From Protein Structure to Function with Bioinformatics.pdf

186 N.J. Burgoyne and R.M. JacksonLijnzaad P, Berendsen HJ, Argos P (1996) Hydrophobic patches on the surfaces of protein structures.Proteins 25:389–397.Lo Conte L, Chothia C, Janin J (1999) The atomic structure of protein-protein recognition sites.J Mol Biol 285:2177–2198.Ma B, Elkayam T, Wolfson H, et al. (2003) Protein-protein interactions: structurally conservedresidues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad SciUSA 100:5772–5777.Murakami Y, Jones S (2006) SHARP2: protein-protein interaction predictions using patch analysis.Bioinformatics 22:1794–1795.Murga LF, Ondrechen MJ, Ringe D (2008) Prediction of interaction sites from apo 3D structureswhen the holo conformation is different. Proteins 72:980–992.Neuvirth H, Raz R, Schreiber G (2004) ProMate: a structure based prediction program to identifythe location of protein-protein binding sites. J Mol Biol 338:181–199.Newman M, Lunnen K, Wilson G, et al. (1998) Crystal structure of restriction endonuclease BglIbound to its interrupted DNA recognition sequence. EMBO J 17:5466–5476.Nissink JWM, Verdonk ML, Klebe G (2000) Simple knowledge-based descriptors to predict protein-ligandinteractions. methodology and validation. J Comput Aided Mol Des 14:787–803.O’Brien KP, Remm M, Sonnhammer EL (2005) Inparanoid: a comprehensive database of eukaryoticorthologs. Nucleic Acids Res 33:D476–480.Oledzki PR, Laurie AT, Jackson RM (2006) Protein–ligand docking and structure-based drugdesign. Edited by Westhead DR, Dunn MJ In, Encyclopedia of Genetics, Genomics,Proteomics and Bioinformatics, 1–17.Ondrechen MJ, Clifton JG, Ringe D (2001) THEMATICS: a simple computational predictor ofenzyme function from structure. Proc Natl Acad Sci USA 98:12473–12478.Pettit FK, Bare E, Tsai A, et al. (2007) HotPatch: a statistical approach to finding biologically relevantfeatures on protein surfaces. J Mol Biol 369:863–879.Pupko T, Bell RE, Mayrose I, et al. (2002) Rate4Site: an algorithmic tool for the identification offunctional regions in proteins by surface mapping of evolutionary determinants within theirhomologues. Bioinformatics 18(Suppl 1):S71–77.Radzicka A, Pedersen L, Wolfenden R (1988) Influences of solvent water on protein folding: free energiesof solvation of cis and trans peptides are nearly identical. Biochemistry 27:4538–4541.Rocchia W, Sridharan S, Nicholls A, et al. (2002) Rapid grid-based construction of the molecularsurface and the use of induced surface charge to calculate reaction field energies: applicationsto the molecular systems and geometric objects. J Comput Chem 23:128–137.Stawiski EW, Gregoret LM, Mandel-Gutfreund Y (2003) Annotating nucleic acid-binding functionbased on protein structure. J Mol Biol 326:1065–1079.Thorn KS, Bogan AA (2001) ASEdb: a database of alanine mutations and their effects on the freeenergy of binding in protein interactions. Bioinformatics 17:284–285.Todd AE, Orengo CA, Thornton JM (2002) Sequence and structural differences between enzymeand nonenzyme homologs. Structure 10:1435–1451.Tong W, Williams RJ, Wei Y, et al. (2008) Enhanced performance in prediction of protein activesites with THEMATICS and support vector machines. Protein Sci 17:333–341.Tsuchiya Y, Kinoshita K, Nakamura H (2005) PreDs: a server for predicting dsDNA-binding siteon protein molecular surfaces. Bioinformatics 21:1721–1723.Valdar WS (2002) Scoring residue conservation. Proteins 48:227–241.Wang Y, Zhang H, Li W, et al. (1995) Discriminating compact nonnative structures from the nativestructure of globular proteins. Proc Natl Acad Sci USA 92:709–713.Wolfenden R, Andersson L, Cullis PM, et al. (1981) Affinities of amino acid side chains for solventwater. Biochemistry 20:849–855.Xu D, Tsai CJ, Nussinov R (1997) Hydrogen bonds and salt bridges across protein-protein interfaces.Protein Eng 10:999–1012.Yadav A, Jackson RM, Holbrook JJ, et al. (1991) Role of solvent reorganization energies in thecatalytic activity of enzymes. J Am Chem Soc. 113:4800–4805.Zhou H-X, Qin S (2007) Interaction-site prediction for protein complexes: a critical assessment.Bioinformatics 23:2203–2209.