{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,25]],"date-time":"2024-07-25T12:31:32Z","timestamp":1721910692004},"reference-count":66,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2008,10,21]],"date-time":"2008-10-21T00:00:00Z","timestamp":1224547200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2008,12]]},"DOI":"10.1186\/1471-2105-9-448","type":"journal-article","created":{"date-parts":[[2008,10,21]],"date-time":"2008-10-21T18:13:20Z","timestamp":1224612800000},"source":"Crossref","is-referenced-by-count":11,"title":["Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces"],"prefix":"10.1186","volume":"9","author":[{"given":"Salim","family":"Bougouffa","sequence":"first","affiliation":[]},{"given":"Jim","family":"Warwicker","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2008,10,21]]},"reference":[{"key":"2433_CR1","doi-asserted-by":"publisher","first-page":"611","DOI":"10.1002\/1615-9861(200206)2:6<611::AID-PROT611>3.0.CO;2-Y","volume":"2","author":"D Auerbach","year":"2002","unstructured":"Auerbach D, Thaminy S, Hottiger MO, Stagljar I: The post-genomic era of interactive proteomics: facts and perspectives. Proteomics 2002, 2: 611\u2013623. 10.1002\/1615-9861(200206)2:6<611::AID-PROT611>3.0.CO;2-Y","journal-title":"Proteomics"},{"key":"2433_CR2","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1113\/jphysiol.2004.080440","volume":"563","author":"AC Gingras","year":"2005","unstructured":"Gingras AC, Aebersold R, Raught B: Advances in protein complex analysis using mass spectrometry. J Physiol 2005, 563: 11\u201321. 10.1113\/jphysiol.2004.080440","journal-title":"J Physiol"},{"key":"2433_CR3","doi-asserted-by":"publisher","first-page":"1010","DOI":"10.1101\/gad.1528707","volume":"21","author":"X Zhu","year":"2007","unstructured":"Zhu X, Gerstein M, Snyder M: Getting connected: analysis and principles of biological networks. Genes Dev 2007, 21: 1010\u20131024. 10.1101\/gad.1528707","journal-title":"Genes Dev"},{"key":"2433_CR4","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucl Acids Res 2000, 28: 235\u2013242. 10.1093\/nar\/28.1.235","journal-title":"Nucl Acids Res"},{"key":"2433_CR5","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1126\/science.1121018","volume":"311","author":"J-M Chandonia","year":"2006","unstructured":"Chandonia J-M, Brenner SE: The impact of structural genomics: Expectations and outcomes. Science 2006, 311: 347\u2013351. 10.1126\/science.1121018","journal-title":"Science"},{"key":"2433_CR6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.2174\/138920308783565741","volume":"9","author":"DW Ritchie","year":"2008","unstructured":"Ritchie DW: Recent progress and future directions in protein-protein docking. Curr Protein Pept Sci 2008, 9: 1\u201315. 10.2174\/138920308783565741","journal-title":"Curr Protein Pept Sci"},{"key":"2433_CR7","doi-asserted-by":"publisher","first-page":"57","DOI":"10.2174\/138920108783955209","volume":"9","author":"IA Vakser","year":"2008","unstructured":"Vakser IA, Kundrotas P: Predicting 3D structures of protein-protein complexes. Curr Pharm Biotechnol 2008, 9: 57\u201366. 10.2174\/138920108783955209","journal-title":"Curr Pharm Biotechnol"},{"key":"2433_CR8","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1016\/j.bpc.2007.05.021","volume":"129","author":"J Audie","year":"2007","unstructured":"Audie J, Scarlata S: A novel empirical free energy function that explains and predicts protein-protein binding affinities. Biophys Chem 2007, 129: 198\u2013211. 10.1016\/j.bpc.2007.05.021","journal-title":"Biophys Chem"},{"key":"2433_CR9","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1016\/j.crvi.2004.03.006","volume":"327","author":"M Eisenstein","year":"2004","unstructured":"Eisenstein M, Katchalski-Katzir E: On proteins, grids, correlations, and docking. C R Biol 2004, 327: 409\u2013420. 