Структура и функционирование белков. Применение методов биоинформатики - Джон Ригден 2014

Пространственные мотивы
Литература

Artymiuk PJ, Poirrette AR, Grindley HM, et al. (1994) A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side chains in protein structures. J Mol Biol 243:327-344

Ashbumer M, Ball CA, Blake JA, et al. (2000) Gene ontology: tool for the unification of biology.

The Gene Ontology Consortium. Nat Genet 25:25-29

Ausiello G, Via A, Helmer-Citterich M (2005a) Query3d: a new method for high-throughput analysis of functional residues in protein structures. BMC Bioinformatics 6(Suppl 4):S5

Ausiello G, Zanzoni A, Peluso D, et al. (2005b) pdbFun: mass selection and fast comparison of annotated PDB residues. Nucleic Acids Res 33:W133-137

Ausiello G Peluso D, Via A, et al. (2007) Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites. BMC Bioinformatics 8(Suppl 1):S24

Ausiello F Gherardini PF, Marcatili P, et al. (2008) FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinformatics 9(Suppl 2):S2

Babbitt PC (2003) Definitions of enzyme function for the structural genomics era. Curr Opin Chem Biol 7:230-237

Babbitt PC, Gerlt JA (1997) Understanding enzyme superfamilies. Chemistry as the fundamental determinant in the evolution of new catalytic activities. J Biol Chem 272:30591-30594

Babbitt PC, Gerlt JA (2000) New functions from old scaffolds: how nature reengineers enzymes for new functions. Adv Protein Chem 55:1-28

Bagley SC, Altman RB (1995) Characterizing the microenvironment surrounding protein sites. Protein Sci 4:622-635

Barker JA, Thornton JM (2003) An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Bioinformatics 19:1644—1649

Bartlett GJ, Porter CT, Borkakoti N, et al. (2002) Analysis of catalytic residues in enzyme active sites. J Mol Biol 324:105-121

Bartlett GJ, Borkakoti N, Thornton JM (2003) Catalysing new reactions during evolution: economy of residues and mechanism. J Mol Biol 331:829-860

Berman HM, Westbrook J, Feng Z, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28:235-242

Blow DM, Birktoft JJ, Hartley BS (1969) Role of a buried acid group in the mechanism of action of chymotrypsin. Nature 221:337-340

Bradley P, Kim PS, Berger В (2002) TRILOGY: Discovery of sequence-structure patterns across diverse proteins. Proc Natl Acad Sci USA 99:8500-8505

Brakoulias A, Jackson RM (2004) Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: an automated all-against-all structural comparison using geometric matching. Proteins 56:250-260

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

Chang DT, Weng YZ, Lin JH, et al. (2006) Protemot: prediction of protein binding sites with automatically extracted geometrical templates. Nucleic Acids Res 34:W303-309

Chen BY, Fofanov VY, Kristensen DM, et al. (2005) Algorithms for structural comparison and statistical analysis of 3D protein motifs. Рас Symp Biocomput 10:334-345

Chen BY, Fofanov VY, Bryant DH, et al. (2007a) The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs. J Comput Biol 14:791-816

Chen BY, Bryant DH, Cruess AE, et al. (2007b) Composite motifs integrating multiple protein structures increase sensitivity for function prediction. Comput Syst Bioinformatics Conf 6: 343-355

Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5:823-826

Chothia C, Gough J, Vogel C, et al. (2003) Evolution of the protein repertoire. Science 300:1701-1703

Devos D, Valencia A (2001) Intrinsic errors in genome annotation. Trends Genet 17:429-431

Di Gennaro JA, Siew N, Hoffman ВТ, et al. (2001) Enhanced functional annotation of protein sequences via the use of structural descriptors. J Struct Biol 134:232-245

Favia AD, Nobeli I, Glaser F, et al. (2008) Molecular docking for substrate identification: the short-chain dehydrogenases/reductases. J Mol Biol 375:855-874

Fetrow JS, Skolnick J (1998) Method for prediction of protein function from sequence using the sequence-to-strocture-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. J Mol Biol 281:949-968

Fischer D, Wolfson H, Lin SL, et al. (1994) Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding. Protein Sci 3:769-778

Glazer DS, Radmer RJ, Altman RB (2008) Combining molecular dynamics and machine learning to improve protein function recognition. Рас Symp Biocomput 2008:332-343.

