proteins: Struct Funct Bioinform. VL - 59 ID - Crowley2005 ER - TY - JOUR AU - Sillerud, L. O. AU - Larson, R. S. PY - 2005 DA - 2005// TI - Design and structure of peptide and peptidomimetic antagonists of protein-protein interaction JO - Current Protein Peptide Sci. VL - 6 ID - Sillerud2005 ER - TY - JOUR AU - Levy, E. D. PY - 2010 DA - 2010// TI - A simple definition of structural regions in proteins and its use in analyzing interface evolution JO - J Mol Biol. VL - 403 ID - Levy2010 ER - TY - JOUR AU - Peng, K. AU - Radivojac, P. AU - Vucetic, S. AU - Dunker, A. K. AU - Obradovic, Z. PY - 2006 DA - 2006// TI - Length-dependent prediction of protein intrinsic disorder JO - BMC Bioinformatics. VL - 7 ID - Peng2006 ER - TY - JOUR AU - Yang, Z. R. AU - Thomson, R. AU - McNeil, P. AU - Esnouf, R. M. PY - 2005 DA - 2005// TI - Ronn: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins JO - Bioinformatics. VL - 21 ID - Yang2005 ER - TY - JOUR AU - Wright, P. E. AU - Dyson, H. J. PY - 1999 DA - 1999// TI - Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm JO - J Mol Biol. VL - 293 ID - Wright1999 ER - TY - JOUR AU - Dunker, A. K. AU - Brown, C. J. AU - Lawson, J. D. AU - Iakoucheva, L. M. AU - Obradovic, Z. PY - 2002 DA - 2002// TI - Intrinsic disorder and protein function JO - Biochemistry. VL - 41 ID - Dunker2002 ER - TY - JOUR AU - Liu, J. AU - Tan, H. AU - Rost, B. PY - 2002 DA - 2002// TI - Loopy proteins appear conserved in evolution JO - J Mol Biol. VL - 322 ID - Liu2002 ER - TY - JOUR AU - Iakoucheva, L. M. AU - Brown, C. J. AU - Lawson, J. D. AU - Obradović, Z. AU - Dunker, A. K. PY - 2002 DA - 2002// TI - Intrinsic disorder in cell-signaling and cancer-associated proteins JO - J Mol Biol. VL - 323 ID - Iakoucheva2002 ER - TY - JOUR AU - Coleman, R. G. AU - Burr, M. A. AU - Souvaine, D. L. AU - Cheng, A. C. PY - 2005 DA - 2005// TI - An intuitive approach to measuring protein surface curvature JO - Proteins: Struct Funct Bioinform. VL - 61 ID - Coleman2005 ER - TY - JOUR AU - Yuan, Z. AU - Zhao, J. AU - Wang, Z. -. X. PY - 2003 DA - 2003// TI - Flexibility analysis of enzyme active sites by crystallographic temperature factors JO - Protein Eng. VL - 16 ID - Yuan2003 ER - TY - JOUR AU - Baker, N. A. AU - Sept, D. AU - Joseph, S. AU - Holst, M. J. AU - McCammon, J. A. PY - 2001 DA - 2001// TI - Electrostatics of nanosystems: application to microtubules and the ribosome JO - Proc Nat Acad Sci. VL - 98 ID - Baker2001 ER - TY - JOUR AU - Rocchia, W. AU - Alexov, E. AU - Honig, B. PY - 2001 DA - 2001// TI - Extending the applicability of the nonlinear poisson-boltzmann equation: Multiple dielectric constants and multivalent ions JO - J Phys Chem B. VL - 105 ID - Rocchia2001 ER - TY - JOUR AU - Guerois, R. AU - Nielsen, J. E. AU - Serrano, L. PY - 2002 DA - 2002// TI - Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations JO - J Mol Biol. VL - 320 ID - Guerois2002 ER - TY - JOUR AU - Schymkowitz, J. AU - Borg, J. AU - Stricher, F. AU - Nys, R. AU - Rousseau, F. AU - Serrano, L. PY - 2005 DA - 2005// TI - The foldx web server: an online force field JO - Nucleic Acids Res. VL - 33 ID - Schymkowitz2005 ER - TY - JOUR AU - Cole, C. AU - Warwicker, J. PY - 2002 DA - 2002// TI - Side-chain conformational entropy at protein–protein interfaces JO - Protein Sci. VL - 11 ID - Cole2002 ER - TY - JOUR AU - Yu, C. -. M. AU - Peng, H. -. P. AU - Chen, C. AU - Lee, Y. -. C. AU - Chen, J. -. B. AU - Tsai, K. -. C. PY - 2012 DA - 2012// TI - Rationalization and design of the complementarity determining region sequences in an antibody-antigen recognition interface JO - PloS One. VL - 7 ID - Yu2012 ER - TY - JOUR AU - Laskowski, R. A. AU - Thornton, J. M. AU - Humblet, C. AU - Singh, J. PY - 1996 DA - 1996// TI - X-site: use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins JO - J Mol Biol. VL - 259 ID - Laskowski1996 ER - TY - JOUR AU - Zuckerkandl, E. AU - Pauling, L. PY - 1965 DA - 1965// TI - Evolutionary divergence and convergence in proteins JO - Evolving Genes Proteins. VL - 97 ID - Zuckerkandl1965 ER - TY - JOUR AU - Harms, M. J. AU - Thornton, J. W. PY - 2013 DA - 2013// TI - Evolutionary biochemistry: revealing the historical and