Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2005 Jul 1;33(Web Server issue):W72-6.
doi: 10.1093/nar/gki396.

SCRATCH: A Protein Structure and Structural Feature Prediction Server

Affiliations
Free PMC article

SCRATCH: A Protein Structure and Structural Feature Prediction Server

J Cheng et al. Nucleic Acids Res. .
Free PMC article

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.

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.

Similar articles

See all similar articles

Cited by 282 articles

See all "Cited by" articles

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

Publication types

Feedback