10.1016\/j.crvi.2004.03.006","journal-title":"C R Biol"},{"issue":"3","key":"2433_CR10","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1016\/j.tibtech.2004.01.006","volume":"22","author":"S Vajda","year":"2004","unstructured":"Vajda S, Camacho CJ: Protein-protein docking: is the glass half-full or half-empty? Trends Biotechnol 2004, 22(3):110\u2013116. 10.1016\/j.tibtech.2004.01.006","journal-title":"Trends Biotechnol"},{"key":"2433_CR11","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1006\/jmbi.1997.1203","volume":"272","author":"HA Gabb","year":"1997","unstructured":"Gabb HA, Jackson RM, Sternberg MJ: Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 1997, 272: 106\u2013120. 10.1006\/jmbi.1997.1203","journal-title":"J Mol Biol"},{"key":"2433_CR12","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1089\/106652702760277336","volume":"9","author":"E Althaus","year":"2002","unstructured":"Althaus E, Kohlbacher O, Lenhof HP, M\u00fcller P: A combinatorial approach to protein docking with flexible side chains. J Comput Biol 2002, 9: 597\u2013612. 10.1089\/106652702760277336","journal-title":"J Comput Biol"},{"key":"2433_CR13","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1002\/prot.20556","volume":"60","author":"O Schueler-Furman","year":"2005","unstructured":"Schueler-Furman O, Wang C, Baker D: Progress in protein-protein dcking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins 2005, 60: 187\u2013194. 10.1002\/prot.20556","journal-title":"Proteins"},{"key":"2433_CR14","doi-asserted-by":"publisher","first-page":"758","DOI":"10.1002\/prot.21684","volume":"69","author":"C Wang","year":"2007","unstructured":"Wang C, Schueler-Furman O, Sndre I, London N, Fleishman SJ, Bradley P, Qian B, Baker D: RosettaDock in CAPRI rounds 6\u201312. Proteins 2007, 69: 758\u2013763. 10.1002\/prot.21684","journal-title":"Proteins"},{"key":"2433_CR15","doi-asserted-by":"publisher","first-page":"1317","DOI":"10.1038\/nbt1018","volume":"22","author":"P Aloy","year":"2004","unstructured":"Aloy P, Russell RB: Ten thousand interactions for the molecular biologist. Nat Biotechnol 2004, 22: 1317\u20131321. 10.1038\/nbt1018","journal-title":"Nat Biotechnol"},{"key":"2433_CR16","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1146\/annurev.biochem.77.062706.133317","volume":"77","author":"C Kiel","year":"2008","unstructured":"Kiel C, Beltrao P, Serrano L: Analyzing protein interaction networks using structural information. Annu Rev Biochem 2008, 77: 415\u2013441. 10.1146\/annurev.biochem.77.062706.133317","journal-title":"Annu Rev Biochem"},{"key":"2433_CR17","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1002\/pro.5560010117","volume":"1","author":"N Horton","year":"1992","unstructured":"Horton N, Lewis M: Calculation of the free-energy of association for protein complexes. Protein Science 1992, 1: 169\u2013181.","journal-title":"Protein Science"},{"key":"2433_CR18","doi-asserted-by":"publisher","first-page":"123","DOI":"10.2174\/138920108783955164","volume":"9","author":"S Teng","year":"2008","unstructured":"Teng S, Michonova-Alexova E, Alexov E: Approaches and resources for prediction of the effects of non-synonymous single nucleotide polymorphism on protein function and interactions. Curr Pharm Biotechnol 2008, 9: 123\u2013133. 10.2174\/138920108783955164","journal-title":"Curr Pharm Biotechnol"},{"key":"2433_CR19","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1016\/S0022-2836(02)00442-4","volume":"320","author":"R Guerois","year":"2002","unstructured":"Guerois R, Nielsen JE, Serrano L: Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 2002, 320: 369\u2013387. 