physical causes of protein properties JO - Nat Rev Genet. VL - 14 ID - Harms2013 ER - TY - JOUR AU - de Juan, D. AU - Pazos, F. AU - Valencia, A. PY - 2013 DA - 2013// TI - Emerging methods in protein co-evolution JO - Nat Rev Genet. VL - 14 ID - de Juan2013 ER - TY - JOUR AU - Grishin, N. V. AU - Phillips, M. A. PY - 1994 DA - 1994// TI - The subunit interfaces of oligomeric enzymes are conserved to a similar extent to the overall protein sequences JO - Protein Sci. VL - 3 ID - Grishin1994 ER - TY - JOUR AU - Caffrey, D. R. AU - Somaroo, S. AU - Hughes, J. D. AU - Mintseris, J. AU - Huang, E. S. PY - 2004 DA - 2004// TI - Are protein–protein interfaces more conserved in sequence than the rest of the protein surface? JO - Protein Sci. VL - 13 ID - Caffrey2004 ER - TY - JOUR AU - Bradford, J. R. AU - Westhead, D. R. PY - 2003 DA - 2003// TI - Asymmetric mutation rates at enzyme–inhibitor interfaces: implications for the protein–protein docking problem JO - Protein Sci. VL - 12 ID - Bradford2003 ER - TY - JOUR AU - Reddy, B. V. AU - Kaznessis, Y. N. PY - 2005 DA - 2005// TI - A quantitative analysis of interfacial amino acid conservation in protein-protein hetero complexes JO - J Bioinform Comput Biol. VL - 3 ID - Reddy2005 ER - TY - JOUR AU - Ma, B. AU - Elkayam, T. AU - Wolfson, H. AU - Nussinov, R. PY - 2003 DA - 2003// TI - Protein–protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces JO - Proc Nat Acad Sci. VL - 100 ID - Ma2003 ER - TY - JOUR AU - Ofran, Y. AU - Rost, B. PY - 2007 DA - 2007// TI - Protein–protein interaction hotspots carved into sequences JO - PLoS Comput Biol. VL - 3 ID - Ofran2007 ER - TY - JOUR AU - Shoemaker, B. A. AU - Zhang, D. AU - Tyagi, M. AU - Thangudu, R. R. AU - Fong, J. H. AU - Marchler-Bauer, A. PY - 2012 DA - 2012// TI - Ibis (inferred biomolecular interaction server) reports, predicts and integrates multiple types of conserved interactions for proteins JO - Nucleic Acids Res. VL - 40 ID - Shoemaker2012 ER - TY - JOUR AU - Wang, B. AU - Chen, P. AU - Huang, D. -. S. AU - Li, J. -. J. AU - Lok, T. -. M. AU - Lyu, M. R. PY - 2006 DA - 2006// TI - Predicting protein interaction sites from residue spatial sequence profile and evolution rate JO - FEBS Lett. VL - 580 ID - Wang2006 ER - TY - JOUR AU - Chelliah, V. AU - Chen, L. AU - Blundell, T. L. AU - Lovell, S. C. PY - 2004 DA - 2004// TI - Distinguishing structural and functional restraints in evolution in order to identify interaction sites JO - J Mol Biol. VL - 342 ID - Chelliah2004 ER - TY - JOUR AU - Celniker, G. AU - Nimrod, G. AU - Ashkenazy, H. AU - Glaser, F. AU - Martz, E. AU - Mayrose, I. PY - 2013 DA - 2013// TI - Consurf: using evolutionary data to raise testable hypotheses about protein function JO - Israel J Chem. VL - 53 ID - Celniker2013 ER - TY - JOUR AU - Wilkins, A. AU - Erdin, S. AU - Lua, R. AU - Lichtarge, O. PY - 2012 DA - 2012// TI - Evolutionary trace for prediction and redesign of protein functional sites JO - Comput Drug Discov Design. VL - 819 ID - Wilkins2012 ER - TY - JOUR AU - Glaser, F. AU - Pupko, T. AU - Paz, I. AU - Bell, R. E. AU - Bechor-Shental, D. AU - Martz, E. PY - 2003 DA - 2003// TI - Consurf: identification of functional regions in proteins by surface-mapping of phylogenetic information JO - Bioinformatics. VL - 19 ID - Glaser2003 ER - TY - JOUR AU - Capra, J. A. AU - Laskowski, R. A. AU - Thornton, J. M. AU - Singh, M. AU - Funkhouser, T. A. PY - 2009 DA - 2009// TI - Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3d structure JO - PLoS Comput Biol. VL - 5 ID - Capra2009 ER - TY - JOUR AU - Berezin, C. AU - Glaser, F. AU - Rosenberg, J. AU - Paz, I. AU - Pupko, T. AU - Fariselli, P. PY - 2004 DA - 2004// TI - Conseq: the identification of functionally and structurally important residues in protein sequences JO - Bioinformatics. VL - 20 ID - Berezin2004 ER - TY - JOUR AU - Ponomarenko, J. V. AU - Bourne, P. E. PY - 2007 DA - 2007// TI - Antibody-protein interactions: benchmark datasets and prediction tools evaluation JO - BMC Struct Biol. VL - 7 ID - Ponomarenko2007 ER - TY - JOUR AU - Dayhoff, M. AU - Schwartz, R. AU - Orcutt, B. PY - 1978 DA - 1978// TI - A model of evolutionary change in proteins JO - Atlas Protein Seq Struct. VL - 5 ID - Dayhoff1978 ER - TY - JOUR AU - Henikoff, S. AU - Henikoff, J. G. PY - 1992 DA - 1992// TI - Amino acid substitution matrices from protein blocks JO - Proc Nat Acad Sci. VL - 89 ID - Henikoff1992 ER - TY - JOUR AU - Shannon, C. E. PY - 1948 DA - 1948// TI - A mathematical theory of communication JO - Bell Syst Tech J. VL - 27 ID - Shannon1948 ER - TY - JOUR AU - Mayrose, I. AU - Graur, D. AU - Ben-Tal, N. AU - Pupko, T. PY - 2004 DA - 2004// TI - Comparison of site-specific rate-inference methods for protein sequences: empirical bayesian methods are superior JO - Mol Biol Evol. VL - 21 ID - Mayrose2004 ER - TY - JOUR AU - Glaser, F. AU - Rosenberg, Y. AU - Kessel, A. AU - Pupko, T. AU - Ben-Tal, N. PY - 2005 DA - 2005// TI - The consurf-hssp database: the mapping of evolutionary conservation among homologs onto pdb structures JO - PROTEINS: Struct Funct Bioinform. VL - 58 ID - Glaser2005 ER - TY - JOUR AU - Schneider, R. AU - Sander, C. PY - 1996 DA - 1996// TI - The hssp database of protein structure-sequence alignments JO - Nucleic Acids Res. VL - 24 ID - Schneider1996 ER - TY - JOUR AU - Kanamori, E. AU - Murakami, Y. AU - Tsuchiya, Y. AU - Standley, D. M. AU - Nakamura, H. AU - Kinoshita, K. PY - 2007 DA - 2007// TI - Docking of protein molecular surfaces with evolutionary trace analysis JO - Proteins: Struct Funct Bioinform. VL - 69 ID - Kanamori2007 ER - TY - JOUR AU - Lichtarge, O. AU - Bourne, H. R. AU - Cohen, F. E. PY - 1996 DA - 1996// TI - An evolutionary trace method defines binding surfaces common to protein families JO - J Mol Biol. VL - 257 ID - Lichtarge1996 ER - TY - JOUR AU - Lichtarge, O. AU - Sowa, M. E. PY - 2002 DA - 2002// TI - Evolutionary predictions of binding surfaces and interactions JO - Current Opin Struct Biol. VL - 12 ID - Lichtarge2002 ER - TY - JOUR AU - Mihalek, I. AU - Reš, I. AU - Lichtarge, O. PY - 2004 DA - 2004// TI - A family of evolution–entropy hybrid methods for ranking protein residues by importance JO - J Mol Biol. VL - 336 ID - Mihalek2004 ER - TY - JOUR AU - Chothia, C. AU - Lesk, A. M. PY - 1986 DA - 1986// TI - The relation between the divergence of sequence and structure in proteins JO - EMBO J. VL - 5 ID - Chothia1986 ER - TY - JOUR AU - Lesk, A. M. AU - Chothia, C. PY - 1980 DA - 1980// TI - How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins JO - J Mol Biol. VL - 136 ID - Lesk1980 ER - TY - JOUR AU - Petrey, D. AU - Fischer, M. AU - Honig, B. PY - 2009 DA - 2009// TI - Structural relationships among proteins with different global topologies and their implications for function annotation strategies JO - Proc Nat Acad Sci. VL - 106 ID - Petrey2009 ER - TY - JOUR AU - Ingles-Prieto, A. AU - Ibarra-Molero, B. AU - Delgado-Delgado, A. AU - Perez-Jimenez, R. AU - Fernandez, J. M. AU - Gaucher, E. A. PY - 2013 DA - 2013// TI - Conservation of protein structure over four billion years JO - Structure. VL - 21 ID - Ingles-Prieto2013 ER - TY - JOUR AU - Kundrotas, P. J. AU - Zhu, Z. AU - Janin, J. AU - Vakser, I. A. PY - 2012 DA - 2012// TI - Templates are available to model nearly all complexes of structurally characterized proteins JO - Proc Nat Acad Sci. VL - 109 ID - Kundrotas2012 ER - TY - JOUR AU - Monji, H. AU - Koizumi, S. AU - Ozaki, T. AU - Ohkawa, T. PY - 2011 DA - 2011// TI - Interaction site prediction by structural similarity to neighboring clusters in protein-protein interaction networks JO - BMC Bioinformatics. VL - 12 ID - Monji2011 ER - TY - JOUR AU - Goncearenco, A. AU - Shoemaker, B. A. AU - Zhang, D. AU - Sarychev, A. AU - Panchenko, A. R. PY - 2014 DA - 2014// TI - Coverage of protein domain families with structural protein-protein interactions: current progress and future trends JO - Progress Biophys Mol Biol. VL - 116 ID - Goncearenco2014 ER - TY - JOUR AU - Khafizov, K. AU - Madrid-Aliste, C. AU - Almo, S. C. AU - Fiser, A. PY - 2014 DA - 2014// TI - Trends in structural coverage of the protein universe and the impact of the protein structure initiative JO - Proc Nat Acad Sci. VL - 111 ID - Khafizov2014 ER - TY - JOUR AU - Gao, M. AU - Skolnick, J. PY - 2010 DA - 2010// TI - Structural space of protein–protein interfaces is