Структура и функционирование белков. Применение методов биоинформатики - Джон Ригден 2014
Предсказание функции белков на основе их теоретических моделей
Литература
Aloy Р, Russell RB (2002) Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci USA 99:5896-5901
Aloy P, Russell RB (2003) InterPreTS: protein interaction prediction through tertiary structure. Bioinformatics 19:161-162
Aloy P, Russell RB (2006) Structural systems biology: modelling protein interactions. Nat Rev Mol Cell Biol 7:188-197
Baxter SM, Rosenblum JS, Knutson S, et al. (2004) Synergistic computational and experimental proteomics approaches for more accurate detection of active serine hydrolases in yeast. Mol Cell Proteomics 3:209-225
Bonneau R, Strauss CE, Rohl CA, et al. (2002) De novo prediction of three-dimensional structures for major protein families. J Mol Biol 322:65-78
Bradley Р, Misura KM, Baker D (2005) Toward high-resolution de novo structure prediction for small proteins. Science 309:1868-1871
Bujnicki JM (2003) Crystallographic and bioinformatic studies on restriction endonucleases: inference of evolutionary relationships in the “midnight zone” of homology. Curr Protein Pept Sci 4:327-337
Bumbaca D, Littlejohn JE, Nayakanti H, et al. (2007) Genome-based identification and characterization of a putative mucin-binding protein from the surface of Streptococcus pneumoniae. Proteins 66:547-558
Cammer SA, Hoffman ВТ, Speir JA, et al. (2003) Structure-based active site profiles for genome analysis and functional family subclassification. J Mol Biol 334:387-401 Castrignano T, De Meo PD, Cozzetto D, et al. (2006) The PMDB Protein Model Database. Nucleic Acids Res 34:D306-309
Chakravarty S, Sanchez R (2004) Systematic analysis of added-value in simple comparative models of protein structure. Structure 12:1461—1470
Chakravarty S, Wang L, Sanchez R (2005) Accuracy of structure-derived properties in simple comparative models of protein structures. Nucleic Acids Res 33:244-259
Chi A, Kemp RG (2000) The primordial high energy compound: ATP or inorganic pyrophosphate? J Biol Chem 275:35677-35679
Cymerman LA, Meiss Q Bujnicki JM (2005) DNase II is a member of the phospholipase D super- family. Bioinformatics 21:3959-3962
Davis FP, Braberg H, Shen MY, et al. (2006) Protein complex compositions predicted by structural similarity. Nucleic Acids Res 34:2943-2952
Davis FP, Barkan DT, Eswar N, et al. (2007) Host pathogen protein interactions predicted by comparative modeling. Protein Sci 16:2585-2596
Feder M, Bujnicki JM (2005) Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site. BMC Genomics 6:21 Fetrow JS, Skolnick J (1998) Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. J Mol Biol 281:949-968
Fetrow JS, Godzik A, Skolnick J (1998) Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity. J Mol Biol 282:703-711
Fumham N, Ruffle S, Southan C (2004) Splice variants: a homology modeling approach. Proteins 54:596-608
Hattersley AT, Ashcroft FM (2005) Activating mutations in Kir6.2 and neonatal diabetes: new clinical syndromes, new scientific insights, and new therapy. Diabetes 54:2503-2513
Hermann JC, Marti-Arbona R, Fedorov AA, et al. (2007) Structure-based activity prediction for an enzyme of unknown function. Nature 448:775-779
Jacobson M, Sali A (2004) Comparative protein Structure Modelling and its applications to drug discovery. Annu Rep Med Chem 39:259-274
Jordan IK, Wolf YI, Koonin EV (2004) Duplicated genes evolve slower than singletons despite the initial rate increase. BMC Evol Biol 4:22
Kolinski A, Bujnicki JM (2005) Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models. Proteins 61(Suppl 7):84-90 Kopp J, Schwede T (2004) The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. Nucleic Acids Res 32:D230-234
Krishnamurthy N, Brown D, Sjolander К (2007) FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function. BMC Evol Biol 7(Suppl 1):S12 Kryshtafovych A, Venclovas C, Fidelis К, et al. (2005) Progress over the first decade of CASP experiments. Proteins 61(Suppl 7):225-236
Kryshtafovych A, Fidelis К, Moult J (2007) Progress from CASP6 to CASP7. Proteins 69(Suppl 8): 194-207
Lopez C, Chevalier N, Hannaert V, et al. (2002) Leishmania donovani phosphoffuctokinase. Gene characterization, biochemical properties and structure-modeling studies. Eur J Biochem 269:3978-3989
Lu L, Lu H, Skolnick J (2002) MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins 49:350-364