10.1016\/S0022-2836(02)00442-4","journal-title":"J Mol Biol"},{"key":"2433_CR20","doi-asserted-by":"publisher","first-page":"14116","DOI":"10.1073\/pnas.202485799","volume":"99","author":"T Kortemme","year":"2002","unstructured":"Kortemme T, Baker D: A simple model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci USA 2002, 99: 14116\u201314121. 10.1073\/pnas.202485799","journal-title":"Proc Natl Acad Sci USA"},{"key":"2433_CR21","doi-asserted-by":"publisher","first-page":"2860","DOI":"10.1110\/ps.0222702","volume":"11","author":"C Cole","year":"2002","unstructured":"Cole C, Warwicker J: Side-chain conformational entropy at protein-protein interfaces. Protein Science 2002, 11: 2860\u20132870. 10.1110\/ps.0222702","journal-title":"Protein Science"},{"key":"2433_CR22","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1006\/jmbi.1994.1366","volume":"239","author":"P Koehl","year":"1994","unstructured":"Koehl P, Delarue M: Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J Mol Biol 1994, 239: 249\u2013275. 10.1006\/jmbi.1994.1366","journal-title":"J Mol Biol"},{"key":"2433_CR23","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1002\/prot.21099","volume":"66","author":"Z Xiang","year":"2007","unstructured":"Xiang Z, Steinbach PJ, Jacobson MJ, Friesner RA, Honig B: Prediction of side-chain conformations on protein surfaces. Proteins 2007, 66: 814\u2013823. 10.1002\/prot.21099","journal-title":"Proteins"},{"key":"2433_CR24","doi-asserted-by":"publisher","first-page":"2001","DOI":"10.1110\/ps.03154503","volume":"12","author":"AA Canutescu","year":"2003","unstructured":"Canutescu AA, Shelenkov AA, Dunbrack RL Jr: A graph-theory algorithm for rapid protein side-cahin prediction. Protein Science 2003, 12: 2001\u20132014. 10.1110\/ps.03154503","journal-title":"Protein Science"},{"key":"2433_CR25","doi-asserted-by":"publisher","first-page":"1048","DOI":"10.1006\/jmbi.1997.1368","volume":"273","author":"A Tamura","year":"1997","unstructured":"Tamura A, Privalov PL: The entropy cost of protein association. J Mol Biol 1997, 273: 1048\u20131060. 10.1006\/jmbi.1997.1368","journal-title":"J Mol Biol"},{"key":"2433_CR26","doi-asserted-by":"publisher","first-page":"1487","DOI":"10.1006\/jmbi.1998.2559","volume":"286","author":"CK Vaughan","year":"1999","unstructured":"Vaughan CK, Buckle AM, Fersht AR: Structural response to mutation at a protein-protein interface. J Mol Biol 1999, 286: 1487\u20131506. 10.1006\/jmbi.1998.2559","journal-title":"J Mol Biol"},{"key":"2433_CR27","doi-asserted-by":"publisher","first-page":"4105","DOI":"10.1021\/j100299a032","volume":"91","author":"YK Kang","year":"1987","unstructured":"Kang YK, Nemethy G, Scheraga HA: Free energies of hydration of solute molecules 1. Improvement of the hydration shell model by exact computations of overlap volumes. J Chem Phys 1987, 91: 4105\u20134109. 10.1021\/j100299a032","journal-title":"J Chem Phys"},{"key":"2433_CR28","doi-asserted-by":"publisher","first-page":"1103","DOI":"10.1016\/S0006-3495(90)82630-8","volume":"57","author":"F Colonna-Cesari","year":"1990","unstructured":"Colonna-Cesari F, Sander C: Excluded volume approximation to protein-solvent interaction. The solvent contact model. Biophys J 1990, 57: 1103\u20131107.","journal-title":"Biophys J"},{"key":"2433_CR29","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1002\/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO;2-N","volume":"35","author":"T Lazaridis","year":"1999","unstructured":"Lazaridis T, Karplus M: Effective energy function for proteins in solution. Proteins 1999, 35: 133\u2013152. 10.1002\/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO;2-N","journal-title":"Proteins"},{"key":"2433_CR30","doi-asserted-by":"publisher","first-page":"1335","DOI":"10.1093\/bioinformatics\/btl079","volume":"22","author":"NJ Burgoyne","year":"2006","unstructured":"Burgoyne NJ, Jackson RM: Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces. Bioinformatics 2006, 22: 1335\u20131342. 