A database of domain definitions for proteins with complex interdomain geometry

PLoS ONE

Volumn 4, Issue 4, 2009, Pages

  Majumdar, Indraneel ^b   Kinch, Lisa N ^a   Grishin, Nick V ^a,b  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; CONTROLLED STUDY; DATA EXTRACTION; INFORMATION PROCESSING; INFORMATION RETRIEVAL; MOLECULAR EVOLUTION; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; PROTEOMICS; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM;

DNA DIRECTED DNA POLYMERASE; DNA DIRECTED RNA POLYMERASE; PROTEIN;

AUTOMATION; DATABASES, PROTEIN; DNA-DIRECTED DNA POLYMERASE; DNA-DIRECTED RNA POLYMERASES; EVOLUTION, MOLECULAR; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEINS;

EID: 65249164850     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0005084     Document Type: Article

References (28)

1. Janin J, Chothia C (1985) Domains in proteins: definitions, location, and structural principles. Methods Enzymol 115: 420-430.
2. Phillips DC (1966) The three-dimensional structure of an enzyme molecule. Sci Am 215: 78-90.
3. Wetlaufer DB (1973) Nucleation, rapid folding, and globular intrachain regions in proteins. Proc Natl Acad Sci U S A 70: 697-701.
4. Rose GD (1979) Hierarchic organization of domains in globular proteins. J Mol Biol 134: 447-470.
5. Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247: 536-540.
6. Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, et al. (2007) The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res 35: D291-297.
7. Levitt M, Chothia C (1976) Structural patterns in globular proteins. Nature 261: 552-558.
8. Zehfus MH, Rose GD (1986) Compact units in proteins. Biochemistry 25: 5759-5765.
9. Wetlaufer DB, Ristow S (1973) Acquisition of three-dimensional structure of proteins. Annu Rev Biochem 42: 135-158.
10. Hegyi H, Bork P (1997) On the classification and evolution of protein modules. J Protein Chem 16: 545-551.
11. Russell RB (1994) Domain insertion. Protein Eng 7: 1407-1410.
12. Baron M, Norman DG, Campbell ID (1991) Protein modules. Trends Biochem Sci 16: 13-17.
13. Orengo CA, Jones DT, Thornton JM (1994) Protein superfamilies and domain superfolds. Nature 372: 631-634.
14. Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5: 823-826.
15. Murzin AG (1998) How far divergent evolution goes in proteins. Curr Opin Struct Biol 8: 380-387.
16. Siddiqui AS, Barton GJ (1995) Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions. Protein Sci 4: 872-884.
17. Alexandrov N, Shindyalov I (2003) PDP: protein domain parser. Bioinformatics 19: 429-430.
18. Veretnik S, Bourne PE, Alexandrov NN, Shindyalov IN (2004) Toward consistent assignment of structural domains in proteins. J Mol Biol 339: 647-678.
19. DeLano WL (2002) The PyMOL Molecular Graphics System.
20. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28: 235-242.
21. Kamada K, Horiuchi T, Ohsumi K, Shimamoto N, Morikawa K (1996) Structure of a replication-terminator protein complexed with DNA. Nature 383: 598-603.
22. Augustin MA, Huber R, Kaiser JT (2001) Crystal structure of a DNA-dependent RNA polymerase (DNA primase). Nat Struct Biol 8: 57-61.
23. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
24. Kinch LN, Wrabl JO, Krishna SS, Majumdar I, Sadreyev RI, et al. (2003) CASP5 assessment of fold recognition target predictions. Proteins 53 Suppl 6: 395-409.
25. Chandonia JM, Hon G, Walker NS, Lo Conte L, Koehl P, et al. (2004) The ASTRAL Compendium in 2004. Nucleic Acids Res 32: D189-192.
26. Majumdar I, Krishna SS, Grishin NV (2005) PALSSE: a program to delineate linear secondary structural elements from protein structures. BMC Bioinformatics 6: 202.
27. Swindells MB (1995) A procedure for detecting structural domains in proteins. Protein Sci 4: 103-112.
28. Holm L, Park J (2000) DaliLite workbench for protein structure comparison. Bioinformatics 16: 566-567.