Saturating representation of loop conformational fragments in structure databanks

BMC Structural Biology

Volumn 6, Issue , 2006, Pages

  Fernandez Fuentes, Narcis ^a   Fiser, András ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE FRAGMENT; PROTEIN;

ARTICLE; PROTEIN CONFORMATION; PROTEIN DATA BANK; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; DATABASES, PROTEIN; MOLECULAR CONFORMATION; PEPTIDES; PROTEIN STRUCTURE, SECONDARY; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 33748959731     PISSN: 14726807     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-6-15     Document Type: Article

References (40)

1. Todd AE, Orengo CA, Thornton JM: Plasticity of enzyme active sites. Trends BiochemSci 2002, 27(8):419.
2. Rost B: Enzyme function less conserved than anticipated. JMolBiol 2002, 318(2):595.
3. Fiser A: Protein structure modeling in the proteomics era. Expert Rev Proteomics 2004, 1(1):97-110.
4. Burley SK, Almo SC, Bonanno JB, Capel M, Chance MR, Gaasterland T, Lin D, Sali A, Studier FW, Swaminathan S: Structural genomics: beyond the human genome project. NatGenet 1999, 23(2):151.
5. Fiser A, Feig M, Brooks CLIII, Sali A: Evolution and Physics in Comparative Protein Structure Modeling. AccChemRes 2002, 35(6):413.
6. Chance MR, Fiser A, Sali A, Pieper U, Eswar N, Xu G, Fajardo JE, Radhakannan T, Marinkovic N: High-throughput computational and experimental techniques in structural genomics. Genome Res 2004, 14(10B):2145.
7. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM: CATH - a hierarchic classification of protein domain structures. Structure 1997, 5(8):1093.
8. Bystroff C, Baker D: Prediction of local structure in proteins using a library of sequence- structure motifs. JMolBiol 1998, 281(3):565.
9. Rohl CA, Strauss CE, Chivian D, Baker D: Modeling structurally variable regions in homologous proteins with rosetta. Proteins 2004, 55(3):656-677.
10. Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D: Progress in modeling of protein structures and interactions. Science 2005, 310(5748):638-642.
11. Fidelis K, Stern PS, Bacon D, Moult J: Comparison of systematic search and database methods for constructing segments of protein structure. Protein Eng 1994, 7(8):953.
12. Fernandez-Fuentes N, Oliva B, Fiser A: A supersecondary structure library and search algorithm for modeling loops in protein structures. Nucleic Acids Res 2006, 34(7):2085-97. Print 2006..
13. Rufino SD, Donate LE, Canard L, Blundell TL: Analysis, clustering and prediction of the conformation of short and medium size loops connecting regular secondary structures. Pac Symp Biocomput 1996:570-589.
14. Topham CM, McLeod A, Eisenmenger F, Overington JP, Johnson MS, Blundell TL: Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables. JMolBiol 1993, 229(1):194.
15. Claessens M, Van Cutsem E, Lasters I, Wodak S: Modelling the polypeptide backbone with 'spare parts' from known protein structures. Protein Eng 1989, 2(5):335.
16. Chothia C, Lesk AM, Levitt M, Amit AG, Mariuzza RA, Phillips SE, Poljak RJ: The predicted structure of immunoglobulin D1.3 and its comparison with the crystal structure. Science 1986, 233(4765):755.
17. Heuser P, Wohlfahrt G, Schomburg D: Efficient methods for filtering and ranking fragments for the prediction of structurally variable regions in proteins. Proteins 2004, 54(3):583-595.
18. Michalsky E, Goede A, Preissner R: Loops In Proteins (LIP) - a comprehensive loop database for homology modelling. Protein Eng 2003, 16(12):979.
19. Fernandez-Fuentes N, Querol E, Aviles FX, Sternberg MJ, Oliva B: Prediction of the conformation and geometry of loops in globular proteins: testing ArchDB, a structural classification of loops. Proteins 2005, 60(4):746-757.
20. Burke DF, Deane CM: Improved protein loop prediction from sequence alone. Protein Eng 2001, 14(7):473-478.
21. Lessel U, Schomburg D: Creation and characterization of a new, non-redundant fragment data bank. Protein Eng 1997, 10(6):659.
22. Fiser A, Do RK, Sali A: Modeling of loops in protein structures. Protein Sci 2000, 9(9):1753.
23. Jacobson MP, Pincus DL, Rapp CS, Day TJ, Honig B, Shaw DE, Friesner RA: A hierarchical approach to all-atom protein loop prediction. Proteins 2004, 55(2):351.
24. de Bakker PI, DePristo MA, Burke DF, Blundell TL: Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model. Proteins 2003, 51(1):21.
25. Xiang Z, Soto CS, Honig B: Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction. ProcNatlAcadSciUSA 2002.
26. Fiser A, Sali A: ModLoop: automated modeling of loops in protein structures. Bioinformatics 2003, 19(18):2500.
27. Zhang C, Liu S, Zhou Y: Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential. Protein Sci 2004, 13(2):391-399.
28. Du P, Andrec M, Levy RM: Have we seen all structures corresponding to short protein fragments in the Protein Data Bank? An update. Protein Eng 2003, 16(6):407.
29. Oliva B, Bates PA, Querol E, Aviles FX, Sternberg MJ: Automated classification of antibody complementarity determining region 3 of the heavy chain (H3) loops into canonical forms and its application to protein structure prediction. JMolBiol 1998, 279(5):1193.
30. Kabsch W, Sander C: On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. ProcNatlAcadSciUSA 1984, 81(4):1075.
31. Mezei M: Chameleon sequences in the PDB. Protein Eng 1998, 11(6):411.
32. Bourne PE, Addess KJ, Bluhm WF, Chen L, Deshpande N, Feng Z, Fleri W, Green R, Merino-Ott JC, Townsend-Merino W, Weissig H, Westbrook J, Berman HM: The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Res 2004, 32 Database issue:D223.
33. Kabsch W, Sander C: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22(12):2577-2637.
34. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS: The Universal Protein Resource (UniProt). Nucleic Acids Res 2005, 33(Database issue):D154-9.
35. Rost B: PHD: predicting one-dimensional protein structure by profile-based neural networks. Methods Enzymol 1996, 266:525.
36. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003, 31(1):365.
37. Li W, Jaroszewski L, Godzik A: Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 2001, 17(3):282.
38. Sali A, Blundell TL: Comparative protein modeling by satisfaction of spatial restraints. J Mol Biol 1993, 234:779-815.
39. Colloc'h N, Etchebest C, Thoreau E, Henrissat B, Mornon JP: Comparison of three algorithms for the assignment of secondary structure in proteins: the advantages of a consensus assignment. Protein Eng 1993, 6(4):377-382.
40. Carter P, Andersen CA, Rost B: DSSPcont: Continuous secondary structure assignments for proteins. Nucleic Acids Res 2003, 31(13):3293-3295.