Структура и функционирование белков. Применение методов биоинформатики - Джон Ригден 2014
Предсказание функции белка по свойствам его поверхности
Литература
Antosiewicz J, McCammon JA, Gilson MK (1994) Prediction of pH-dependent properties of proteins. J Mol Biol 238:415-436.
Beadle BM, Shoichet BK (2002) Structural bases of stability-function tradeoffs in enzymes. J Mol Biol 321:285-296.
Berchanski A, Shapira B, Eisenstein M (2004) Hydrophobic complementarity in protein-protein docking. Proteins 56:130-142.
Binkowski TA, Naghibzadeh S, Liang J (2003) CASTp: computed atlas of surface topography of proteins. Nucleic Acids Res 31:3352—3355.
Bogan AA, Thom KS (1998) Anatomy of hot spots in protein interfaces. J Mol Biol 280:1-9.
Bordner AJ, Abagyan R (2005) Statistical analysis and prediction of protein-protein interfaces. Proteins 60:353-366.
Bradford JR, Westhead DR (2005) Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics 21:1487-1494.
Brady GP Jr, Stouten PF (2000) Fast prediction and visualization of protein binding pockets with PASS. J Comput Aided Mol Des 14:383-401.
Brown D, Superti-Fuiga G (2003) Rediscovering the sweet spot in drug discovery. Drug Discov Today 8:1067-1077.
Burgoyne NJ, Jackson RM (2006) Predicting protein interaction sites: binding hot-spots in protein- protein and protein-ligand interfaces. Bioinformatics 22:1335-1342.
Cheng AC, Coleman RG, Smyth KT, et al. (2007) Structure-based maximal affinity model predicts small-molecule druggability. Nat Biotechnol 25:71-75.
Chothia C., Janin J (1975) Principles of protein-protein recognition. Nature 256: 705-708.
Clackson T, Wells JA (1995) A hot spot of binding energy in a hormone-receptor interface. Science 267:383-386.
Connolly ML (1984) Analytical molecular surface calculation. J Appl Cryst 16:548-558.
Devos D, Valencia A (2000) Practical limits of function prediction. Proteins 41:98-107.
Ebner S, Sharon N, Ben-Tal N (2003) Evolutionary analysis reveals collective properties and specificity in the C-type lectin and lectin-like domain superfamily. Proteins 53:44-55.
Elcock AH (2001) Prediction of functionally important residues based solely on the computed energetics of protein structure. J Mol Biol 312:885-896.
Fauchere JL, Pliska V (1983) Hydrophobic paramaters-pi of amino-acid side-chains from the partitioning of N-acetyl-amino-acid amides. Eur J Med Chem 18:369-375.
Fogolari F, Brigo A, Molinari H (2002) The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology. J Mol Recognit 15:377-392.
Garvie CW, Phillips SE (2000) Direct and indirect readout in mutant Met repressor-operator complexes. Structure 8:905-914.
Getzoff ED, Tainer JA, Weiner PK, et al. (1983) Electrostatic recognition between superoxide and copper, zinc superoxide dismutase. Nature 306:287-290.
Goodford PJ (1985) A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem 28:849-857.
Hajduk PJ, Huth JR, Fesik SW (2005) Druggability indices for protein targets derived from NMR-based screening data. J Med Chem 48:2518-2525.
Hendlich M, Rippmann F, Bamickel G (1997) LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J Mol Graph Model 15:359-363.
Hopkins AL, Groom CR (2002) The druggable genome. Nat Rev Drug Discov 1:727-730.
Jackson RM (2002) Q-fit: a probabilistic method for docking molecular fragments by sampling low energy conformational space. J Comput Aided Mol Des 16:43-57.
Jackson RM, Sternberg MJE (1993) Protein surface area defined. Nature 366:638.
Janin J, Chothia C (1990) The structure of protein-protein recognition sites. J Biol Chem 265:16027-16030.
