3D motifs

From Protein Structure to Function with Bioinformatics

Volumn , Issue , 2009, Pages 187-216

  Meng, Elaine C ^a   Polacco, Benjamin J ^a   Babbitt, Patricia C ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84862613064     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4020-9058-5_8     Document Type: Chapter

References (85)

1. 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
2. Ashburner 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
3. 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
4. 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
5. 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
6. Ausiello G, 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
7. Babbitt PC (2003) Definitions of enzyme function for the structural genomics era. Curr Opin Chem Biol 7:230-237
8. 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
9. Babbitt PC, Gerlt JA (2000) New functions from old scaffolds: how nature reengineers enzymes for new functions. Adv Protein Chem 55:1-28
10. Bagley SC, Altman RB (1995) Characterizing the microenvironment surrounding protein sites. Protein Sci 4:622-635
11. Barker JA, Thornton JM (2003) An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Bioinformatics 19:1644-1649
12. Bartlett GJ, Porter CT, Borkakoti N, et al. (2002) Analysis of catalytic residues in enzyme active sites. J Mol Biol 324:105-121
13. Bartlett GJ, Borkakoti N, Thornton JM (2003) Catalysing new reactions during evolution: economy of residues and mechanism. J Mol Biol 331:829-860
14. Berman HM, Westbrook J, Feng Z, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28:235-242
15. Blow DM, Birktoft JJ, Hartley BS (1969) Role of a buried acid group in the mechanism of action of chymotrypsin. Nature 221:337-340
16. Bradley P, Kim PS, Berger B (2002) TRILOGY: Discovery of sequence-structure patterns across diverse proteins. Proc Natl Acad Sci USA 99:8500-8505
17. 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
18. Cammer SA, Hoffman BT, Speir JA, et al. (2003) Structure-based active site profiles for genome analysis and functional family subclassification. J Mol Biol 334:387-401
19. 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
20. Chen BY, Fofanov VY, Kristensen DM, et al. (2005) Algorithms for structural comparison and statistical analysis of 3D protein motifs. Pac Symp Biocomput 10:334-345
21. 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
22. 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
23. Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5:823-826
24. Chothia C, Gough J, Vogel C, et al. (2003) Evolution of the protein repertoire. Science 300:1701-1703
25. Devos D, Valencia A (2001) Intrinsic errors in genome annotation. Trends Genet 17:429-431
26. Di Gennaro JA, Siew N, Hoffman BT, et al. (2001) Enhanced functional annotation of protein sequences via the use of structural descriptors. J Struct Biol 134:232-245
27. 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
28. 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
29. 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
30. Glazer DS, Radmer RJ, Altman RB (2008) Combining molecular dynamics and machine learning to improve protein function recognition. Pac Symp Biocomput 2008:332-343.
31. Goyal K, Mande SC (2008) Exploiting 3D structural templates for detection of metal-binding sites in protein structures. Proteins 70:1206-1218
32. Goyal K, Mohanty D, Mande SC (2007) PAR-3D: a server to predict protein active site residues. Nucleic Acids Res 35:W503-505
33. Hermann JC, Ghanem E, Li Y, et al. (2006) Predicting substrates by docking high-energy intermediates to enzyme structures. J Am Chem Soc 128:15882-15891
34. Hermann JC, Marti-Arbona R, Fedorov AA, et al. (2007) Structure-based activity prediction for an enzyme of unknown function. Nature 448:775-779
35. 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
36. 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
37. 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
38. 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
39. Jambon M, Andrieu O, Combet C, et al. (2005) The SuMo server: 3D search for protein functional sites. Bioinformatics 21:3929-3930
40. Kalyanaraman C, Bernacki K, Jacobson MP (2005) Virtual screening against highly charged active sites: identifying substrates of alpha-beta barrel enzymes. Biochemistry 44:2059-2071
