Bioinformatics Links Directory : 3-D Structure Prediction

This section contains links to resources to aid in protein 3D structure prediction.

CaspR - (Found June 24, 2008 )

CaspR is a web tool for building structural models for protein sequences using molecular replacement and homology modelling. The software implements an automated approach that uses T-COFFEE to produce alignments, MODELLER to produce homology models, and finally uses AMoRe and CNS to produce the structural model.
http://igs-server.cnrs-mrs.fr/Caspr/index.cgi

Bioverse - (Found June 24, 2008 )

Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.
http://bioverse.compbio.washington.edu/

BhairPred - (Found June 24, 2008 )

BhairPred is a tool for predicting beta-hairpins in protein sequences using a support vector machine.
http://www.imtech.res.in/raghava/bhairpred/

Berkeley Phylogenomics Group - (Found June 24, 2008 )

The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.
http://phylogenomics.berkeley.edu/

AS2TS - (Found June 24, 2008 )

The AS2TS (Amino acid Sequence to Tertiary Structure) system consists of servers for protein structure analysis and modelling.
http://as2ts.llnl.gov/AS2TS/as2ts.html

ArchPred - (Found June 24, 2008 )

ArchPRED predicts the structure of loop regions in protein structures based on a fragment-search based method. Given a query loop of unknown structure, ArchPRED identifies which loops of know structures are likely to share conformational similarity with the query loop.
http://manaslu.aecom.yu.edu/loopred/

Andrej Sali Lab - (Found June 24, 2008 )

This page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).
http://salilab.org/our_resources.shtml

3D-pssm - (Found June 24, 2008 )

Protein fold recognition using 1d and 3d sequence profiles coupled with secondary structure and solvation potential information.
http://www.sbg.bio.ic.ac.uk/~3dpssm/

3D-Jury - (Found June 24, 2008 )

3D-Jury is a protein structure prediction server that collects predictions from multiple servers and generates the final model using a consensus approach.
http://bioinfo.pl/Meta/

DIAL - (Found June 24, 2008 )

DIAL (Domain Identification Algorithm) is a web server for the automatic identification of structural domains given the three-dimensional coordinates of a protein.
http://caps.ncbs.res.in/DIAL/home.html