Janin J, Miller S, Chothia C (1988) Surface, subunit interfaces and interior of oligomeric proteins. J Mol Biol 204:155-164.
Jones S, Thornton JM (1995) Protein-protein interactions: a review of protein dimer structures. Prog Biophys Mol Biol 63:31-65.
Jones S, Thornton JM (1996) Principles of protein-protein interactions. Proc Natl Acad Sei USA93:13-20.
Jones S, Thornton JM (1997) Prediction of protein-protein interaction sites using patch analysis. J Mol Biol 272:133-143.
Kinoshita K, Nakamura H (2003) Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Sei 12:1589-1595.
Ko J, Murga LF, Andre P, et al. (2005) Statistical criteria for the identification of protein active sites using Theoretical Microscopic Titration Curves. Proteins 59:183-95.
Laskowski RA (1995) SURFNET: a program for visualizing molecular surfaces, cavities, and in- termolecular interactions. J Mol Graph 13:323-330.
Laskowski RA, Luscombe NM, Swindells MB, et al. (1996) Protein clefts in molecular recognition and function. Protein Sсi 5:2438-2452.
Laskowski RA, Chistyakov W, Thornton JM (2005) PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res 33:D266-268.
Laurie AT, Jackson RM (2005) Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 21:1908-1916.
Laurie AT, Jackson RM (2006) Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening. Curr Protein Pept Sсi 7:395-406.
Lee B, Richards FM (1971) The interpretation of protein structures: estimation of static accessibility. J Mol Biol 55:379-400.
Levitt DG, Banaszak LJ (1992) POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J Mol Graph 10:229-234.
Lichtarge О, Bourne HR, Cohen FE (1996) Evolutionarily conserved Galphabetagamma binding surfaces support a model of the G protein-receptor complex. Proc Natl Acad Sсi USA 93:7507-7511.
Lijnzaad Р, Berendsen HJ, Argos Р (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 conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sei USA 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 structures when the holo conformation is different. Proteins 72:980-992.
Neuvirth H, Raz R, Schreiber G (2004) ProMate: a structure based prediction program to identify the 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 Bgll bound 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-ligand interactions, methodology and validation. J Comput Aided Mol Des 14:787-803.
O’Brien KP, Remm M, Sonnhammer EL (2005) Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res 33:D476-480.
Olędzki PR, Laurie AT, Jackson RM (2006) Protein-ligand docking and structure-based drug design. 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 of enzyme function from structure. Proc Natl Acad Sсi USA 98:12473-12478.
Pettit FK, Ваге E, Tsai A, et al. (2007) HotPatch: a statistical approach to finding biologically relevant features 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 of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18(Suppl 1 ):S71—77.
Radzicka A, Pedersen L, Wolfenden R (1988) Influences of solvent water on protein folding: free energies of 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 molecular surface and the use of induced surface charge to calculate reaction field eneigies: applications to the molecular systems and geometric objects. J Comput Chem 23:128-137.
Stawiski EW, Gregoret LM, Mandel-Gutfreund Y (2003) Annotating nucleic acid-binding function based on protein structure. J Mol Biol 326:1065-1079.
Thom KS, Bogan AA (2001) ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics 17:284-285.
Todd AE, Orengo CA, Thornton JM (2002) Sequence and structural differences between enzyme and nonenzyme homologs. Structure 10:1435-1451.
Tong W, Williams RJ, Wei Y, et al. (2008) Enhanced performance in prediction of protein active sites with THEMATICS and support vector machines. Protein Sсi 17:333-341.
Tsuchiya Y, Kinoshita K, Nakamura H (2005) PreDs: a server for predicting dsDNA-binding site on 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 native structure of globular proteins. Proc Natl Acad Sсi USA 92:709-713.
Wolfenden R, Andersson L, Cullis PM, et al. (1981) Affinities of amino acid side chains for solvent water. 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 the catalytic 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.