Goyal K, Mande SC (2008) Exploiting 3D structural templates for detection of metal-binding sites in protein structures. Proteins 70:1206-1218

Goyal K, Mohanty D, Mande SC (2007) PAR-3D: a server to predict protein active site residues. Nucleic Acids Res 35:W503-505

Hermann JC, Ghanem Е, Li Y, et al. (2006) Predicting substrates by docking high-energy intermediates to enzyme structures. J Am Chem Soc 128:15882-15891

Hermann JC, Marti-Arbona R, Fedorov AA, et al. (2007) Structure-based activity prediction for an enzyme of unknown function. Nature 448:775-779

International Union of Biochemistry and Molecular Biology: Nomenclature Committee, Webb EC (1992) Enzyme nomenclature 1992: recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzymes. Academic, San Diego, CA Ivanisenko VA, Pintus SS, Grigorovich DA, et al. (2004) PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. Nucleic Acids Res 32:W549-554

Ivanisenko VA, Pintus SS, Grigorovich DA, et al. (2005) PDBSite: a database of the 3D structure of protein functional sites. Nucleic Acids Res 33:D183-187

Jambon M, Imberty A, Deleage G, et al. (2003) A new bioinformatic approach to detect common 3D sites in protein structures. Proteins 52:137-145 Jambon M, Andrieu O, Combet C, et al. (2005) The SuMo server: 3D search for protein functional sites. Bioinformatics 21:3929-3930

Kalyanaraman C, Bemacki K, Jacobson MP (2005) Virtual screening against highly charged active sites: identifying substrates of alpha-beta barrel enzymes. Biochemistry 44:2059-2071

Kleywegt GJ (1999) Recognition of spatial motifs in protein structures. J Mol Biol 285:1887-1897

Kobayashi N, Go N (1997) A method to search for similar protein local structures at ligand binding sites and its application to adenine recognition. Eur Biophys J 26:135-144

Kristensen DM, Chen BY, Fofanov VY, et al. (2006) Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity. Protein Sci 15:1530-1536

Kuhn D, Weskamp N, Schmitt S, et al. (2006) From the similarity analysis of protein cavities to the functional classification of protein families using cavbase. J Mol Biol 359:1023-1044

RA, Watson JD, Thornton JM (2005a) Protein function prediction using local 3D templates. J Mol Biol 351:614-626

Laskowski RA, Watson JD, Thornton JM (2005b) ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 33:W89-93

Liang MP, Banatao DR, Klein TE, et al. (2003) WebFEATURE: an interactive web tool for identifying and visualizing functional sites on macromolecular structures. Nucleic Acids Res 31:3324-3327

Macchiarulo A, Nobeli I, Thornton JM (2004) Ligand selectivity and competition between enzymes in silico. Nat Biotechnol 22:1039-1045

Meng EC, Polacco BJ, Babbitt PC (2004) Superfamily active site templates. Proteins 55:962-976

Milik M, Szalma S, Olszewski KA (2003) Common Structural Cliques: a tool for protein structure and function analysis. Protein Eng 16:543-552

Mooney SD, Liang MH, DeConde R, et al. (2005) Structural characterization of proteins using residue environments. Proteins 61:741-747

Murzin AG, Brenner SE, Hubbard T, et al. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247:536-540

Nebel JC (2006) Generation of 3D templates of active sites of proteins with rigid prosthetic groups. Bioinformatics 22:1183-1189

Nebel JC, Herzyk P, Gilbert DR (2007) Automatic generation of 3D motifs for classification of protein binding sites. BMC Bioinformatics 8:321

