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. 2005 Jul 1;33(Web Server issue):W72-6.
doi: 10.1093/nar/gki396.

SCRATCH: a protein structure and structural feature prediction server

J Cheng  1 , A Z Randall, M J Sweredoski, P Baldi
Affiliations

SCRATCH: a protein structure and structural feature prediction server

J Cheng et al. Nucleic Acids Res. .

Abstract

SCRATCH is a server for predicting protein tertiary structure and structural features. The SCRATCH software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure. The user simply provides an amino acid sequence and selects the desired predictions, then submits to the server. Results are emailed to the user. The server is available at http://www.igb.uci.edu/servers/psss.html.

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Figures

Figure 1
Figure 1
Flow diagram for the SCRATCH server. DISpro, DOMpro, CONpro and DIpro are grouped together because they have the same inputs and their outputs are not used by other predictors; however, they are standalone programs.
See this image and copyright information in PMC

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References

    1. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 2000;28:235–242. - PMC - PubMed
    1. Pollastri G., Przybylski D., Rost B., Baldi P. Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins. 2002;47:228–235. - PubMed
    1. Pollastri G., Baldi P., Fariselli P., Casadio R. Prediction of coordination number and relative solvent accessibility in proteins. Proteins. 2002;47:142–153. - PubMed
    1. Baldi P., Cheng J., Vullo A. Large-scale prediction of disulphide bond connectivity. Adv. Neural Inf. Process Syst. 2004;17:97–104.
    1. Pollastri G., Baldi P. Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. Bioinformatics. 2002;18(Suppl. 1):S62–S70. - PubMed

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