41. Kleywegt GJ (1999) Recognition of spatial motifs in protein structures. J Mol Biol 285:1887-1897
42. 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
43. 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
44. 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
45. Laskowski RA, Watson JD, Thornton JM (2005a) Protein function prediction using local 3D templates. J Mol Biol 351:614-626
46. Laskowski RA, Watson JD, Thornton JM (2005b) ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 33:W89-93
47. 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
48. Macchiarulo A, Nobeli I, Thornton JM (2004) Ligand selectivity and competition between enzymes in silico. Nat Biotechnol 22:1039-1045
49. Meng EC, Polacco BJ, Babbitt PC (2004) Superfamily active site templates. Proteins 55:962-976
50. Milik M, Szalma S, Olszewski KA (2003) Common Structural Cliques: a tool for protein structure and function analysis. Protein Eng 16:543-552
51. Mooney SD, Liang MH, De Conde R, et al. (2005) Structural characterization of proteins using residue environments. Proteins 61:741-747
52. 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
53. Nebel JC (2006) Generation of 3D templates of active sites of proteins with rigid prosthetic groups. Bioinformatics 22:1183-1189
54. Nebel JC, Herzyk P, Gilbert DR (2007) Automatic generation of 3D motifs for classification of protein binding sites. BMC Bioinformatics 8:321
55. Oldfield TJ (2002) Data mining the protein data bank: residue interactions. Proteins 49:510-528
56. Orengo CA, Michie AD, Jones S, et al. (1997) CATH-a hierarchic classification of protein domain structures. Structure 5:1093-1108
57. Pal D, Eisenberg D (2005) Inference of protein function from protein structure. Structure 13:121-130
58. 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
59. Pennec X, Ayache N (1998) A geometric algorithm to find small but highly similar 3D substructures in proteins. Bioinformatics 14:516-522
60. 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
61. 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
62. Polacco BJ, Babbitt PC (2006) Automated discovery of 3D motifs for protein function annotation. Bioinformatics 22:723-730
63. 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
64. Richardson JS (1981) The anatomy and taxonomy of protein structure. Adv Protein Chem 34:167-339
65. Rost B (1997) Protein structures sustain evolutionary drift. Fold Des 2:S19-24
66. Rost B (2002) Enzyme function less conserved than anticipated. J Mol Biol 318:595-608
67. Russell RB (1998) Detection of protein three-dimensional side chain patterns: new examples of convergent evolution. J Mol Biol 279:1211-1227
68. 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
69. Shulman-Peleg A, Nussinov R, Wolfson HJ (2004) Recognition of functional sites in protein structures. J Mol Biol 339:607-633
70. 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
71. 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
72. 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
73. Stark A, Russell RB (2003) Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. Nucleic Acids Res 31:3341-3344
74. Stark A, Sunyaev S, Russell RB (2003) A model for statistical significance of local similarities in structure. J Mol Biol 326:1307-1316
75. Stark A, Shkumatov A, Russell RB (2004) Finding functional sites in structural genomics proteins. Structure 12:1405-1412
76. Todd AE, Orengo CA, Thornton JM (2001) Evolution of function in protein superfamilies, from a structural perspective. J Mol Biol 307:1113-1143
77. Todd AE, Orengo CA, Thornton JM (2002) Plasticity of enzyme active sites. Trends Biochem Sci 27:419-426
78. Torrance JW, Bartlett GJ, Porter CT, et al. (2005) Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families. J Mol Biol 347:565-581
79. Tyagi S, Pleiss J (2006) Biochemical profiling in silico-predicting substrate specificities of large enzyme families. J Biotechnol 124:108-116
80. 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
81. 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
82. 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
83. Wright CS, Alden RA, Kraut J (1969) Structure of subtilisin BPN' at 2.5 angstrom resolution. Nature 221:235-242
84. 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
85. Xie L, Bourne PE (2008) Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc Natl Acad Sci USA 105:5441-5446