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.

TMBETA-NET - (Found July 2, 2008 )

Tool that predicts transmembrane beta strands in an outer membrane protein from its amino acid sequence.
http://psfs.cbrc.jp/tmbeta-net/

TMH Benchmark - (Found July 2, 2008 )

The Transmembrane Helix (TMH) Benchmark server provides a standard benchmark evaluation for helical trans-membrane prediction methods.
http://cubic.bioc.columbia.edu/services/tmh_benchmark/

TMpred - (Found July 2, 2008 )

Prediction of transmembrane regions and their orientation.
http://www.ch.embnet.org/software/TMPRED_form.html

TRAMPLE - (Found July 2, 2008 )

TRAMPLE is a tool for the prediction of transmembrane helices, transmembrane strands, secondary structure, and signal peptides.
http://gpcr.biocomp.unibo.it/biodec/

transFold - (Found July 2, 2008 )

transFold predicts the super-secondary structure of transmembrane beta-barrel (TMB) proteins including side-chain orientation and topology of transmembrane segments.
http://bioinformatics.bc.edu/clotelab/transFold

PROFtmb - (Found July 2, 2008 )

PROFtmb predicts transmembrane beta-barrel (TMB) proteins in Gram-negative bacteria. In addition to running your own predictions, you can also download predictions for all proteins in 78 Gram-Negative bacterial genomes.
http://cubic.bioc.columbia.edu/services/proftmb/

PredictProtein - (Found July 2, 2008 )

PredictProtein is a protein sequence analysis and structure prediction tool. Users provide a protein sequence, and PredictProtein reports similar sequences, PROSITE sequence motifs, and various types of structure prediction information. You can also use META PredictProtein to submit a sequence to one web form and query several other servers at once, retrieving the results by e-mail.
http://www.predictprotein.org

PRED-TMBB - (Found July 2, 2008 )

PRED-TMBB is a tool that takes a Gram-negative bacteria protein sequence as input and predicts the transmembrane strands and the probability of it being an outer membrane beta-barrel protein. The user has a choice of three different decoding methods.
http://bioinformatics.biol.uoa.gr/PRED-TMBB/

PRALINE - (Found July 2, 2008 )

Praline is a multiple sequence alignment program that can integrate information from sequence similarity searches and secondary structure prediction.
http://ibivu.cs.vu.nl/programs/pralinewww/

PONGO - (Found July 2, 2008 )

PONGO allows users to compare topology predictions of membrane proteins made by four different predictors (MEMSAT, TMHMM, ENSEMBLE, and PRODIV). It also displays a signal peptide prediction determined with SPEP.
http://pongo.biocomp.unibo.it/pongo