TY - JOUR AU - Jones, S. AU - Thornton, J. M. PY - 1996 DA - 1996// TI - Principles of protein-protein interactions JO - Proc Natl Acad Sci U S A VL - 93 UR - https://doi.org/10.1073/pnas.93.1.13 DO - 10.1073/pnas.93.1.13 ID - Jones1996 ER - TY - JOUR AU - Sheinerman, F. B. AU - Norel, R. AU - Honig, B. PY - 2000 DA - 2000// TI - Electrostatic aspects of protein-protein interactions JO - Curr Opin Struct Biol VL - 10 UR - https://doi.org/10.1016/S0959-440X(00)00065-8 DO - 10.1016/S0959-440X(00)00065-8 ID - Sheinerman2000 ER - TY - JOUR AU - Nooren, I. M. 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 UR - https://doi.org/10.1016/S0022-2836(02)01281-0 DO - 10.1016/S0022-2836(02)01281-0 ID - Nooren2003 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 VL - 60 UR - https://doi.org/10.1002/prot.20433 DO - 10.1002/prot.20433 ID - Bordner2005 ER - TY - JOUR AU - Bordner, A. J. AU - Gorin, A. A. PY - 2007 DA - 2007// TI - Protein docking using surface matching and supervised machine learning JO - Proteins VL - 68 UR - https://doi.org/10.1002/prot.21406 DO - 10.1002/prot.21406 ID - Bordner2007 ER - TY - JOUR AU - Aloy, P. AU - Russell, R. B. PY - 2002 DA - 2002// TI - Interrogating protein interaction networks through structural biology JO - Proc Natl Acad Sci U S A VL - 99 UR - https://doi.org/10.1073/pnas.092147999 DO - 10.1073/pnas.092147999 ID - Aloy2002 ER - TY - JOUR AU - Lu, L. AU - Lu, H. AU - Skolnick, J. PY - 2002 DA - 2002// TI - MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading JO - Proteins VL - 49 UR - https://doi.org/10.1002/prot.10222 DO - 10.1002/prot.10222 ID - Lu2002 ER - TY - JOUR AU - Ponstingl, H. AU - Henrick, K. AU - Thornton, J. M. PY - 2000 DA - 2000// TI - Discriminating between homodimeric and monomeric proteins in the crystalline state JO - Proteins VL - 41 UR - https://doi.org/3.0.CO;2-8 DO - 3.0.CO;2-8 ID - Ponstingl2000 ER - TY - JOUR AU - Valdar, W. S. AU - Thornton, J. M. PY - 2001 DA - 2001// TI - Conservation helps to identify biologically relevant crystal contacts JO - J Mol Biol VL - 313 UR - https://doi.org/10.1006/jmbi.2001.5034 DO - 10.1006/jmbi.2001.5034 ID - Valdar2001 ER - TY - JOUR AU - Bahadur, R. P. 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 UR - https://doi.org/10.1016/j.jmb.2003.12.073 DO - 10.1016/j.jmb.2003.12.073 ID - Bahadur2004 ER - TY - JOUR AU - Ponstingl, H. AU - Kabir, T. AU - Thornton, J. M. PY - 2003 DA - 2003// TI - Automatic inference of protein quaternary structure from crystals JO - J Appl Cryst VL - 36 UR - https://doi.org/10.1107/S0021889803012421 DO - 10.1107/S0021889803012421 ID - Ponstingl2003 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 UR - https://doi.org/10.1016/S0968-0004(98)01253-5 DO - 10.1016/S0968-0004(98)01253-5 ID - Henrick1998 ER - TY - STD TI - PQS Protein Quaternary Structure server[http://pqs.ebi.ac.uk] UR - http://pqs.ebi.ac.uk ID - ref13 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 UR - https://doi.org/10.1016/j.jmb.2007.05.022 DO - 10.1016/j.jmb.2007.05.022 ID - Krissinel2007 ER - TY - STD TI - PISA (Protein Interfaces, Surfaces, and Assemblies) server[http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html] UR - http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html ID - ref15 ER - TY - JOUR AU - Davis, F. P. AU - Sali, A. PY - 2005 DA - 2005// TI - PIBASE: a comprehensive database of structurally defined protein interfaces JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti277 DO - 10.1093/bioinformatics/bti277 ID - Davis2005 ER - TY - JOUR AU - Kundrotas, P. J. AU - Alexov, E. PY - 2007 DA - 2007// TI - PROTCOM: searchable database of protein complexes enhanced with domain-domain structures JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkl768 DO - 10.1093/nar/gkl768 ID - Kundrotas2007 ER - TY - JOUR AU - Levy, E. D. AU - Pereira-Leal, J. B. AU - Chothia, C. AU - Teichmann, S. A. PY - 2006 DA - 2006// TI - 3D Complex: A Structural Classification of Protein Complexes JO - PLoS Comput Biol VL - 2 UR - https://doi.org/10.1371/journal.pcbi.0020155 DO - 10.1371/journal.pcbi.0020155 ID - Levy2006 ER - TY - JOUR AU - Ogmen, U. AU - Keskin, O. AU - Aytuna, A. S. AU - Nussinov, R. AU - Gursoy, A. PY - 2005 DA - 2005// TI - PRISM: protein interactions by structural matching JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki585 DO - 10.1093/nar/gki585 ID - Ogmen2005 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 UR - https://doi.org/10.1093/nar/gki037 DO - 10.1093/nar/gki037 ID - Stein2005 ER - TY - JOUR AU - Jefferson, E. R. AU - Walsh, T. P. AU - Roberts, T. J. AU - Barton, G. J. PY - 2007 