Improving protein structure similarity searches using domain boundaries based on conserved sequence information

BMC Structural Biology

Volumn 9, Issue , 2009, Pages

  Thompson, Kenneth Evan ^a,b   Wang, Yanli ^a   Madej, Tom ^a   Bryant, Stephen H ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA TOPOISOMERASE; FIBRONECTIN;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; MOLECULAR MODEL; NUCLEOTIDE SEQUENCE; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; ALGORITHM; BIOLOGY; CHEMISTRY; HUMAN; METHODOLOGY; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DATABASES, PROTEIN; DNA TOPOISOMERASES; FIBRONECTINS; HUMANS; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 67649322466     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-9-33     Document Type: Article

References (34)

1. Improved tools for biological sequence comparison. WR Pearson DJ Lipman, Proc Natl Acad Sci USA 1988 85 8 2444 2448 3162770 10.1073/pnas.85.8.2444
2. Basic local alignment search tool. SF Altschul W Gish W Miller EW Myers DJ Lipman, J Mol Biol 1990 215 403 410 2231712
3. The relation between the divergence of sequence and structure in proteins. C Chothia A Lesk, EMBO J 1986 5 4 823 826 3709526
4. Similar amino acid sequences: chance or common ancestry? R Doolittle, Science 1981 214 4517 149 159 10.1126/science.7280687 7280687 (Pubitemid 12243411)
5. Sensitivity and selectivity in protein structure comparison. M Sierk W Pearson, Protein Sci 2004 13 3 773 785 14978311 10.1110/ps.03328504
6. Evolution of protein sequences and structures. T Wood W Pearson, J Mol Biol 1999 291 4 977 995 10.1006/jmbi.1999.2972 10452901
7. Surprising similarities in structure comparison. J Gibrat T Madej S Bryant, Curr Opin Struct Biol 1996 6 3 377 385 10.1016/S0959-440X(96)80058-3 8804824
8. Protein structure comparison by alignment of distance matrices. L Holm C Sander, J Mol Biol 1993 233 1 123 138 10.1006/jmbi.1993.1489 8377180
9. Protein structure alignment using environmental profiles. J Jung B Lee, Protein Eng 2000 13 8 535 543 10.1093/protein/13.8.535 10964982
10. A unified statistical framework for sequence comparison and structure comparison. M Levitt M Gerstein, Proc Natl Acad Sci USA 1998 95 11 5913 5920 9600892 10.1073/pnas.95.11.5913
11. Structural characterization of proteins using residue environments. S Mooney M Liang R DeConde R Altman, Proteins 2005 61 4 741 747 16245324 10.1002/prot.20661
12. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. I Shindyalov P Bourne, Protein Eng 1998 11 9 739 747 10.1093/protein/11.9.739 9796821 (Pubitemid 28434482)
13. Protein structure alignment using a genetic algorithm. J Szustakowski Z Weng, Proteins 2000 38 4 428 440 10.1002/(SICI)1097-0134(20000301)38:4<428:: AID-PROT8>3.0.CO;2-N 10707029 (Pubitemid 30112445)
14. Protein structure comparison using iterated double dynamic programming. W Taylor, Protein Sci 1999 8 3 654 665 10091668 (Pubitemid 29117980)
15. Representing and comparing protein structures as paths in three-dimensional space. D Zhi S Krishna H Cao P Pevzner A Godzik, BMC Bioinformatics 2006 7 460 17052359 10.1186/1471-2105-7-460
16. MMDB: Entrez's 3D-structure database. J Chen J Anderson C DeWeese-Scott N Fedorova L Geer S He D Hurwitz J Jackson A Jacobs C Lanczycki, Nucleic Acids Res 2003 31 1 474 477 12520055 10.1093/nar/gkg086
17. SCOP: a structural classification of proteins database for the investigation of sequences and structures. A Murzin S Brenner T Hubbard C Chothia, J Mol Biol 1995 247 4 536 540 7723011
18. CATH: a hierarchic classification of protein domain structures. C Orengo A Michie S Jones D Jones M Swindells J Thornton, Structure 1997 5 8 1093 1108 10.1016/S0969-2126(97)00260-8 9309224 (Pubitemid 27393093)
19. The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. F Pearl A Todd I Sillitoe M Dibley O Redfern T Lewis C Bennett R Marsden A Grant D Lee, Nucleic Acids Res 2005 33 Database D247 251 15608188
20. The three-dimensional structure of an enzyme molecule. C Philips David, Sci Am 1966 215 5 78 90
21. The covalent structure of an entire gammaG immunoglobulin molecule. G Edelman B Cunningham W Gall P Gottlieb U Rutishauser M Waxdal, Proc Natl Acad Sci USA 1969 63 1 78 85 5257969 10.1073/pnas.63.1.78
22. The covalent structure of a human gamma G-immunoglobulin. XI. Functional implications. G Edelman, Biochemistry 1970 9 16 3197 3205 10.1021/bi00818a012 5489773
23. Partitioning protein structures into domains: why is it so difficult? T Holland S Veretnik I Shindyalov P Bourne, J Mol Biol 2006 361 3 562 590 10.1016/j.jmb.2006.05.060 16863650
24. Toward consistent assignment of structural domains in proteins. S Veretnik P Bourne N Alexandrov I Shindyalov, J Mol Biol 2004 339 3 647 678 10.1016/j.jmb.2004.03.053 15147847
25. Pfam: clans, web tools and services. R Finn J Mistry B Schuster-Böckler S Griffiths-Jones V Hollich T Lassmann S Moxon M Marshall A Khanna R Durbin, Nucleic Acids Res 2006 34 Database D247 251 16381856 10.1093/nar/gkj149
26. SMART, a simple modular architecture research tool: identification of signaling domains. J Schultz F Milpetz P Bork C Ponting, Proc Natl Acad Sci USA 1998 95 11 5857 5864 9600884 10.1073/pnas.95.11.5857
27. SMART 5: domains in the context of genomes and networks. I Letunic R Copley B Pils S Pinkert J Schultz P Bork, Nucleic Acids Res 2005 34 Database issue D257 260
28. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. A Marchler-Bauer A Panchenko B Shoemaker P Thiessen L Geer S Bryant, Nucleic Acids Res 2001 30 1 281 283 10.1093/nar/30.1.281
29. CDD: a Conserved Domain Database for protein classification. A Marchler-Bauer J Anderson P Cherukuri C DeWeese-Scott L Geer M Gwadz S He D Hurwitz J Jackson Z Ke, Nucleic Acids Res 2005 33 Database D192 196 15608175
30. VAST Help. 2007 http://www.ncbi.nlm.nih.gov/Structure/VAST/vasthelp.html
31. A genomic perspective on protein families. R Tatusov E Koonin D Lipman, Science 1997 278 5338 631 637 10.1126/science.278.5338.631 9381173
32. The COG database: an updated version includes eukaryotes. R Tatusov N Fedorova J Jackson A Jacobs B Kiryutin E Koonin D Krylov R Mazumder S Mekhedov A Nikolskaya, BMC Bioinformatics 2003 4 41 12969510 10.1186/1471-2105-4-41
33. The PyMol Molecular Graphics System. M DeLano, Palo Alto, CA, USA: DeLano Scientific 2002
34. Cn3D: sequence and structure views for Entrez. Y Wang L Geer C Chappey J Kans S Bryant, Trends Biochem Sci 2000 25 6 300 302 10.1016/S0968-0004(00)01561- 9 10838572