Predicting structures for genome proteins

Current Opinion in Structural Biology

Volumn 9, Issue 2, 1999, Pages 208-211

  Fischer, Daniel ^a   Eisenberg, David ^b  

^a Dept of Math and Computer Science   (Israel)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; CRYSTALLIZATION; GENE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; SEQUENCE HOMOLOGY; SHORT SURVEY;

EID: 0033117760     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(99)80029-3     Document Type: Article

References (22)

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2. Frishman D, Mewes H-W: Protein structural classes in five complete genomes. Nat Struct Biol 1997, 4:626-628. An extensive analysis and classification of open reading frames (ORFs) from various genomes using sequence-based techniques. The numbers reported in this paper have been superseded by more recent computations, available at the authors' web site (http://pedant.mips.biochem.mpg.de). This site contains the authors' analysis of 40 complete and unfinished genomes! The fraction of ORFs with assigned folds ranges from 10% for an archeon, up to 18% for M. tuberculosis.
3. Sanchez R, Sali A: Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc Natl Acad Sci USA 1998, 95:13597-13602. An interesting and original procedure for building homology models for complete genomes. The procedure includes a validation step, which uses a potential of mean force. The procedure was applied to yeast, E. coli, M. genitalium, C. elegans and M. jannaschii, resulting in homology models for 17%, 18%, 19%, 20% and 16% of the open reading frames, respectively. (See, also, http://www.guitar.rockefeller.edu.)
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8. Bork P, Gibson TJ: Applying motif and profile searches. Methods Enzymol 1996, 266:162-184.
9. Fischer D, Rice DW, Bowie JU, Eisenberg D: Assigning amino acid sequences to 3D protein folds. FASEB J 1996, 10:126-136.
10. Altschul SF, Madden TL, Schaffer AA, Zhang J, ZHang Z, Miller W, Lipman DJ: Gapped blast and PSI-BLAST: A new generation of protein database search programs. Nucleic Acid Res 1997, 25:3389-3402. An extension of the widely used BLAST method, which allows gapped alignments and iterative database searches using a position-specific score matrix or profile. PSI-BLAST is a very sensitive method that is able to detect weak, but biologically relevant, sequence similarities. The increased sensitivity is mainly due to the use of evolutionary information from sequence neighbors in the form of a profile.
11. CASP3 - critical assessment of protein structure prediction methods, round III, 1998 on World Wide Web URL: http://Predictioncenter.llnl.gov/casp3/Over 40 targets for protein structure prediction were compiled in this experiment, with the participation of dozens of predictors. This computer-aided (i.e. person plus machine) structure prediction experiment demonstrated the progress in the field. A special issue devoted to this experiment will appear in Proteins in 1999.
12. Huynen M, Doerks T, Eisenhaber F, Orengo C, Sunyaev S, Yuan Y, Bork P: Homology-based fold predictions for Mycoplasma genitalium proteins. J Mol Biol 1998, 280:323-326. PSI-BLAST was used to find structures for 37% and 33% of the M. genitalium and E. coli open reading frames, respectively. An accuracy of 98% is estimated! A very useful automated web server implementing this procedure is available at http://dove.embl-heidelberg.de/3D/.
13. Rychlewski L, Zhang B, Godzik A: Fold and function predictions for Mycoplasma genitalium proteins. Fold Des 1998, 3:229-236. Structures homologous to the sequences of the M. genitalium genome were searched using two sequence-only tools: PSI-BLAST and BASIC (a new profile-profile method developed by the authors). The fraction of assigned sequences reported is 27% and 38%, respectively. A comparison of the predictions from both methods showed that there were open reading frames for which different folds had been predicted, indicating that both predictions can not be correct. An interesting structural and functional analysis of the predictions is included.
14. Wolf Yl, Brenner SE, Bash PA, Koonin EV: Distribution of protein folds in the three super-kingdoms of life. Genome Res 1999, in press. Using PSI-BLAST and a collection of 1193 position-dependent weight matrices, the authors assigned folds for 20-30% of the open reading frames of 14 completely sequenced genomes. The authors analysed both the distribution of the most common folds and the observed diversity of protein folds in different proteomes. The fold predictions are available at ftp://ncbi.nlm.nih.gov/pub/koonin/FOLDS/index.html.
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16. 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. The first application of a structure-based fold-assignment method to a complete genome. Using an automated computer server (http://www.doe-mbi.ucla.edu/people/frsvr/frsvr.html) with rather conservative thresholds, 25% of the M, genitalium genome was assigned a 3D fold. The authors repeated their assignments 18 months later, resulting in an assigned fraction of 32%. A list of attractive targets for crystallization is given at http://www.doe-mbi.ucla.edu/people/frsvr/preds/MG/MG.html.
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19. CAFASP1 on World Wide Web URL: http://www.cs.bgu.ac.il/≃dfischer/cafasp1/cafasp1.html. The first experiment on the critical assessment of fully automated structure-prediction methods. The evaluation of the performance of fully automated (no human intervention) fold-recognition methods is required to assess their future applicability at genomic scales.
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