Malmstrom L, Riffle M, Strauss CE, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5:e76 McGovern SL, Shoichet BK (2003) Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J Med Chem 46:2895-2907
McGuffin LJ (2008) The ModFOLD server for the quality assessment of protein structural models. Bioinformatics 24:586-587
Melo F, Feytmans E (1998) Assessing protein structures with a non-local atomic interaction energy. J Mol Biol 277:1141-1152
Melo F, Sanchez R, Sali A (2002) Statistical potentials for fold assessment. Protein Sei 11:430-448
Michels PA, Chevalier N, Opperdoes FR, et al. (1997) The glycosomal ATP-dependent phospho-fructokinase of Trypanosoma brucei must have evolved from an ancestral pyrophosphate- dependent enzyme. Eur J Biochem 250:698-704
Oshiro C, Bradley EK, Eksterowicz J, et al. (2004) Performance of 3D-database molecular docking studies into homology models. J Med Chem 47:764-767
Pawłowski К, Godzik A (2001) Surface map comparison: studying function diversity of homologous proteins. J Mol Biol 309:793-806
Pawłowski M, Gajda MJ, Matlak R, et al. (2008) Meta-MQAP: a meta-server for the quality assessment of protein models. BMC Bioinformatics in press Pieper U, Eswar N, Davis FP, et al. (2006) MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 34:D291-295
Quiocho F, Vyas N (1999) Atomic interactions between proteins/enzymes and carbohydrates, ln: Hecht SM (ed.), Bioinorganic Chemistry: Carbohydrates. Oxford University Press, New York, NY Raes J, Harrington ED, Singh AH, et al. (2007) Protein function space: viewing the limits or limited by our view? Curr Opin Struct Biol 17:362-369
Rigden DJ, Galperin MY (2008) Sequence analysis of GerM and SpoVS, uncharacterised bacterial ’sporulation’ proteins with widespread phylogenetic distribution. Bioinformatics, accepted DOI 10.1093/bioinformatics/btn314
Roberts RJ (2004) Identifying protein fimetion-a call for community action. PLoS Biol 2:E42 Sasin JM, Godzik A, Bujnicki JM (2007) SURF’S UP! - protein classification by surface comparisons. J Biosci 32:97-100
Schafer P, Cymerman LA, Bujnicki JM, et al. (2007) Human lysosomal DNase Ilalpha contains two requisite PLD-signature (HxK) motifs: evidence for a pseudodimeric structure of the active enzyme species. Protein Sei 16:82-91
Service RF (2008a) Structural biology. Protein structure initiative: phase 3 or phase out. Science 319:1610-1613
Service RF (2008b) Structural biology. Researchers hone their homology tools. Science 319:1612
Silveira NJ, Uchoa HB, Pereira JH, et al. (2005) Molecular models of protein targets from Mycobacterium tuberculosis. J Mol Model 11:160-166
Sodhi JS, Bryson K, McGuffin LJ, et al. (2004) Predicting metal-binding site residues in low- resolution structural models. J Mol Biol 342:307-320
Song L, Kalyanaraman C, Fedorov AA, et al. (2007) Prediction and assignment of function for a divergent N-succinyl amino acid racemase. Nat Chem Biol 3:486-491
Szilagyi A, Skolnick J (2006) Efficient prediction of nucleic acid binding function from low- resolution protein structures. J Mol Biol 358:922-933
Tammaro P, Flanagan SE, Zadek В, et al. (2008) A Kir6.2 mutation causing severe functional effects in vitro produces neonatal diabetes without the expected neurological complications. Diabetologia 51:802-810
Tamulaitiene Q Jakubauskas A, Urbanke C, et al. (2006) The crystal structure of the rare-cutting restriction enzyme Sdal reveals unexpected domain architecture. Structure 14:1389-1400
Tatusov RL, Fedorova ND, Jackson JD, et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41
Tress M, Bujnicki JM, Valencia A (2008) Integrating structures, functions, and interactions. In: Bujnicki JM (ed.), Prediction of Protein Structures, Functions and Interactions. Wiley.
Tress ML, Martelli PL, Frankish A, et al. (2007) The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci USA 104:5495-5500
van Gunsteren W (1996) Biomolecular Simulations: The GROMOS96 Manual and User Guide. Biomos : Groningen
Wallner B, Elofsson A (2003) Can correct protein models be identified? Protein Sci 12:1073-1086
Wallner B, Elofsson A (2006) Identification of correct regions in protein models using structural, alignment, and consensus information. Protein Sci 15:900-913
Wang P, Yan B, Guo JT, et al. (2005) Structural genomics analysis of alternative splicing and application to isoform structure modeling. Proc Natl Acad Sci USA 102:18920-18925
Xu LZ, Sanchez R, Sali A, et al. (1996) Ligand specificity of brain lipid-binding protein. J Biol Chem 271:24711-24719
Yooseph S, Sutton G Rusch DB, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol 5:e16