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. 2003 Jul 1;31(13):3300-4.
doi: 10.1093/nar/gkg508.

The PredictProtein server

Burkhard Rost  1 , Jinfeng Liu
Affiliations

The PredictProtein server

Burkhard Rost et al. Nucleic Acids Res. .

Abstract

PredictProtein (PP, http://cubic.bioc.columbia.edu/pp/) is an internet service for sequence analysis and the prediction of aspects of protein structure and function. Users submit protein sequence or alignments; the server returns a multiple sequence alignment, PROSITE sequence motifs, low-complexity regions (SEG), ProDom domain assignments, nuclear localisation signals, regions lacking regular structure and predictions of secondary structure, solvent accessibility, globular regions, transmembrane helices, coiled-coil regions, structural switch regions and disulfide-bonds. Upon request, fold recognition by prediction-based threading is available. For all services, users can submit their query either by electronic mail or interactively from World Wide Web.

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Figures

Figure 1
Figure 1
Data flow for PredictProtein (PP). Users query PP with their protein and receive a single file with results from database comparisons and prediction methods. Users can query PP through email and web interfaces.
Figure 2
Figure 2
Usage of PredictProtein. The number of requests to PP continues to rise (A); over one million requests came from 95 countries. Almost half of all the requests originated from North America (B).
See this image and copyright information in PMC

References

    1. Rost B. and Sander,C. (1992) Jury returns on structure prediction. Nature, 360, 540. - PubMed
    1. Henikoff S. (1993) Sequence analysis by electronic mail server. Trends Biochem. Sci., 18, 267–268. - PubMed
    1. Rost B. (1999) Twilight zone of protein sequence alignments. Protein Eng, 12, 85–94. - PubMed
    1. Altschul S.F. and Gish,W. (1996) Local alignment statistics. Methods Enzymol., 266, 460–480. - PubMed
    1. Altschul S., Madden,T., Shaffer,A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D. (1997) Gapped BLAST and PSI-Blast: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389–3402. - PMC - PubMed

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