Oldfield TJ (2002) Data mining the protein data bank: residue interactions. Proteins 49:510-528

Orengo CA, Michie AD, Jones S, et al. (1997) CATH-a hierarchic classification of protein domain structures. Structure 5:1093—1108

Pal D, Eisenberg D (2005) Inference of protein function from protein structure. Structure 13:121-130

Paul N, Kellenberger E, Bret G, et al. (2004) Recovering the true targets of specific ligands by virtual screening of the protein data bank. Proteins 54:671-680

Pennec X, Ayache N (1998) A geometric algorithm to find small but highly similar 3D substructures in proteins. Bioinformatics 14:516-522

Peters B, Moad C, Youn E, et al. (2006) Identification of similar regions of protein structures using integrated sequence and structure analysis tools. BMC Struct Biol 6:4

Pettersen EF, Goddard TD, Huang CC, et al. (2004) UCSF Chimera a visualization system for exploratory research and analysis. J Comput Chem 25:1605-1612

Polacco BJ, Babbitt PC (2006) Automated discovery of 3D motifs for protein function annotation. Bioinformatics 22:723-730

Porter CT, Bartlett GJ, Thornton JM (2004) The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 32:D129-133

Richardson JS (1981) The anatomy and taxonomy of protein structure. Adv Protein Chem 34:167-339

Rost В (1997) Protein structures sustain evolutionary drift. Fold Des 2:S 19-24

Rost В (2002) Enzyme function less conserved than anticipated. J Mol Biol 318:595-608

Russell RB (1998) Detection of protein three-dimensional side chain patterns: new examples of convergent evolution. J Mol Biol 279:1211-1227

Schmitt S, Kuhn D, Klebe G (2002) A new method to detect related function among proteins independent of sequence and fold homology. J Mol Biol 323:387-406

Shulman-Peleg A, Nussinov R, Wolfson HJ (2004) Recognition of functional sites in protein structures. J Mol Biol 339:607-633

Shulman-Peleg A, Nussinov R, Wolfson HJ (2005) SiteEngines: recognition and comparison of binding sites and protein-protein interfaces. Nucleic Acids Res 33:W337-341

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

Spriggs RV, Artymiuk PJ, Willett P (2003) Searching for patterns of amino acids in 3D protein structures. J Chem Inf Comput Sci 43:412-421

Stark A, Russell RB (2003) Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. Nucleic Acids Res 31:3341-3344 Stark A, Sunyaev S, Russell RB (2003) A model for statistical significance of local similarities in structure. J Mol Biol 326:1307-1316

Stark A, Shkumatov A, Russell RB (2004) Finding functional sites in structural genomics proteins. Structure 12:1405-1412

Todd AE, Orengo CA, Thornton JM (2001) Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol 307:1113-1143

Todd AE, Orengo CA, Thornton JM (2002) Plasticity of enzyme active sites. Trends Biochem Sci 27:419-426

Torrance JW, Bartlett GJ, Porter CT, et al. (2005) Using a library of structural templates to recognize catalytic sites and explore their evolution in homologous families. J Mol Biol 347:565-581

Tyagi S, Pleiss J (2006) Biochemical profiling in silico-predicting substrate specificities of large enzyme families. J Biotechnol 124:108-116

Wallace AC, Laskowski RA, Thornton JM (1996) Derivation of 3D coordinate templates for searching structural databases: application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein Sci 5:1001-1013

Wallace AC, Borkakoti N, Thornton JM (1997) TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci 6:2308-2323

Wangikar PP, Tendulkar AV, Ramya S, et al. (2003) Functional sites in protein families uncovered via an objective and automated graph theoretic approach. J Mol Biol 326:955-978

Wright CS, Alden RA, Kraut J (1969) Structure of subtilisin BPN’ at 2.5 angstrom resolution. Nature 221:235-242

Xie L, Bourne PE (2007) A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites. BMC Bioinformatics 8(Suppl 4):S9

Xie L, Bourne PE (2008) Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natl Acad Sei USA 105:5441 5446