10.1093\/bioinformatics\/btl079","journal-title":"Bioinformatics"},{"key":"2433_CR31","doi-asserted-by":"publisher","first-page":"1618","DOI":"10.1529\/biophysj.104.040964","volume":"87","author":"T Wang","year":"2004","unstructured":"Wang T, Tomic S, Gabdoulline RR, Wade RC: How optimal are the binding energetics of barnase and barstar? Biophys J 2004, 87: 1618\u20131630. 10.1529\/biophysj.104.040964","journal-title":"Biophys J"},{"key":"2433_CR32","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1093\/bioinformatics\/17.3.284","volume":"17","author":"KS Thorn","year":"2001","unstructured":"Thorn KS, Bogan AA: ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics 2001, 17: 284\u2013285. 10.1093\/bioinformatics\/17.3.284","journal-title":"Bioinformatics"},{"key":"2433_CR33","doi-asserted-by":"publisher","first-page":"D195","DOI":"10.1093\/nar\/gkj017","volume":"34","author":"MD Kumar","year":"2006","unstructured":"Kumar MD, Gromiha MM: PINT: Protein-protein Interactions Thermodynamic Database. Nucl Acids Res 2006, 34: D195-D198. 10.1093\/nar\/gkj017","journal-title":"Nucl Acids Res"},{"key":"2433_CR34","doi-asserted-by":"publisher","first-page":"D120","DOI":"10.1093\/nar\/gkh082","volume":"32","author":"KA Bava","year":"2004","unstructured":"Bava KA, Gromiha MM, Uedaira H, Kitajima K, Sarai A: ProTherm, version 4.0; thermodynamic database for proteins and mutants. Nucl Acids Res 2004, 32: D120-D121. 10.1093\/nar\/gkh082","journal-title":"Nucl Acids Res"},{"key":"2433_CR35","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/protein\/3.1.1","volume":"3","author":"AV Finkelstein","year":"1989","unstructured":"Finkelstein AV, Janin J: The price of lost freedom: the entropy of bimolecular complex formation. Protein Eng 1989, 3: 1\u20133. 10.1093\/protein\/3.1.1","journal-title":"Protein Eng"},{"key":"2433_CR36","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1002\/(SICI)1097-0134(199706)28:2<144::AID-PROT2>3.0.CO;2-F","volume":"28","author":"LM Amzel","year":"1997","unstructured":"Amzel LM: Loss of translational entropy in binding, folding, and catalysis. Proteins 1997, 28: 144\u2013149. 10.1002\/(SICI)1097-0134(199706)28:2<144::AID-PROT2>3.0.CO;2-F","journal-title":"Proteins"},{"key":"2433_CR37","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1002\/jcc.10379","volume":"25","author":"H Gohlke","year":"2004","unstructured":"Gohlke H, Case DA: Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. J Comput Chem 2004, 25: 238\u2013250. 10.1002\/jcc.10379","journal-title":"J Comput Chem"},{"key":"2433_CR38","doi-asserted-by":"publisher","first-page":"2925","DOI":"10.1073\/pnas.71.8.2925","volume":"71","author":"JA Reynolds","year":"1974","unstructured":"Reynolds JA, Gilbert DB, Tanford C: Empirical correlation between hydrophobic free energy and aqueous cavity surface area. Proc Natl Acad Sci USA 1974, 71: 2925\u20132927. 10.1073\/pnas.71.8.2925","journal-title":"Proc Natl Acad Sci USA"},{"key":"2433_CR39","doi-asserted-by":"publisher","first-page":"622","DOI":"10.1073\/pnas.80.2.622","volume":"80","author":"B Lee","year":"1983","unstructured":"Lee B: Calculation of volume fluctuations for globular protein models. Proc Natl Acad Sci USA 1983, 80: 622\u2013626. 10.1073\/pnas.80.2.622","journal-title":"Proc Natl Acad Sci USA"},{"key":"2433_CR40","doi-asserted-by":"publisher","first-page":"3494","DOI":"10.1002\/pmic.200500534","volume":"6","author":"P Chan","year":"2006","unstructured":"Chan P, Lovric J, Warwicker J: Subcellular pH and the predicted pH-dependent features of proteins. Proteomics 2006, 6: 3494\u20133501. 