degenerate, close to complete, and highly connected JO - Proc Nat Acad Sci. VL - 107 ID - Gao2010 ER - TY - JOUR AU - Tuncbag, N. AU - Gursoy, A. AU - Nussinov, R. AU - Keskin, O. PY - 2011 DA - 2011// TI - Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using prism JO - Nat Protoc. VL - 6 ID - Tuncbag2011 ER - TY - JOUR AU - Garma, L. AU - Mukherjee, S. AU - Mitra, P. AU - Zhang, Y. PY - 2012 DA - 2012// TI - How many protein-protein interactions types exist in nature? JO - PloS One. VL - 7 ID - Garma2012 ER - TY - JOUR AU - Xie, L. AU - Xie, L. AU - Bourne, P. E. PY - 2011 DA - 2011// TI - Structure-based systems biology for analyzing off-target binding JO - Current Opin Struct Biol. VL - 21 ID - Xie2011 ER - TY - JOUR AU - Xie, L. AU - Bourne, P. E. PY - 2005 DA - 2005// TI - Functional coverage of the human genome by existing structures, structural genomics targets, and homology models JO - PLoS Comput Biol. VL - 1 ID - Xie2005 ER - TY - JOUR AU - Kundrotas, P. J. AU - Vakser, I. A. PY - 2010 DA - 2010// TI - Accuracy of protein-protein binding sites in high-throughput template-based modeling JO - PLoS Comput Biol. VL - 6 ID - Kundrotas2010 ER - TY - JOUR AU - Koike, A. AU - Takagi, T. PY - 2004 DA - 2004// TI - Prediction of protein–protein interaction sites using support vector machines JO - Protein Eng Des Sel. VL - 17 ID - Koike2004 ER - TY - JOUR AU - Glaser, F. AU - Steinberg, D. M. AU - Vakser, I. A. AU - Ben-Tal, N. PY - 2001 DA - 2001// TI - Residue frequencies and pairing preferences at protein–protein interfaces JO - Proteins: Struct Funct Bioinform. VL - 43 ID - Glaser2001 ER - TY - JOUR AU - Miller, S. PY - 1989 DA - 1989// TI - The structure of interfaces between subunits of dimeric and tetrameric proteins JO - Protein Eng. VL - 3 ID - Miller1989 ER - TY - JOUR AU - Bouvier, B. AU - Grünberg, R. AU - Nilges, M. AU - Cazals, F. PY - 2009 DA - 2009// TI - Shelling the voronoi interface of protein–protein complexes reveals patterns of residue conservation, dynamics, and composition JO - Proteins: Struct Funct Bioinformatics. VL - 76 ID - Bouvier2009 ER - TY - JOUR AU - Bordner, A. J. AU - Abagyan, R. PY - 2005 DA - 2005// TI - Statistical analysis and prediction of protein–protein interfaces JO - Proteins: Struct Funct Bioinform. VL - 60 ID - Bordner2005 ER - TY - JOUR AU - Prasad Bahadur, R. AU - Chakrabarti, P. AU - Rodier, F. AU - Janin, J. PY - 2004 DA - 2004// TI - A dissection of specific and non-specific protein–protein interfaces JO - J Mol Biol. VL - 336 ID - Prasad Bahadur2004 ER - TY - JOUR AU - Bahadur, R. P. AU - Chakrabarti, P. AU - Rodier, F. AU - Janin, J. PY - 2003 DA - 2003// TI - Dissecting subunit interfaces in homodimeric proteins JO - Proteins: Struct Funct Bioinform. VL - 53 ID - Bahadur2003 ER - TY - JOUR AU - Hu, Z. AU - Ma, B. AU - Wolfson, H. AU - Nussinov, R. PY - 2000 DA - 2000// TI - Conservation of polar residues as hot spots at protein interfaces JO - Proteins: Struct Funct Bioinform. VL - 39 ID - Hu2000 ER - TY - JOUR AU - Lukatsky, D. AU - Shakhnovich, B. AU - Mintseris, J. AU - Shakhnovich, E. PY - 2007 DA - 2007// TI - Structural similarity enhances interaction propensity of proteins JO - J Mol Biol. VL - 365 ID - Lukatsky2007 ER - TY - JOUR AU - Murakami, Y. AU - Jones, S. PY - 2006 DA - 2006// TI - Sharp2: protein–protein interaction predictions using patch analysis JO - Bioinformatics. VL - 22 ID - Murakami2006 ER - TY - JOUR AU - Negi, S. S. AU - Schein, C. H. AU - Oezguen, N. AU - Power, T. D. AU - Braun, W. PY - 2007 DA - 2007// TI - Interprosurf: a web server for predicting interacting sites on protein surfaces JO - Bioinformatics. VL - 23 ID - Negi2007 ER - TY - JOUR AU - Hamer, R. AU - Luo, Q. AU - Armitage, J. P. AU - Reinert, G. AU - Deane, C. M. PY - 2010 DA - 2010// TI - i-patch: Interprotein contact prediction using local network information JO - Proteins: Struct Funct Bioinform. VL - 78 ID - Hamer2010 ER - TY - JOUR AU - Warme, P. K. AU - Morgan, R. S. PY - 1978 DA - 1978// TI - A survey of atomic interactions in 21 proteins JO - J Mol Biol. VL - 118 ID - Warme1978 ER - TY - JOUR AU - Xu, D. AU - Lin, S. L. AU - Nussinov, R. PY - 1997 DA - 1997// TI - Protein binding