TY - JOUR AU - Clackson, T. AU - Wells, J. A. PY - 1995 DA - 1995// TI - A hot spot of binding energy in a hormone-receptor interface JO - Science VL - 1995 UR - https://doi.org/10.1126/science.7529940 DO - 10.1126/science.7529940 ID - Clackson1995 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 - 1998 UR - https://doi.org/10.1006/jmbi.1998.1843 DO - 10.1006/jmbi.1998.1843 ID - Bogan1998 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 UR - https://doi.org/10.1186/1471-2105-10-365 DO - 10.1186/1471-2105-10-365 ID - Lise2009 ER - TY - JOUR AU - Keskin, O. AU - Ma, B. AU - Nussinov, R. PY - 2005 DA - 2005// TI - Hot regions in protein–protein interactions: the organization and contribution of structurally conserved hot spot residues JO - J Mol Biol VL - 345 UR - https://doi.org/10.1016/j.jmb.2004.10.077 DO - 10.1016/j.jmb.2004.10.077 ID - Keskin2005 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 VL - 68 UR - https://doi.org/10.1002/prot.21396 DO - 10.1002/prot.21396 ID - Moreira2007 ER - TY - JOUR AU - Thorn, K. S. AU - Bogan, A. A. PY - 2001 DA - 2001// TI - ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions JO - Bioinformatics VL - 17 UR - https://doi.org/10.1093/bioinformatics/17.3.284 DO - 10.1093/bioinformatics/17.3.284 ID - Thorn2001 ER - TY - JOUR AU - Fischer, T. B. AU - Arunachalam, K. V. AU - Bailey, D. AU - Mangual, V. AU - Bakhru, S. AU - Russo, R. AU - Huang, D. AU - Paczkowski, M. AU - Lalchandani, V. AU - Ramachandra, C. AU - Ellison, B. AU - Galer, S. AU - Shapley, J. AU - Fuentes, E. AU - Tsai, J. PY - 2003 DA - 2003// TI - The binding interface database (BID): a compilation of amino acid hot spots in protein interfaces JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg163 DO - 10.1093/bioinformatics/btg163 ID - Fischer2003 ER - TY - JOUR AU - Burgoyne, N. AU - Jackson, R. PY - 2006 DA - 2006// TI - Predicting protein interaction sites: binding hotspots in protein-protein and protein-ligand interfaces JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl079 DO - 10.1093/bioinformatics/btl079 ID - Burgoyne2006 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 Natl Acad Sci VL - 102 UR - https://doi.org/10.1073/pnas.0505425102 DO - 10.1073/pnas.0505425102 ID - Guharoy2005 ER - TY - JOUR AU - Li, J. AU - Liu, Q. PY - 2009 DA - 2009// TI - ‘Double water exclusion’: a hypothesis refining the O-ring theory for the hot spots at protein interfaces JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp058 DO - 10.1093/bioinformatics/btp058 ID - Li2009 ER - TY - JOUR AU - Liu, Q. AU - Li, J. PY - 2010 DA - 2010// TI - Propensity vectors of low-ASA residue pairs in the distinction of protein interactions JO - Proteins VL - 78 ID - Liu2010 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 UR - https://doi.org/10.1002/pro.5560031231 DO - 10.1002/pro.5560031231 ID - Grishin1994 ER - TY - JOUR AU - Valdar, W. S. AU - Thornton, J. M. PY - 2001 DA - 2001// TI - Protein-protein interfaces: analysis of amino acid conservation in homodimers JO - Proteins VL - 42 UR - https://doi.org/3.0.CO;2-O DO - 3.0.CO;2-O ID - Valdar2001 ER - TY - JOUR AU - Fraser, H. B. AU - Hirsh, A. E. AU - Steinmetz, L. M. AU - Scharfe, C. AU - Feldman, M. W. PY - 2002 DA - 2002// TI - Evolutionary rate in the protein interaction network JO - Science VL - 296 UR - https://doi.org/10.1126/science.1068696 DO - 10.1126/science.1068696 ID - Fraser2002 ER - TY - JOUR AU - Caffrey, D. R. AU - Somaroo, S. AU - Hughes, J. D. AU - Mintseris, J. AU - Huang, H. 