10.1002\/pmic.200500534","journal-title":"Proteomics"},{"key":"2433_CR41","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1016\/S0022-5193(86)80093-5","volume":"121","author":"J Warwicker","year":"1986","unstructured":"Warwicker J: Continuum dielectric modelling of the protein-solvent system, and calculation of the long-range electrostatic field of the enzyme phosphoglycerate mutase. J Theor Biol 1986, 121: 199\u2013210. 10.1016\/S0022-5193(86)80093-5","journal-title":"J Theor Biol"},{"key":"2433_CR42","doi-asserted-by":"publisher","first-page":"2793","DOI":"10.1110\/ps.04785604","volume":"13","author":"J Warwicker","year":"2004","unstructured":"Warwicker J: Improved pKa calculations through flexibility based sampling of a water-dominated interaction scheme. Protein Science 2004, 13: 2793\u20132805. 10.1110\/ps.04785604","journal-title":"Protein Science"},{"key":"2433_CR43","doi-asserted-by":"publisher","first-page":"5804","DOI":"10.1073\/pnas.88.13.5804","volume":"88","author":"P Beroza","year":"1991","unstructured":"Beroza P, Fredkin DR, Okamura MY, Feher G: Protonation of interacting residues in a protein by a Monte Carlo method: application to lysozyme abd the photosynthetic reaction center of Rhodobacter sphaeroides . Proc Natl Acad Sci USA 1991, 88: 5804\u20135808. 10.1073\/pnas.88.13.5804","journal-title":"Proc Natl Acad Sci USA"},{"key":"2433_CR44","doi-asserted-by":"publisher","first-page":"10219","DOI":"10.1021\/bi00496a010","volume":"29","author":"D Bashford","year":"1990","unstructured":"Bashford D, Karplus : pKa's of ionisable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry 1990, 29: 10219\u201310225. 10.1021\/bi00496a010","journal-title":"Biochemistry"},{"key":"2433_CR45","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1006\/jmbi.1994.1301","volume":"238","author":"J Antosiewicz","year":"1994","unstructured":"Antosiewicz J, McCammon JA, Gilson MK: Prediction of the pH-dependent properties of proteins. J Mol Biol 1994, 238: 415\u2013436. 10.1006\/jmbi.1994.1301","journal-title":"J Mol Biol"},{"key":"2433_CR46","doi-asserted-by":"publisher","first-page":"809","DOI":"10.1093\/protein\/10.7.809","volume":"10","author":"J Warwicker","year":"1997","unstructured":"Warwicker J: Improving pKa calculations with consideration of hydration entropy. Protein Eng 1997, 10: 809\u2013814. 10.1093\/protein\/10.7.809","journal-title":"Protein Eng"},{"key":"2433_CR47","unstructured":"Gnu Regression, Econometrics and Time-series Library[ http:\/\/gretl.sourceforge.net\/ ]"},{"key":"2433_CR48","doi-asserted-by":"publisher","first-page":"2714","DOI":"10.1002\/elps.1150181505","volume":"18","author":"N Guex","year":"1997","unstructured":"Guex N, Peitsch MC: Swiss-Model and the Swiss-PdbViewer: an environment for comparative protein modelling. Electrophoresis 1997, 18: 2714\u20132723. 10.1002\/elps.1150181505","journal-title":"Electrophoresis"},{"key":"2433_CR49","doi-asserted-by":"publisher","first-page":"11435","DOI":"10.1021\/bi960515w","volume":"35","author":"MJM Castro","year":"1996","unstructured":"Castro MJM, Anderson S: Alanine point-mutations in the reactive region of bovine pancreatic trypsin inhibitor: Effects on the kinetics and thermodynamics of binding to beta-trypsin and alpha-chymotrypsin. Biochemistry 1996, 35: 11435\u201311446. 10.1021\/bi960515w","journal-title":"Biochemistry"},{"key":"2433_CR50","doi-asserted-by":"publisher","first-page":"696","DOI":"10.1006\/jmbi.1997.0892","volume":"267","author":"C Frisch","year":"1997","unstructured":"Frisch C, Schreiber G, Johnson CM, Fersht AR: Thermodynamics of the interaction of barnase and barstar: changes in free energy versus changes in enthalpy on mutation. J Mol Biol 1997, 267: 696\u2013706. 10.1006\/jmbi.1997.0892","journal-title":"J Mol Biol"},{"key":"2433_CR51","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1016\/S0022-2836(03)00783-6","volume":"331","author":"JR Horn","year":"2003","unstructured":"Horn JR, Ramaswamy S, Murphy KP: Structure and Energetics of Protein-Protein Interactions: The Role of Conformational Heterogeneity in OMTKY3 Binding to Serine Proteases. J Mol Biol 2003, 331: 497\u2013508. 