DA - 2007// TI - SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkl836 DO - 10.1093/nar/gkl836 ID - Jefferson2007 ER - TY - JOUR AU - Winter, C. AU - Henschel, A. AU - Kim, W. K. AU - Schroeder, M. PY - 2006 DA - 2006// TI - SCOPPI: a structural classification of protein-protein interfaces JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkj099 DO - 10.1093/nar/gkj099 ID - Winter2006 ER - TY - JOUR AU - Breiman, L. PY - 2001 DA - 2001// TI - Random forests JO - Machine Learning VL - 45 UR - https://doi.org/10.1023/A:1010933404324 DO - 10.1023/A:1010933404324 ID - Breiman2001 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 UR - https://doi.org/10.1002/bip.360221211 DO - 10.1002/bip.360221211 ID - Kabsch1983 ER - TY - CHAP AU - Abagyan, R. AU - Totrov, M. PY - 2007 DA - 2007// BT - ICM PB - dMolsoft LLC CY - La Jolla, CA ID - Abagyan2007 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schaffer, A. A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. AU - Lipman, D. J. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 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 UR - https://doi.org/10.1093/bioinformatics/btl158 DO - 10.1093/bioinformatics/btl158 ID - Li2006 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: multiple sequence alignment with high accuracy and high throughput JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh340 DO - 10.1093/nar/gkh340 ID - Edgar2004 ER - TY - CHAP AU - Lehmann, E. L. PY - 1975 DA - 1975// BT - Nonparametric Statistical Methods Based on Ranks PB - New York CY - McGraw-Hill ID - Lehmann1975 ER - TY - JOUR AU - Keskin, O. AU - Tsai, C. J. AU - Wolfson, H. AU - Nussinov, R. PY - 2004 DA - 2004// TI - A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications JO - Protein Sci VL - 13 UR - https://doi.org/10.1110/ps.03484604 DO - 10.1110/ps.03484604 ID - Keskin2004 ER - TY - JOUR AU - Bateman, A. AU - Coin, L. AU - Durbin, R. AU - Finn, R. D. AU - Hollich, V. AU - Griffiths-Jones, S. AU - Khanna, A. AU - Marshall, M. AU - Moxon, S. AU - Sonnhammer, E. L. AU - Studholme, D. J. AU - Yeats, C. AU - Eddy, S. R. PY - 2004 DA - 2004// TI - The Pfam protein families database JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh121 DO - 10.1093/nar/gkh121 ID - Bateman2004 ER - TY - JOUR PY - 2007 DA - 2007// TI - The Universal Protein Resource (UniProt) JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkl929 DO - 10.1093/nar/gkl929 ID - ref32 ER - TY - JOUR AU - Rice, P. AU - Longden, I. AU - Bleasby, A. PY - 2000 DA - 2000// TI - EMBOSS: the European Molecular Biology Open Software Suite JO - Trends Genet VL - 16 UR - https://doi.org/10.1016/S0168-9525(00)02024-2 DO - 10.1016/S0168-9525(00)02024-2 ID - Rice2000 ER - TY - CHAP AU - DeLano, W. L. PY - 2002 DA - 2002// BT - The PyMOL Molecular Graphics System PB - DeLano Scientific CY - Palo Alto, CA, USA ID - DeLano2002 ER - TY - CHAP PY - 2005 DA - 2005// BT - R: A language and environment for statistical computing PB - R Foundation for Statistical Computing CY - Vienna, Austria ID - ref35 ER - TY - JOUR AU - Liaw, A. AU - Wiener, M. PY - 2002 DA - 2002// TI - Classification and Regression by randomForest JO - R news VL - 2 ID - Liaw2002 ER - TY - JOUR AU - Janin, J. PY - 1997 DA - 1997// TI - Specific versus non-specific contacts in protein crystals JO - Nat Struct Biol VL - 4 UR - https://doi.org/10.1038/nsb1297-973 DO - 10.1038/nsb1297-973 ID - Janin1997 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 - Progress in biophysics and molecular biology VL - 63 UR - https://doi.org/10.1016/0079-6107(94)00008-W DO - 10.1016/0079-6107(94)00008-W ID - Jones1995 ER - TY - JOUR AU - Xu, D. AU - Tsai, C. J. AU - Nussinov, R. PY - 1997 DA - 1997// TI - Hydrogen bonds and salt bridges across protein-protein interfaces JO - Protein engineering VL - 10 UR - https://doi.org/10.1093/protein/10.9.999 DO - 10.1093/protein/10.9.999 ID - Xu1997 ER - TY - JOUR AU - Fersht, A. R. PY - 1984 DA - 1984// TI - Basis of biological specificity JO - Trends Biochem Sci VL - 9 UR - https://doi.org/10.1016/0968-0004(84)90122-1 DO - 10.1016/0968-0004(84)90122-1 ID - Fersht1984 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 the PDB at domain and amino acid resolutions JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti011 DO - 10.1093/bioinformatics/bti011 ID - Finn2005 ER - TY - JOUR AU - Deng, M. AU - Mehta, S. AU - Sun, F. AU - Chen, T. PY - 2002 DA - 2002// TI - Inferring domain-domain interactions from protein-protein interactions JO - Genome research VL - 12 UR - https://doi.org/10.1101/gr.153002 DO - 10.1101/gr.153002 ID - Deng2002 ER -