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 UR - https://doi.org/10.1110/ps.03323604 DO - 10.1110/ps.03323604 ID - Caffrey2004 ER - TY - JOUR AU - Panchenko, A. R. AU - Kondrashov, F. AU - Bryant, S. PY - 2004 DA - 2004// TI - Prediction of functional sites by analysis of sequence and structure conservation JO - Protein Sci VL - 13 UR - https://doi.org/10.1110/ps.03465504 DO - 10.1110/ps.03465504 ID - Panchenko2004 ER - TY - JOUR AU - Yogurtcu, O. N. AU - Erdemli, S. B. AU - Nussinov, R. AU - Turkay, M. AU - Keskin, O. PY - 2008 DA - 2008// TI - Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations JO - Biophys J VL - 94 UR - https://doi.org/10.1529/biophysj.107.114835 DO - 10.1529/biophysj.107.114835 ID - Yogurtcu2008 ER - TY - JOUR AU - Kim, J. AU - Mao, J. AU - Gunner, M. R. PY - 2005 DA - 2005// TI - Are acidic and basic groups in buried proteins predicted to be ionized? JO - J Mol Biol VL - 348 UR - https://doi.org/10.1016/j.jmb.2005.03.051 DO - 10.1016/j.jmb.2005.03.051 ID - Kim2005 ER - TY - JOUR AU - Glaser, F. AU - Pupko, T. AU - Paz, I. AU - Bell, R. E. AU - Bechor-Shental, D. AU - Martz, E. AU - Ben-Tal, N. PY - 2003 DA - 2003// TI - ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/19.1.163 DO - 10.1093/bioinformatics/19.1.163 ID - Glaser2003 ER - TY - JOUR AU - Wells, J. A. PY - 1991 DA - 1991// TI - Systematic mutational analyses of protein-protein interfaces JO - Methods Enzymol VL - 202 UR - https://doi.org/10.1016/0076-6879(91)02020-A DO - 10.1016/0076-6879(91)02020-A ID - Wells1991 ER - TY - JOUR AU - Jin, L. AU - Wells, J. A. PY - 1994 DA - 1994// TI - Dissecting the energetics of an antibody-antigen interface by alanine shaving and molecular grafting JO - Protein Sci VL - 3 UR - https://doi.org/10.1002/pro.5560031219 DO - 10.1002/pro.5560031219 ID - Jin1994 ER - TY - JOUR AU - Kortemme, T. AU - Baker, D. PY - 2002 DA - 2002// TI - A simple physical model for binding energy hot spots in protein-protein complexes JO - Proc Natl Acad Sci U S A VL - 99 UR - https://doi.org/10.1073/pnas.202485799 DO - 10.1073/pnas.202485799 ID - Kortemme2002 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 UR - https://doi.org/10.1016/S0022-2836(02)00442-4 DO - 10.1016/S0022-2836(02)00442-4 ID - Guerois2002 ER - TY - JOUR AU - Darnell, S. J. AU - LeGault, L. AU - Mitchell, J. C. PY - 2008 DA - 2008// TI - KFC Server: interactive forecasting of protein interaction hot spots JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkn346 DO - 10.1093/nar/gkn346 ID - Darnell2008 ER - TY - JOUR AU - Cho, K. I. AU - Kim, D. AU - Lee, D. PY - 2009 DA - 2009// TI - A feature-based approach to modelling protein–protein interaction hot spots JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkp132 DO - 10.1093/nar/gkp132 ID - Cho2009 ER - TY - JOUR AU - Tuncbag, N. AU - Keskin, O. AU - Gursoy, A. PY - 2010 DA - 2010// TI - HotPoint: hot spot prediction server for protein interfaces JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkq323 DO - 10.1093/nar/gkq323 ID - Tuncbag2010 ER - TY - JOUR AU - Zhu, X. AU - Mitchell, J. C. PY - 2011 DA - 2011// TI - KFC2: a knowledge-based hot spot prediction method based on interface solvation, atomic density, and plasticity features JO - Proteins VL - 79 UR - https://doi.org/10.1002/prot.23094 DO - 10.1002/prot.23094 ID - Zhu2011 ER - TY - JOUR AU - Landon, M. R. AU - Lancia, D. R. AU - Yu, J. AU - Thiel, S. C. AU - Vajda, S. PY - 2007 DA - 2007// TI - Identification of hot spots within druggable binding regions by computational solvent mapping of proteins JO - J Med Chem VL - 50 UR - https://doi.org/10.1021/jm061134b DO - 10.1021/jm061134b ID - Landon2007 ER - TY - JOUR AU - Guney, E. AU - Tuncbag, N. AU - Keskin, O. AU - Gursoy, A. PY - 2008 DA - 2008// TI - HotSprint: database of computational hot spots in protein interfaces JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkm813 DO - 10.1093/nar/gkm813 ID - Guney2008 ER - TY - JOUR AU - Tuncbag, N. AU - Gursoy, A. AU - Keskin, O. PY - 2009 DA - 2009// TI - Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp240 