10.1016\/S0022-2836(03)00783-6","journal-title":"J Mol Biol"},{"key":"2433_CR52","doi-asserted-by":"publisher","first-page":"6794","DOI":"10.1074\/jbc.271.36.21848","volume":"271","author":"C Herrmann","year":"1996","unstructured":"Herrmann C, Horn G, Spaargaren M, Wittinghofer A: Differential Interaction of the Ras Family GTP-binding Proteins H-Ras, Rap1A, and R-Ras with the Putative Effector Molecules Raf Kinase and Ral-Guanine Nucleotide Exchange Factor. J Biol Chem 1996, 271: 6794\u20136800. 10.1074\/jbc.271.12.6794","journal-title":"J Biol Chem"},{"key":"2433_CR53","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1016\/j.jmb.2005.02.048","volume":"348","author":"S Wohlgemuth","year":"2005","unstructured":"Wohlgemuth S, Kiel C, Kr\u00e4mer A, Serrano L, Wittinghofer F, Herrmann C: Recognizing and Defining True Ras Binding Domains I: Biochemical Analysis. J Mol Biol 2005, 348: 741\u2013758. 10.1016\/j.jmb.2005.02.048","journal-title":"J Mol Biol"},{"key":"2433_CR54","doi-asserted-by":"publisher","first-page":"9667","DOI":"10.1021\/bi960819i","volume":"35","author":"W Dall'Acqua","year":"1996","unstructured":"Dall'Acqua W, Goldman ER, Eisenstein E, Mariuzza RA: A mutational analysis of the binding of two different proteins to the same antibody. Biochemistry 1996, 35: 9667\u20139676. 10.1021\/bi960819i","journal-title":"Biochemistry"},{"key":"2433_CR55","doi-asserted-by":"publisher","first-page":"1534","DOI":"10.1126\/science.2451287","volume":"239","author":"M Verhoeyen","year":"1988","unstructured":"Verhoeyen M, Milstein C, Winter G: Reshaping human antibodies: Grafting an antilysozyme activity. Science 1988, 239: 1534\u20131536. 10.1126\/science.2451287","journal-title":"Science"},{"key":"2433_CR56","doi-asserted-by":"publisher","first-page":"1868","DOI":"10.1002\/pro.5560070903","volume":"7","author":"A Rajpal","year":"1998","unstructured":"Rajpal A, Taylor MG, Kirsch JF: Quantitative evaluation of the chicken lysozyme epitope in the HyHEL-10 Fab complex: Free energies and kinetics. Protein Science 1998, 7: 1868\u20131874.","journal-title":"Protein Science"},{"key":"2433_CR57","doi-asserted-by":"publisher","first-page":"1039","DOI":"10.1016\/j.jmb.2004.05.050","volume":"340","author":"C Kiel","year":"2004","unstructured":"Kiel C, Serrano L, Herrmann C: A Detailed Thermodynamic Analysis of Ras\/Effector Complex Interfaces. J Mol Biol 2004, 340: 1039\u20131058. 10.1016\/j.jmb.2004.05.050","journal-title":"J Mol Biol"},{"issue":"3","key":"2433_CR58","doi-asserted-by":"publisher","first-page":"167","DOI":"10.3109\/14756368809040723","volume":"2","author":"P Ascenzi","year":"1988","unstructured":"Ascenzi P, Amiconi G, Menegatti E, Guarneri M, Bolognesi M, Schnebli HP: Binding of the recombinant proteinase inhibitor eglin c from leech Hirudo medicinalis to human leukocyte elastase, bovine alpha-chymotrypsin and subtilisin Carlsberg: Thermodynamic study. J Enzyme Inhib 1988, 2(3):167\u2013172. 10.3109\/14756368809040723","journal-title":"J Enzyme Inhib"},{"key":"2433_CR59","doi-asserted-by":"publisher","first-page":"476","DOI":"10.1021\/bi971884a","volume":"37","author":"R Wallis","year":"1998","unstructured":"Wallis R, Leung KY, Osborne MJ, James R, Moore GR, Kleanthous C: Specificity in Protein-Protein Recognition: Conserved Im9 Residues Are the Major Determinants of Stability in the Colicin E9 DNase-Im9 Complex. Biochemistry 1998, 37: 476\u2013485. 