CASP2 knowledge-based approach to distant homology recognition and fold prediction in CASP4

Proteins: Structure, Function and Genetics

Volumn 45, Issue SUPPL. 5, 2001, Pages 76-85

  Murzin, Alexey G ^a   Bateman, Alex ^b  

^a MEDICAL RESEARCH COUNCIL   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

Fold recognition; SCOP; Structural similarity; Structure prediction; Superfamily

Indexed keywords

PROTEIN; ABC TRANSPORTER; ARCHAEAL PROTEIN; BACTERIOCIN; BACTERIOCIN AS 48; BACTERIOCIN AS-48; CHORISMATE PYRUVATE LYASE; DEOXYRIBONUCLEASE; LYASE; MALK PROTEIN, THERMOCOCCUS LITORALIS;

ACCURACY; ARTICLE; COMPARATIVE STUDY; EVALUATION; MODEL; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; ARTIFICIAL INTELLIGENCE; BACTERIOPHAGE T7; CHEMICAL STRUCTURE; CHEMISTRY; ENTEROCOCCUS FAECALIS; ESCHERICHIA COLI; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS;

ARCHAEAL PROTEINS; ARTIFICIAL INTELLIGENCE; ATP-BINDING CASSETTE TRANSPORTERS; BACTERIOCINS; BACTERIOPHAGE T7; ENDODEOXYRIBONUCLEASES; ENTEROCOCCUS FAECALIS; ESCHERICHIA COLI; MODELS, MOLECULAR; OXO-ACID-LYASES; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY;

EID: 0035747811     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10037     Document Type: Article

References (28)

1. Distant homology recognition using structural classification of proteins
2. SCOP: A structural classification of proteins database for the investigation of sequences and structures
3. Structure classification-based assessment of CASP3 predictions for the fold recognition targets
4. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
5. The Pfam protein families database
6. Comparative protein structure modeling. Introduction and practical examples with MODELLER
7. Improved methods for building protein models in electron density maps and the location of errors in these models
8. New folds for all-β proteins
9. A new family of bacterial regulatory proteins
10. A new mutation in Spo0A with intragenic suppressors in the effector domain
11. The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains
12. Crystal structure of the M-fragment of α-catenin: Implications for modulation of cell adhesion
13. Characterization of a novel, antifungal, chitin-binding protein from Streptomyces tendae Tu901 that interferes with growth polarity
14. NMR structure of Streptomyces killer toxin-like protein, SKLP: Further evidence for the wide distribution of single-domain βγ-crystallin superfamily proteins
15. Crystal structure of MalK, the ATPase subunit of the trehalose/maltose ABC transporter of the archaeon Thermococcus litoralis
16. Catalytic and binding mutants of the junction-resolving enzyme endonuclease I of bacteriophage T7: Role of acidic residues
17. Crystal structure of the Holliday junction resolving enzyme T7 endonuclease I
18. The crystal structure of chorismate lyase shows a new fold and a tightly retained product
19. Characterization of the Saccharomyces cerevisiae cyclic nucleotide phosphodiesterase involved in the metabolism of ADP-ribose 1″,2″-cyclic phosphate
20. Structure and mechanism of activity of the cyclic phosphodiesterase of Appr>p, a product of the tRNA splicing reaction
21. Sequence-specific 1H assignment and secondary structure of the bacteriocin AS-48 cyclic peptide
22. General architecture of the α-helical globule
23. Bacteriocin AS-48, a microbial cyclic polypeptide structurally and functionally related to mammalian NK-lysin
24. Assessment of the CASP4 fold recognition category
25. A six-stranded double-psi β barrel is shared by several protein superfamilies
26. Structure of the AAA ATPase p97
27. The solution structure of the S1 RNA binding domain: A member of an ancient nucleic acid-binding fold
28. An extended RNA binding surface through arrayed S1 and KH domains in transcription factor NusA