Modeling three-dimensional protein structures for amino acid sequences of the CASP3 experiment using sequence-derived predictions

Proteins: Structure, Function and Genetics

Volumn 37, Issue SUPPL. 3, 1999, Pages 61-65

  Fischer, Daniel ^a  

^a BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

Author keywords

Critical assessment of protein structure prediction; Homology modeling; Protein fold assignment; Protein structure prediction; Sequence structure alignment; Threading

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; MODEL; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; PROTEIN TARGETING; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; ANIMAL; BACILLUS SUBTILIS; CHEMICAL STRUCTURE; CHEMISTRY; MOLECULAR GENETICS; PLASMODIUM; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT;

BACTERIAL PROTEIN; FLAD PROTEIN, BACTERIA; INITIATION FACTOR;

AMINO ACID SEQUENCE; ANIMALS; BACILLUS SUBTILIS; BACTERIAL PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDE INITIATION FACTORS; PLASMODIUM; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT;

EID: 0032606139     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(1999)37:3+<61::AID-PROT9>3.0.CO;2-9     Document Type: Article

References (15)

1. Fischer D, Eisenberg D. Protein fold recognition using sequence-derived predictions. Protein Sci 1996;5:947-955.
2. Fischer D, Elofsson A, Rice DW, Eisenberg D. Assessing the performance of inverted protein folding methods by means of an extensive benchmark. Proceedings 1st Pacific Symposium on Biocomputing 1996;January:300-318. http://www.mbi.ucla.edu/ people/fischer/BENCH/benchmark1.html.
3. Elofsson A, Fischer D, Rice DW, Le Grand S, Eisenberg D. A study of combined structure-sequence profiles. Folding Design 1996;1: 451-461.
4. Rost B, Sander C. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol 1993;232:584-599.
5. Rost B. TOPITS: threading one-dimensional predictions into three-dimensional structures. Proceedings Conference Intelligent Systems in Molecular Biology, ISMB-95 1995;314-321.
6. Gonnet GH, Cohen MA, Benner SA. Exhaustive matching of the entire protein sequence database. Science 1992;256:1433-1445.
7. Genetic Computer Group. 1991.
8. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment tool. J Mol Biol 1990;215:403-410.
9. Bairoch A, Boeckmann B. The swiss-prot protein sequence data bank. Nucleic Acids Res 1992;20:2019-2022.
10. Rice DW, Fischer D, Weiss R, Eisenberg D. Fold assignments for amino acid sequences of the CASP2 experiment. Proteins Suppl 1997;1:113-122.
11. Bernstein FC, Koetzle TF, Williams GJB, et al. The Protein Data Bank: a Computer-based Archival File for Macromolecular Structures. J Mol Biol 1977;112:535-542.
12. Fischer D, Eisenberg D. Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. Proc Natl Acad Sci USA 1997;94:11929-11934.
13. Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acid Res 1997;25:3389-3402.
14. Fischer D, Eisenberg D. Predicting structures for genome sequences. Curr Opin Struct Biol 1999;9:208-211.
15. Sanchez R, Sali A. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc Natl Acad Sci USA 1998; 95:13597-13602.