10.1021\/bi971884a","journal-title":"Biochemistry"},{"key":"2433_CR60","doi-asserted-by":"crossref","first-page":"503","DOI":"10.4049\/jimmunol.148.2.503","volume":"148","author":"TB Lavoie","year":"1992","unstructured":"Lavoie TB, Drohan WN, Smith-Gill SJ: Experimental analysis by site-directed mutagenesis of somatic mutation effects on affinity and fine specificity in antibodies specific for lysozyme. J Immunol 1992, 148: 503\u2013513.","journal-title":"J Immunol"},{"key":"2433_CR61","doi-asserted-by":"publisher","first-page":"4420","DOI":"10.1021\/bi00288a012","volume":"22","author":"RJ Read","year":"1983","unstructured":"Read RJ, Fujinaga M, Sielecki AR, James MNG: Structure of the complex of Streptomyces griseus protease B and the third domain of the turkey ovomucoid inhibitor at 1.8 \u00c5 resolution. Biochemistry 1983, 22: 4420\u20134433. 10.1021\/bi00288a012","journal-title":"Biochemistry"},{"key":"2433_CR62","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1006\/jmbi.2000.4075","volume":"302","author":"R Shapiro","year":"2000","unstructured":"Shapiro R, Ruiz-Gutierrez M, Chen CZ: Analysis of the interactions of human ribonuclease inhibitor with angiogenin and ribonuclease A by mutagenesis: Importance of inhibitor residues inside versus outside the C-terminal 'hot spot'. J Mol Biol 2000, 302: 497\u2013519. 10.1006\/jmbi.2000.4075","journal-title":"J Mol Biol"},{"key":"2433_CR63","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1006\/abio.1999.4183","volume":"273","author":"AA Kortt","year":"1999","unstructured":"Kortt AA, Nice E, Gruen LC: Analysis of the Binding of the Fab Fragment of Monoclonal Antibody NC10 to Influenza Virus N9 Neuraminidase from Tern and Whale Using the BIAcore Biosensor: Effect of Immobilization Level and Flow Rate on Kinetic Analysis. Anal Biochem 1999, 273: 133\u2013141. 10.1006\/abio.1999.4183","journal-title":"Anal Biochem"},{"key":"2433_CR64","doi-asserted-by":"crossref","first-page":"1195","DOI":"10.1093\/oxfordjournals.jbchem.a132236","volume":"84","author":"Y Uehara","year":"1978","unstructured":"Uehara Y, Tonomura B, Hiromi K: Direct fluorometric determination of a dissociation constant as low as 10\u201310 M for the subtilisin BPN'-protein proteinase inhibitor (Streptomyces subtilisin inhibitor) complex by a single photon counting technique. J Biochem 1978, 84: 1195\u20131202.","journal-title":"J Biochem"},{"key":"2433_CR65","doi-asserted-by":"publisher","first-page":"32015","DOI":"10.1074\/jbc.M205009200","volume":"277","author":"AO Pineda","year":"2002","unstructured":"Pineda AO, Cantwell AM, Bush LA, Rose T, Cera ED: The thrombin epitope recognizing thrombomodulin is a highly cooperative hot spot in exosite I. J Biol Chem 2002, 277: 32015\u201332019. 10.1074\/jbc.M205009200","journal-title":"J Biol Chem"},{"key":"2433_CR66","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1016\/0022-2836(83)90078-5","volume":"164","author":"Z Chen","year":"1983","unstructured":"Chen Z, Bode W: Refined 2\u00b75 \u00c5 X-ray crystal structure of the complex formed by porcine kallikrein A and the bovine pancreatic trypsin inhibitor. Crystallization, Patterson search, structure determination, refinement, structure and comparison with its components and with the bovine trypsin-pancreatic trypsin inhibitor complex. J Mol Biol 1983, 164: 283\u2013311. 10.1016\/0022-2836(83)90078-5","journal-title":"J Mol Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-448.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-9-448\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-448.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,20]],"date-time":"2023-05-20T16:52:33Z","timestamp":1684601553000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-448"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,10,21]]},"references-count":66,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["2433"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-448","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,10,21]]},"article-number":"448"}}