DO - 10.1093/bioinformatics/btp240 ID - Tuncbag2009 ER - TY - JOUR AU - Li, L. AU - Zhao, B. AU - Cui, Z. AU - Gan, J. AU - Sakharkar, M. K. AU - Kangueane, P. PY - 2006 DA - 2006// TI - Identification of hot spot residues at protein-protein interface JO - Bioinformation VL - 1 UR - https://doi.org/10.6026/97320630001121 DO - 10.6026/97320630001121 ID - Li2006 ER - TY - JOUR AU - Li, X. AU - Keskin, O. AU - Ma, B. AU - Nussinov, R. AU - Liang, J. PY - 2004 DA - 2004// TI - Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking JO - J Mol Biol VL - 344 UR - https://doi.org/10.1016/j.jmb.2004.09.051 DO - 10.1016/j.jmb.2004.09.051 ID - Li2004 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 VL - 39 UR - https://doi.org/3.0.CO;2-A DO - 3.0.CO;2-A ID - Hu2000 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 Natl Acad Sci U S A VL - 100 UR - https://doi.org/10.1073/pnas.1030237100 DO - 10.1073/pnas.1030237100 ID - Ma2003 ER - TY - JOUR AU - Ma, B. AU - Nussinov, R. PY - 2007 DA - 2007// TI - Trp/Met/Phe hot spots in protein-protein interactions: potential targets in drug design JO - Curr Top Med Chem VL - 7 UR - https://doi.org/10.2174/156802607780906717 DO - 10.2174/156802607780906717 ID - Ma2007 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 UR - https://doi.org/10.1371/journal.pcbi.0030119 DO - 10.1371/journal.pcbi.0030119 ID - Ofran2007 ER - TY - JOUR AU - Hsu, C. M. AU - Chen, C. Y. AU - Liu, B. J. AU - Huang, C. C. AU - Laio, M. H. AU - Lin, C. C. AU - Wu, T. L. PY - 2007 DA - 2007// TI - Identification of hot regions in protein-protein interactions by sequential pattern mining JO - BMC Bioinformatics VL - 8 UR - https://doi.org/10.1186/1471-2105-8-S5-S8 DO - 10.1186/1471-2105-8-S5-S8 ID - Hsu2007 ER - TY - JOUR AU - DeLano, W. L. PY - 2002 DA - 2002// TI - Unraveling hot spots in binding interfaces: progress and challenges JO - Curr Opin Struct Biol VL - 12 UR - https://doi.org/10.1016/S0959-440X(02)00283-X DO - 10.1016/S0959-440X(02)00283-X ID - DeLano2002 ER - TY - JOUR AU - Diller, D. J. AU - Humblet, C. AU - Zhang, X. AU - Westerhoff, L. M. PY - 2010 DA - 2010// TI - Computational alanine scanning with linear scaling semiempirical quantum mechanical methods JO - Proteins VL - 78 UR - https://doi.org/10.1002/prot.22745 DO - 10.1002/prot.22745 ID - Diller2010 ER - TY - JOUR AU - Massova, I. AU - Kollman, P. A. PY - 1999 DA - 1999// TI - Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies JO - J Am Chem Soc VL - 121 UR - https://doi.org/10.1021/ja990935j DO - 10.1021/ja990935j ID - Massova1999 ER - TY - JOUR AU - Assi, S. A. AU - Tanaka, T. AU - Rabbitts, T. H. AU - Fernandez-Fuentes, N. PY - 2010 DA - 2010// TI - PCRPi: presaging critical residues in protein interfaces, a new computational tool to chart hot spots in protein interfaces JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkp1158 DO - 10.1093/nar/gkp1158 ID - Assi2010 ER - TY - JOUR AU - Darnell, S. J. AU - Page, D. AU - Mitchell, J. C. PY - 2007 DA - 2007// TI - An automated decision-tree approach to predicting protein interaction hot spots JO - Proteins VL - 68 UR - https://doi.org/10.1002/prot.21474 DO - 10.1002/prot.21474 ID - Darnell2007 ER - TY - JOUR AU - Wang, L. AU - Liu, Z. P. AU - Zhang, X. S. AU - Chen, L. PY - 2012 DA - 2012// TI - Prediction of hot spots in protein interfaces using a random forest model with hybrid features JO - Protein Eng Des Sel VL - 25 UR - https://doi.org/10.1093/protein/gzr066 DO - 10.1093/protein/gzr066 ID - Wang2012 ER - TY - JOUR AU - Grosdidier, S. AU - Fernandez-Recio, J. PY - 2008 DA - 2008// TI - Identification of hot spot residues in protein–protein interactions by computational docking JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-447 DO - 10.1186/1471-2105-9-447 