Automated search of natively folded protein fragments for high-throughput structure determination in structural genomics

Protein Science

Volumn 9, Issue 12, 2000, Pages 2313-2321

  Kuroda, Yutaka ^a,c   Tani, Kazutoshi ^a   Matsuo, Yo ^a   Yokoyama, Shigeyuki ^a,b  

^a INST OF PHYS AND CHEMICAL RESEARCH   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c RIKEN YOKOHAMA INSTITUTE   (Japan)

Author keywords

Automated procedure; Computing tool; PASS; Protein structure determination; Sequence similarity; Stable protein fragment; Structural genomics

Indexed keywords

AMINO ACID ANALYSIS; AMINO ACID SEQUENCE; ARTICLE; AUTOANALYZER; COMPUTER PROGRAM; DATA BASE; GEOMETRY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

EID: 0034493084     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.9.12.2313     Document Type: Article

References (40)

1. Basic local alignment search tool
2. Gapped BLAST and PSI-BLAST: A new generation of protein data-base search programs
3. The SWISS-PROT protein sequence data bank and its new supplement TREMBL
4. Structure of the fibronectin type I module
5. GenBank
6. The PRESAGE database for structural genomics
7. Structural genomics: Beyond the human genome project
8. Building protein structure and function from modular units
9. NMR structures of proteins and protein complexes beyond 20,000 M(r)
10. The ProDom database of protein domain families
11. A comparison of sequence and structure protein domain families as a basis for structural genomics
12. Structural genomics: Bioinformatics in the driver's seat
13. Sequence analysis of the genome of Bombyx mori uucleopolyhedrovirus
14. Automated protein Sequence database classification. I. Integration of compositional similarity search, local similarity search, and multiple sequence alignment
15. Blocks+: A non-redundant database Of protein alignment blocks derived from multiple compilations
16. Touring protein fold space with Dali/FSSP
17. Directed evolution of thermostable kanamycin-resistance gene: A convenient selection marker for Thermus thermophilus
18. The structural aspects of limited proteolysis of native proteins
19. SCOP: A Structural classification of proteins database
20. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
21. Shining a light on structural genomics
22. Solution structure of the SH3 domain of phospholipase C-gamma
23. Solution structure of the link module: A hyalurouan-binding domain involved in extracellular matrix stability and cell migration
24. Solution structure Of the Eps15 homology domain of a human POB1 (partner of RalBP1)
25. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
26. Solution structure of the CIDE-N domain of CIDE-B and a model for CIDE-N/CIDE-N interactions in the DNA fragmentation pathway of apoptosis
27. Selecting protein targets for Structural genomics of Pyrobaculum aerophilum: Validating automated fold assignment methods by using binary hypothesis testing
28. SCOP: A structural classification of proteins database for the investigation of sequences and structures
29. Crystal structure of Thermus thermophilus HB8 UvrB protein, a key enzyme of nucleotide excision repair
30. SSMAL: Similarity searching with alignment graphs
31. Protein superfamilies and domain superfolds
32. CATH - A hierarchic classification of protein domain structures
33. From protein structure to function
34. TROSY in triple-resonance experiments: New perspectives for sequential NMR assignment of large proteins
35. The Argonne Structural Genomics Workshop: Lamaze class for the birth of a new science
36. Pfam: A comprehensive database of protein domain families based on seed alignments
37. Modular arrangement of proteins as inferred from analysis of homology
38. The second decade - Into the third millennium
39. Structural genomics projects in Japan
40. Solution structure of the SH3 domain of Src and -identification of its ligand-binding site