versus protein folding: the role of hydrophilic bridges in protein associations JO - J Mol Biol. VL - 265 ID - Xu1997 ER - TY - JOUR AU - Tsai, C. -. J. AU - Lin, S. L. AU - Wolfson, H. J. AU - Nussinov, R. PY - 1997 DA - 1997// TI - Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect JO - Protein Sci. VL - 6 ID - Tsai1997 ER - TY - JOUR AU - Liu, S. AU - Zhang, C. AU - Zhou, H. AU - Zhou, Y. PY - 2004 DA - 2004// TI - A physical reference state unifies the structure-derived potential of mean force for protein folding and binding JO - Proteins: Struct Funct Bioinform. VL - 56 ID - Liu2004 ER - TY - JOUR AU - Tsai, C. -. J. AU - Xu, D. AU - Nussinov, R. PY - 1997 DA - 1997// TI - Structural motifs at protein-protein interfaces: Protein cores versus two-state and three-state model complexes JO - Protein Sci. VL - 6 ID - Tsai1997 ER - TY - JOUR AU - McConkey, B. J. AU - Sobolev, V. AU - Edelman, M. PY - 2003 DA - 2003// TI - Discrimination of native protein structures using atom–atom contact scoring JO - Proc Nat Acad Sci. VL - 100 ID - McConkey2003 ER - TY - JOUR AU - Lawrence, M. C. AU - Colman, P. M. PY - 1993 DA - 1993// TI - Shape complementarity at protein/protein interfaces JO - J Mol Biol. VL - 234 ID - Lawrence1993 ER - TY - JOUR AU - de Vries, S. J. AU - Bonvin, A. M. PY - 2008 DA - 2008// TI - How proteins get in touch: interface prediction in the study of biomolecular complexes JO - Current Protein Peptide Sci. VL - 9 ID - de Vries2008 ER - TY - JOUR AU - Wass, M. N. AU - David, A. AU - Sternberg, M. J. PY - 2011 DA - 2011// TI - Challenges for the prediction of macromolecular interactions JO - Current Opinion Struct Biol. VL - 21 ID - Wass2011 ER - TY - JOUR AU - Yu, L. AU - Liu, H. PY - 2004 DA - 2004// TI - Efficient feature selection via analysis of relevance and redundancy JO - J Mach Learn Res. VL - 5 ID - Yu2004 ER - TY - JOUR AU - Booker, L. B. AU - Goldberg, D. E. AU - Holland, J. H. PY - 1989 DA - 1989// TI - Classifier systems and genetic algorithms JO - Artif Intell. VL - 40 ID - Booker1989 ER - TY - CHAP AU - Andrew Moore, M. S. L. ED - Cohen, W. W. ED - Hirsh, H. PY - 1994 DA - 1994// TI - Efficient algorithms for minimizing cross validation error BT - Proceedings of the 11th International Confonference on Machine Learning PB - Morgan Kaufmann CY - Burlington, Massachusetts, USA ID - Andrew Moore1994 ER - TY - JOUR AU - Matthews, B. W. PY - 1975 DA - 1975// TI - Comparison of the predicted and observed secondary structure of t4 phage lysozyme JO - Biochimica et Biophysica Acta (BBA)-Protein Struct. VL - 405 ID - Matthews1975 ER - TY - JOUR AU - Maron, O. AU - Moore, A. W. PY - 1993 DA - 1993// TI - Hoeffding races: Accelerating model selection search for classification and function approximation JO - Adv Neural Inform Process Syst. VL - 6 ID - Maron1993 ER - TY - JOUR AU - Hoeffding, W. PY - 1963 DA - 1963// TI - Probability inequalities for sums of bounded random variables JO - J Am Stat Assoc. VL - 58 ID - Hoeffding1963 ER - TY - JOUR AU - Peng, H. AU - Long, F. AU - Ding, C. PY - 2005 DA - 2005// TI - Feature selection based on mutual information criteria of max-dependency, max-relevance, and min-redundancy JO - Pattern Anal Mach Intell IEEE Trans. VL - 27 ID - Peng2005 ER - TY - JOUR AU - Ding, C. AU - Peng, H. PY - 2005 DA - 2005// TI - Minimum redundancy feature selection from microarray gene expression data JO - J Bioinform Comput Biol. VL - 3 ID - Ding2005 ER - TY - CHAP AU - Cover, T. M. AU - Thomas, J. A. PY - 1991 DA - 1991// TI - Entropy, relative entropy and mutual information BT - Elements Inform Theory PB - Sons, Inc. CY - Hoboken, NJ ID - Cover1991 ER - TY - JOUR AU - Li, B. -. Q. AU - Hu, L. -. L. AU - Niu, S. AU - Cai, Y. -. D. AU - Chou, K. -. C. PY - 2012 DA - 2012// TI - Predict and analyze s-nitrosylation modification sites with the mrmr and ifs approaches JO - J Proteomics. VL - 75 ID - Li2012 ER - TY - JOUR AU - Li, B. -. Q. AU - Hu, L. -. L. AU - Chen, L. AU - Feng, K. -. Y. AU - Cai, Y. -. D. AU - Chou, K. -. C. PY - 2012 DA - 2012// TI - Prediction of protein domain with mrmr feature selection and analysis JO - PLoS One. VL - 7 ID - Li2012 ER - TY - JOUR AU - Hotelling, H. PY - 1933 DA - 1933// TI - Analysis of a complex of statistical variables into principal components JO - J Educ Psychol. VL - 24 ID - Hotelling1933 ER - TY - CHAP AU - Jolliffe, I. PY - 2005 DA - 2005// TI - Principal component analysis BT - Encyclopedia of Statistics in Behavioral Science PB - Wiley Online Library CY - Chichester, England ID - Jolliffe2005 ER - TY - STD TI - Jackson DA. Stopping rules in principal components analysis: a comparison of heuristical and statistical approaches. Ecology. 