ID - Grosdidier2008 ER - TY - JOUR AU - Gao, Y. AU - Wang, R. AU - Lai, L. PY - 2004 DA - 2004// TI - Structure-based method for analyzing protein-protein interfaces JO - J Mol Model VL - 10 UR - https://doi.org/10.1007/s00894-003-0168-3 DO - 10.1007/s00894-003-0168-3 ID - Gao2004 ER - TY - JOUR AU - Gonzalez-Ruiz, D. AU - Gohlke, H. PY - 2006 DA - 2006// TI - Targeting protein-protein interactions with small molecules: challenges and perspectives for computational binding epitope detection and ligand finding JO - Curr Med Chem VL - 13 UR - https://doi.org/10.2174/092986706778201530 DO - 10.2174/092986706778201530 ID - Gonzalez-Ruiz2006 ER - TY - JOUR AU - Xia, J. F. AU - Zhao, X. M. AU - Song, J. AU - Huang, D. S. PY - 2010 DA - 2010// TI - APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility JO - BMC Bioinformatics VL - 11 UR - https://doi.org/10.1186/1471-2105-11-174 DO - 10.1186/1471-2105-11-174 ID - Xia2010 ER - TY - JOUR AU - Sukhwal, A. AU - Sowdhamini, R. PY - 2013 DA - 2013// TI - Oligomerisation status and evolutionary conservation of interface of protein structural domain superfamilies JO - Mol BioSyst VL - 9 UR - https://doi.org/10.1039/c3mb25484d DO - 10.1039/c3mb25484d ID - Sukhwal2013 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schäffer, 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 - Larkin, M. A. AU - Blackshields, G. AU - Brown, N. P. AU - Chenna, R. AU - McGettigan, P. A. AU - McWilliam, H. AU - Valentin, F. AU - Wallace, I. M. AU - Wilm, A. AU - Lopez, R. AU - Thompson, J. D. AU - Gibson, T. J. AU - Higgins, D. G. PY - 2007 DA - 2007// TI - ClustalW and ClustalX version 2 JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm404 DO - 10.1093/bioinformatics/btm404 ID - Larkin2007 ER - TY - JOUR AU - Johnson, M. S. AU - Overington, J. P. AU - Blundell, T. L. PY - 1993 DA - 1993// TI - A structural basis for sequence comparisons: an evaluation of scoring methodologies JO - J Mol Biol VL - 233 UR - https://doi.org/10.1006/jmbi.1993.1548 DO - 10.1006/jmbi.1993.1548 ID - Johnson1993 ER - TY - JOUR AU - Pugalenthi, G. AU - Suganthan, P. N. AU - Sowdhamini, R. AU - Chakrabarti, S. PY - 2007 DA - 2007// TI - SMotif: a server for structural motifs in proteins JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btl679 DO - 10.1093/bioinformatics/btl679 ID - Pugalenthi2007 ER - TY - JOUR AU - Wallis, R. AU - Leung, K. Y. AU - Osborne, M. J. AU - James, R. AU - Moore, G. R. AU - Kleanthous, C. PY - 1998 DA - 1998// TI - Specificity in protein–protein recognition: conserved Im9 residues are the major determinants of stability in the colicin E9 dnase Im9 complex JO - Biochemistry VL - 37 UR - https://doi.org/10.1021/bi971884a DO - 10.1021/bi971884a ID - Wallis1998 ER - TY - JOUR AU - Curtis, M. D. AU - James, R. PY - 1991 DA - 1991// TI - Investigation of the specificity of the interaction between colicin E9 and its immunity protein by site-directed mutagenesis JO - Mol Microbiol VL - 5 UR - https://doi.org/10.1111/j.1365-2958.1991.tb01981.x DO - 10.1111/j.1365-2958.1991.tb01981.x ID - Curtis1991 ER - TY - JOUR AU - Radisky, E. S. AU - Lu, C. J. K. AU - Kwan, G. AU - Koshland, D. E. PY - 2005 DA - 2005// TI - Role of the intermolecular hydrogen bond network in the inhibitory power of chymotrypsin inhibitor 2 JO - Biochemistry VL - 44 UR - https://doi.org/10.1021/bi047301w DO - 10.1021/bi047301w ID - Radisky2005 ER - TY - JOUR AU - Radisky, E. S. AU - Kwan, G. AU - Lu, C. J. K. AU - Koshland, D. E. PY - 2004 DA - 2004// TI - Binding, proteolytic, and crystallographic analyses of mutations at the protease − inhibitor interface of the subtilisin BPN‘/chymotrypsin inhibitor 2 complex JO - Biochemistry VL - 43 UR - https://doi.org/10.1021/bi048797k DO - 10.1021/bi048797k ID - Radisky2004 ER -