Protein Secondary Structure Prediction Servers and FTP Sites

Web sites which perform protein secondary structure prediction. Some implement very new procedures, and some implement older ones. Organized by method.

Parametric and Semiparametric Methods

• (Local) QL server (Munson, NIH) Quadratic-Logistic prediction method is based on maximum-likelihood methods.
• (Local) QL with homologs (Munson, NIH) Allows prediction from multiple sequences.
• SSP Program Description (Solovyev, Baylor College) for secondary structure prediction uses linear discriminant analysis. The actual prediction server for SSP and NNSSP is: pssprediction
• (Local) GOR-IV server (Garnier, NIH) from the Garnier group
• Download GOR-IV code from NCBI
• Download GOR-IV code from Jouy, France

Neural Network Methods

• PHD (Rost&Sander, EMBL) Email service for prediction of protein structure. This is the PHD/MaxHom server of Rost and Sander.
• NNPRED (Fred Cohen , UCSF) D. G. Kneller, F. E. Cohen and R. Langridge (1990) "Improvements in Protein Secondary Structure Prediction by an Enhanced Neural Network" J. Mol. Biol. (214) 171-182.

Nearest-Neighbor Methods

• Program, NNSSP (Salamov, Baylor), nnssprediction is an implementation and improvement of a nearest-neighbor/neural network method by Yi and Lander
• The actual prediction server for SSP and NNSSP is: pssprediction
• Anonymous FTP of program code for the SIMPA96 program from the Garnier group

Hybrid Methods

• PREDATOR (Frishman&Argos, EMBL) allows you to submit by email or WWW and receive a response by email.
• SSPRED Documentation (Prediction by Mehta, Heringa, Argos , EMBL) "Prediction of protein secondary structure using exchange statistics in multiply aligned sequences"
• SOPMA (Geourjon at IBCP, Lyon, France)

Secondary Structure Content Prediction

• SSCP Documentation Secondary Structure Content Prediction by Frank Eisenhaber of the Argos group
• SSCP seq-request form

OTHER INTERESTING SITES

• STRIDE Documentation, an alternative method to DSSP for secondary structure assignment.
• A related, interesting server is search-launcher by Randal Smith at Baylor College of Med
• ExPASy - Tools Nice collection of protein sequence analysis tools collected at University of Geneva. Includes pointers to many local sequence servers and pointers to many other servers

Next are the ISREC(Swiss Institute for Experimental Cancer Research in Epalinges/Lausanne, Switzerland sites:ISREC COILS Server coiled coil prediction search form

• ISREC SAPS server SAPS (Statistical Analysis of Proteins, Brendel....Karlin, PNAS 1992) server
• ISREC TMpred Server Transmembrane region orientation prediction by Hoffman and StoffelCPE Protein Structure Prediction Pages MRC Center for Protein Engineering (Tim Hubbard) pointers to interesting secondary structure prediction issues, including a course being run at Rome, Italy on the net
• The NCSA Biology Workbench site
• Boston University site including state-space modeling by White, Stulz, Smith
• Pedro's Biomelcular Research Tools

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