Bioinformatics Links Directory : 2-D Structure Prediction

This sections contains links to several programs which predict protein secondary structure. A link to resources for the evaluation of protein structure prediction is also found here.

VAST - (Found July 2, 2008 )

Vector Alignment Search Tool for viewing protein structure neighbours.
http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml

Protein Peeling - (Found July 2, 2008 )

Protein Peeling is an approach for splitting a protein three dimensional (3D) structure into protein units, an intermediate level of protein structure description between protein domains and secondary structures.
http://www.ebgm.jussieu.fr/~gelly/index.html

PSA - (Found July 2, 2008 )

Prediction of probable secondary structures and fold-class; good for visualizing amphipathic helices, where present.
http://bmerc-www.bu.edu/psa/request.htm

PSIPRED - (Found July 2, 2008 )

An excellent tool for prediction of secondary structure, with access to GenTHREADER for protein fold recognition and MEMSAT-2 transmembrane topology prediction.
http://bioinf.cs.ucl.ac.uk/psipred/

SAPS - Statistical Analysis of Protein Sequences - (Found July 2, 2008 )

Calculations include compositional analysis, charge distribution, identification of highly hydrophobic (transmembrane) segments, sequence repeats, and more.
http://www.ch.embnet.org/software/SAPS_form.html

SCRATCH - (Found July 2, 2008 )

SCRATCH is a suite of protein structure software and servers for the prediction of secondary structure, solvent accessibility, disulphide bridges, stability effects of single amino acid mutations, disordered regions, domains, beta-residue and beta-strand pairings, amino acid contact maps, and tertiary structure.
http://www.igb.uci.edu/servers/psss.html

SSEP - (Found July 2, 2008 )

Secondary Structural Elements of Proteins (SSEP) provides access to information about secondary structural elements present in non-redundant sets of proteins from the PDB.
http://cluster.physics.iisc.ernet.in/ssep/options.html

STRIDE - (Found July 2, 2008 )

STRIDE takes a PDB structure as input and reports back either secondary structure assignments, a Ramachandran plot or a contact map.
http://webclu.bio.wzw.tum.de/stride/

SVMtm - (Found July 2, 2008 )

Support Vector Machine Transmembrane (SVMtm) predicts transmembrane helices when given protein sequences in FASTA format.
http://ccb.imb.uq.edu.au/svmtm/svmtm_predictor.shtml

TMB-Hunt - (Found July 2, 2008 )

TMB-Hunt (Transmembrane Barrel - Hunt) classifies protein sequences as transmembrane B-barrel (TMB) or non-TMB based on amino acid composition.
http://www.bioinformatics.leeds.ac.uk/betaBarrel/