Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 10, 2014, Pages 3733-3738

  Khafizov, Kamil ^a,b   Madrid Aliste, Carlos ^a   Almo, Steven C ^a   Fiser, Andras ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^b MOSCOW INSTITUTE OF PHYSICS AND TECHNOLOGY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; CELLULAR DISTRIBUTION; HUMAN; NONHUMAN; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE DATABASE; STRUCTURAL GENOMICS;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MOLECULAR SEQUENCE ANNOTATION; PROTEINS; PROTEOMICS; SPECIES SPECIFICITY;

EID: 84896271802     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1321614111     Document Type: Article

References (25)

1. Levitt M (2009) Nature of the protein universe. Proc Natl Acad Sci USA 106(27): 11079-11084.
2. Chandonia JM, Brenner SE (2006) The impact of structural genomics: Expectations and outcomes. Science 311(5759):347-351.
3. Terwilliger TC (2011) The success of structural genomics. J Struct Funct Genomics 12(2):43-44.
4. Fajardo JE, Fiser A (2013) Protein structure-based prediction of catalytic residues. BMC Bioinformatics 14:63.
5. Jhoti H, Leach AR (2007) Structure-Based Drug Discovery (Springer, Dordrecht), p xii.
6. Stein A, Céol A, Aloy P (2011) 3did: Identification and classification of domain-based interactions of known three-dimensional structure. Nucleic Acids Res 39(Database issue):D718-D723.
7. Zhang Y, et al. (2009) Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science 325(5947):1544-1549.
8. Kim J, et al. (2013) Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function. Nature 498(7452):123-126.
9. Zhao S, et al. (2013) Discovery of new enzymes and metabolic pathways by using structure and genome context. Nature 502(7473):698-702.
10. Montelione GT (2012) The Protein Structure Initiative: Achievements and visions for the future. F1000 Biol Rep 4:7.
11. Fernandez-Fuentes N, Rai BK, Madrid-Aliste CJ, Fajardo JE, Fiser A (2007) Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments. Bioinformatics 23(19):2558-2565.
12. Punta M, et al. (2009) Structural genomics target selection for the New York Consortium on Membrane Protein Structure. J Struct Funct Genomics 10(4):255-268.
13. Gifford LK, Carter LG, Gabanyi MJ, Berman HM, Adams PD (2012) The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: A structural biology web resource. J Struct Funct Genomics 13(2):57-62.
14. Cormier CY, et al. (2011) PSI:Biology-materials repository: A biologist's resource for protein expression plasmids. J Struct Funct Genomics 12(2):55-62.
15. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2009) GenBank. Nucleic Acids Res 37(Database issue):D26-D31.
16. Liu J, Montelione GT, Rost B (2007) Novel leverage of structural genomics. Nat Biotechnol 25(8):849-851.
17. Punta M, et al. (2012) The Pfam protein families database. Nucleic Acids Res 40(Database issue):D290-D301.
18. Nair R, et al. (2009) Structural genomics is the largest contributor of novel structural leverage. J Struct Funct Genomics 10(2):181-191.
19. Levitt M (2007) Growth of novel protein structural data. Proc Natl Acad Sci USA 104(9):3183-3188.
20. Cuff A, et al. (2009) The CATH hierarchy revisited: Structural divergence in domain superfamilies and the continuity of fold space. Structure 17(8):1051-1062.
21. Liu X, Fan K, Wang W (2004) The number of protein folds and their distribution over families in nature. Proteins 54(3):491-499.
22. Pagani I, et al. (2012) The Genomes OnLine Database (GOLD) v.4: Status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 40(Database issue):D571-D579.
23. Grant A, Lee D, Orengo C (2004) Progress towards mapping the universe of protein folds. Genome Biol 5(5):107.
24. Almo SC, et al. (2013) Protein production from the structural genomics perspective: Achievements and future needs. Curr Opin Struct Biol 23(3):335-344.
25. Berry IM, et al. (2006) SPINE high-throughput crystallization, crystal imaging and recognition techniques: Current state, performance analysis, new technologies, and future aspects. Acta Crystallogr D Biol Crystallogr 62(Pt 10):1137-1149.