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.

Phobius - (Found July 2, 2008 )

Phobius is a combined transmembrane topology and signal peptide predictor. The server also allows for constrained and homology-enriched predictions.
http://phobius.cgb.ki.se/

BPROMPT - (Found July 2, 2008 )

Bayesian PRediction Of Membrane Protein Topology (BPROMPT) uses a Bayesian Belief Network to combine the results of other membrane protein prediction methods for a protein sequence.
http://www.jenner.ac.uk/BPROMPT/

COILS - (Found July 2, 2008 )

Prediction of coiled coil regions.
http://www.ch.embnet.org/software/COILS_form.html

ConPred II - (Found July 2, 2008 )

ConPred II is a tool for predicting transmembrane topology for a user-supplied query sequence. Results are presented in a variety of forms including hydropathy plots.
http://bioinfo.si.hirosaki-u.ac.jp/~ConPred2/

DICHROWEB - (Found July 2, 2008 )

A server that supports several different algorithms for the analysis of Circular Dichroism (CD) spectra for the prediction of protein secondary structure. Results also contain a graphical comparison of calculated versus experimental results.
http://public-1.cryst.bbk.ac.uk/cdweb/html/

DSSPcont - (Found July 2, 2008 )

DSSPcont automates protein secondary structure prediction from PDB structures to reflect structural variations due to thermal fluctuations.
http://cubic.bioc.columbia.edu/services/DSSPcont/

ENDscript - (Found July 2, 2008 )

ENDscript is a tool for creating, visualizing, and interpreting multiple sequence alignments overlayed with known structural information.
http://espript.ibcp.fr/ESPript/ENDscript/index.php

GlobPlot - (Found July 2, 2008 )

GlobPlot has the ability to plot the tendency towards globularity for a given protein sequence. Can also perform SMARTPfam domain prediction.
http://globplot.embl.de/

HHrep - (Found July 2, 2008 )

HHrep is a tool for the de novo identification of repeats in protein sequences based on the pairwise comparison of profile hidden Markov models (HMMs).
http://toolkit.tuebingen.mpg.de/index.php?view=hhrep

iMolTalk - (Found July 2, 2008 )

iMolTalk is a set of tools for protein structure analysis. Users have access to tools to extract information from PDB files, create Ramachandran plots or alpha-carbon distance matrices, align two structures or a sequence to a structure, search for contacts for a residue, and identify the interface between chains.
http://i.moltalk.org