1993:2204–14. ID - ref229 ER - TY - JOUR AU - Jones, S. AU - Thornton, J. M. PY - 1995 DA - 1995// TI - Protein-protein interactions: a review of protein dimer structures JO - Prog Biophys Mol Biol. VL - 63 ID - Jones1995 ER - TY - JOUR AU - De Vries, S. J. AU - Bonvin, A. M. PY - 2006 DA - 2006// TI - Intramolecular surface contacts contain information about protein–protein interface regions JO - Bioinformatics. VL - 22 ID - De Vries2006 ER - TY - JOUR AU - Petrey, D. AU - Honig, B. PY - 2002 DA - 2002// TI - Grasp2: visualization, surface properties, and electrostatics of macromolecular structures and sequences JO - Methods Enzymol. VL - 374 ID - Petrey2002 ER - TY - JOUR AU - Yang, A. -. S. AU - Honig, B. PY - 2000 DA - 2000// TI - An integrated approach to the analysis and modeling of protein sequences and structures. i. protein structural alignment and a quantitative measure for protein structural distance JO - J Mol Biol. VL - 301 ID - Yang2000 ER - TY - JOUR AU - Cortes, C. AU - Vapnik, V. PY - 1995 DA - 1995// TI - Support-vector networks JO - Mach Learn. VL - 20 ID - Cortes1995 ER - TY - JOUR AU - Jones, D. T. AU - Taylor, W. R. AU - Thornton, J. M. PY - 1992 DA - 1992// TI - The rapid generation of mutation data matrices from protein sequences JO - Comput Appl Biosci CABIOS. VL - 8 ID - Jones1992 ER - TY - JOUR AU - Gascuel, O. PY - 1997 DA - 1997// TI - Bionj: an improved version of the nj algorithm based on a simple model of sequence data JO - Mol Biol Evol. VL - 14 ID - Gascuel1997 ER - TY - JOUR AU - Saitou, N. AU - Nei, M. PY - 1987 DA - 1987// TI - The neighbor-joining method: a new method for reconstructing phylogenetic trees JO - Mol Biol Evol. VL - 4 ID - Saitou1987 ER - TY - JOUR AU - Guindon, S. AU - Gascuel, O. PY - 2003 DA - 2003// TI - A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood JO - Syst Biol. VL - 52 ID - Guindon2003 ER - TY - JOUR AU - Breiman, L. PY - 2001 DA - 2001// TI - Random forests JO - Mach Learn. VL - 45 ID - Breiman2001 ER - TY - JOUR AU - Loriot, S. AU - Cazals, F. PY - 2010 DA - 2010// TI - Modeling macro–molecular interfaces with intervor JO - Bioinformatics. VL - 26 ID - Loriot2010 ER - TY - CHAP AU - Freund, Y. AU - Mason, L. PY - 1999 DA - 1999// TI - The alternating decision tree learning algorithm BT - Proceedings of the Sixteenth International Conference on Machine Learning. ICML ’99 PB - Morgan Kaufmann Publishers Inc. CY - San Francisco, CA, USA ID - Freund1999 ER - TY - STD TI - Pfahringer B, Holmes G, Kirkby R. Optimizing the induction of alternating decision trees. Adv Knowl Discov Data Mining. 2001:477–87. ID - ref242 ER - TY - JOUR AU - Aurenhammer, F. PY - 1991 DA - 1991// TI - Voronoi diagrams—a survey of a fundamental geometric data structure JO - ACM Comput Surv (CSUR). VL - 23 ID - Aurenhammer1991 ER - TY - JOUR AU - da Silveira, C. H. AU - Pires, D. E. AU - Minardi, R. C. AU - Ribeiro, C. AU - Veloso, C. J. PY - 2009 DA - 2009// TI - Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins JO - Proteins: Struct Funct Bioinform. VL - 74 ID - da Silveira2009 ER - TY - JOUR AU - Fisher, R. A. PY - 1936 DA - 1936// TI - The use of multiple measurements in taxonomic problems JO - Ann Eugen. VL - 7 ID - Fisher1936 ER - TY - BOOK AU - Venables, W. N. AU - Ripley, B. D. PY - 2002 DA - 2002// TI - Modern applied statistics with s PB - Springer CY - New York, NY, USA ID - Venables2002 ER - TY - BOOK AU - Rumelhart, D. E. AU - Hinton, G. E. AU - Williams, R. J. PY - 1986 DA - 1986// TI - Parallel distributed processing: Explorations in the microstructure of cognition, vol. 1 PB - MIT Press CY - Cambridge, MA, USA ID - Rumelhart1986 ER - TY - STD TI - Haykin S, 1st edn. Upper Saddle River, NJ, USA: Prentice Hall PTR; 1994. ID - ref248 ER - TY - CHAP AU - Riedmiller, M. AU - Braun, H. PY - 1993 DA - 1993// TI - A direct adaptive method for faster backpropagation learning: The rprop algorithm BT - Neural Networks, 1993., IEEE International Conference On PB - IEEE CY - Washington, DC, USA ID - Riedmiller1993 ER - TY - JOUR AU - Breiman, L. PY - 1996 DA - 1996// TI - Bagging predictors JO - Mach Learn. VL - 24 ID - Breiman1996 ER - TY - JOUR AU - Fawcett, T. PY - 2006 DA - 2006// TI - An introduction to roc analysis JO - Pattern Recognit Lett. VL - 27 ID - Fawcett2006 ER - TY - JOUR AU - Bradley, A. P. PY - 1997 DA - 1997// TI - The use of the area under the roc curve in the evaluation of machine learning algorithms JO - Pattern Recognit. VL - 30 ID - Bradley1997 ER - TY - JOUR AU - Sørensen, T. PY - 1948 DA - 1948// TI - A method of establishing groups of equal amplitude in plant sociology based on similarity of species and its application to analyses of the vegetation on danish commons JO - Biol Skr. VL - 5 ID - Sørensen1948 ER - TY - JOUR AU - Dice, L. R. PY - 1945 DA - 1945// TI - Measures of the amount of ecologic association between species JO - Ecology. VL - 26 ID - Dice1945 ER - TY - JOUR AU - Baldi, P. AU - Brunak, S. AU - Chauvin, Y. AU - Andersen, C. A. AU - Nielsen, H. PY - 2000 DA - 2000// TI - Assessing the accuracy of prediction algorithms for classification: an overview JO - Bioinformatics. VL - 16 ID - Baldi2000 ER - TY - STD TI - Peng K, Obradovic Z, Vucetic S. Exploring bias in the protein data bank using contrast classifiers. In: Pacific Symposium on Biocomputing 2004: Hawaii, USA, 6-10 January 2004. World Scientific: 2003. p. 435. ID - ref256 ER - TY - JOUR AU - Kirchmair, J. AU - Markt, P. AU - Distinto, S. AU - Schuster, D. AU - Spitzer, G. M. AU - Liedl, K. R. AU - Langer, T. AU - Wolber, G. PY - 2008 DA - 2008// TI - The protein data bank (pdb), its related services and software tools as key components for in silico guided drug discovery JO - J Med Chem. VL - 51 ID - Kirchmair2008 ER - TY - JOUR AU - Bouman, C. A. AU - Shapiro, M. PY - 1994 DA - 1994// TI - A multiscale random field model for bayesian image segmentation JO - Image Process IEEE Trans. VL - 3 ID - Bouman1994 ER - TY - CHAP AU - He, X. AU - Zemel, R. S. AU - Carreira-Perpindn, M. PY - 2004 DA - 2004// TI - Multiscale conditional random fields for image labeling BT - Computer Vision and Pattern Recognition, 2004. CVPR 2004. Proceedings of the 2004 IEEE Computer Society Conference On, vol. 2 PB - IEEE CY - Washington, DC, USA ID - He2004 ER - TY - JOUR AU - Li, X. AU - Moal, I. H. AU - Bates, P. A. PY - 2010 DA - 2010// TI - Detection and refinement of encounter complexes for protein–protein docking: taking account of macromolecular crowding JO - Proteins: Struct Funct Bioinform. VL - 78 ID - Li2010 ER - TY - CHAP AU - Mnih, V. AU - Szepesvári, C. AU - Audibert, J. -. Y. PY - 2008 DA - 2008// TI - Empirical bernstein stopping BT - Proceedings of the 25th International Conference on Machine Learning PB - ACM CY - New York, NY, USA ID - Mnih2008 ER - TY - JOUR AU - Schölkopf, B. AU - Smola, A. AU - Müller, K. -. R. PY - 1998 DA - 1998// TI - Nonlinear component analysis as a kernel eigenvalue problem JO - Neural Comput. VL - 10 ID - Schölkopf1998 ER - TY - JOUR AU - Hinton, G. E. AU - Salakhutdinov, R. R. PY - 2006 DA - 2006// TI - Reducing the dimensionality of data with neural networks JO - Science. VL - 313 ID - Hinton2006 ER - TY - JOUR AU - Lise, S. AU - Archambeau, C. AU - Pontil, M. AU - Jones, D. T. PY - 2009 DA - 2009// TI - Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods JO - BMC Bioinformatics. VL - 10 ID - Lise2009 ER - TY - JOUR AU - Xu, B. AU - Wei, X. AU - Deng, L. AU - Guan, J. AU - Zhou, S. PY - 2012 DA - 2012// TI - A semi-supervised boosting svm for predicting hot spots at protein-protein interfaces JO - BMC Syst Biol. VL - 6 ID - Xu2012 ER - TY - JOUR AU - Qi, Y. AU - Tastan, O. AU - Carbonell, J. G. AU - Klein-Seetharaman, J. AU - Weston, J. PY - 2010 DA - 2010// TI - Semi-supervised multi-task learning for predicting interactions between hiv-1 and human proteins JO - Bioinformatics. VL - 26 ID - Qi2010 ER - TY - JOUR AU - Bruzzone, L. AU - Persello, C. PY - 2009 DA - 2009// TI - A novel context-sensitive semisupervised svm classifier robust to mislabeled training samples JO - Geosci Remote Sensing IEEE Trans. VL - 47 ID - Bruzzone2009 ER - TY - JOUR AU - Frénay, B. AU - Verleysen, M. PY - 2014 DA - 2014// TI - Classification in the presence of label noise: a survey JO - IEEE Trans Neural Netw Learn Syst. VL - 25 ID - Frénay2014 ER - TY - JOUR AU - Tan, A. AU - Gilbert, D. AU - Deville, Y. PY - 2003 DA - 2003// TI - Multi-class protein fold classification using a new ensemble machine learning approach JO - Genome Inform. VL - 14 ID - Tan2003 ER - TY - STD TI - Weston J, Watkins C. Support vector machines for multi-class pattern recognition, vol. 99. In: ESANN: 1999. p. 219–24. ID - ref270 ER - TY - JOUR AU - Moreira, I. S. AU - Fernandes, P. A. AU - Ramos, M. J. PY - 2007 DA - 2007// TI - Hot spots—a review of the protein–protein interface determinant amino-acid residues JO - Proteins: Struct Funct Bioinform. VL - 68 ID - Moreira2007 ER - TY - JOUR AU - Geppert, T. AU - Reisen, F. AU - Pillong, M. AU - Hähnke, V. AU - Tanrikulu, Y. AU - Koch, C. P. PY - 2012 DA - 2012// TI - Virtual screening for compounds that mimic protein–protein interface epitopes JO - J Comput Chem. VL - 33 ID - Geppert2012 ER - TY - JOUR AU - Bogan, A. A. AU - Thorn, K. S. PY - 1998 DA - 1998// TI - Anatomy of hot spots in protein interfaces JO - J Mol Biol. VL - 280 ID - Bogan1998 ER - TY - JOUR AU - Livnah, O. AU - Stura, E. A. AU - Johnson, D. L. AU - Middleton, S. A. AU - Mulcahy, L. S. AU - Wrighton, N. C. PY - 1996 DA - 1996// TI - Functional mimicry of a protein hormone by a peptide agonist: the epo receptor complex at 2.8 å JO - Science. VL - 273 ID - Livnah1996 ER - TY - JOUR AU - Johnson, D. L. AU - Farrell, F. X. AU - Barbone, F. P. AU - McMahon, F. J. AU - Tullai, J. AU - Hoey, K. PY - 1998 DA - 1998// TI - Identification of a 13 amino acid peptide mimetic of erythropoietin and description of amino acids critical for the mimetic activity of emp1 JO - Biochemistry. VL - 37 ID - Johnson1998 ER - TY - JOUR AU - Tinberg, C. E. AU - Khare, S. D. AU - Dou, J. AU - Doyle, L. AU - Nelson, J. W. AU - Schena, A. PY - 2013 DA - 2013// TI - Computational design of ligand-binding proteins with high affinity and selectivity JO - Nature. VL - 501 ID - Tinberg2013 ER - TY - JOUR AU - Schreiber, G. AU - Fleishman, S. J. PY - 2013 DA - 2013// TI - Computational design of protein–protein interactions JO - Current Opin Struct Biol. VL - 23 ID - Schreiber2013 ER - TY - JOUR AU - De Vries, S. J. AU - van Dijk, M. AU - Bonvin, A. M. PY - 2010 DA - 2010// TI - The haddock web server for data-driven biomolecular docking JO - Nat Protocols. VL - 5 ID - De Vries2010 ER - TY - JOUR AU - Dominguez, C. AU - Boelens, R. AU - Bonvin, A. M. PY - 2003 DA - 2003// TI - Haddock: a protein-protein docking approach based on biochemical or biophysical information JO - J Am Chem Soci. VL - 125 ID - Dominguez2003 ER - TY - JOUR AU - Lopes, A. AU - Sacquin-Mora, S. AU - Dimitrova, V. AU - Laine, E. AU - Ponty, Y. AU - Carbone, A. PY - 2013 DA - 2013// TI - Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information JO - PLoS Comput Biol. VL - 9 ID - Lopes2013 ER - TY - JOUR AU - Kuzu, G. AU - Keskin, O. AU - Gursoy, A. AU - Nussinov, R. PY - 2012 DA - 2012// TI - Constructing structural networks of signaling pathways on the proteome scale JO - Current Opinion Struct Biol. VL - 22 ID - Kuzu2012 ER - TY - JOUR AU - Bandyopadhyay, S. AU - Sharan, R. AU - Ideker, T. PY - 2006 DA - 2006// TI - Systematic identification of functional orthologs based on protein network comparison JO - Genome Research. VL - 16 ID - Bandyopadhyay2006 ER - TY - JOUR AU - Phan, H. T. AU - Sternberg, M. J. PY - 2012 DA - 2012// TI - Pinalog: a novel approach to align protein interaction networks—implications for complex detection and function prediction JO - Bioinformatics. VL - 28 ID - Phan2012 ER - TY - JOUR AU - Singh, R. AU - Xu, J. AU - Berger, B. PY - 2008 DA - 2008// TI - Global alignment of multiple protein interaction networks with application to functional orthology detection JO - Proc Nat Acad Sci. VL - 105 ID - Singh2008 ER -