Bioinformatics Links Directory : 3-D Structure Prediction

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

Services from Zhou Laboratory - (Found June 24, 2008 )

Tools from the Zhou laboratory including predictors of transmembrane topology (THUMBUP, UMDHMM-TMHP, TUPS); predictionanalysis tools for tertiary structure (SPARKS2, SP3); and, predictionanalysis tools for interactions (DMONOMER, DLOOP, DMUTANT, DCOMPLEX, DDNA, TCD, DOGMA).
http://theory.med.buffalo.edu/

Servers at University College London - (Found June 24, 2008 )

A suite of tools that includes: PSIPRED, a protein structure prediction server; GenTHREADER, for genomic protein fold recognition; MEMSAT2, for transmembrane protein structure prediction; GTD, the genomic threading database; DISOPRED, a dynamic disorder prediction server; DomPred, a domain prediction server; and COPS, for the comparison of protein structure classifications.
http://bioinf.cs.ucl.ac.uk/software.html

SDPMOD - (Found June 24, 2008 )

SDPMOD is a comparative modelling tool for small disulfide-bonded proteins (SDPs).
http://proline.bic.nus.edu.sg/sdpmod/

SABBAC - (Found June 24, 2008 )

Structural Alphabet based protein Backbone Builder from Alpha Carbon trace (SABBAC) is a tool for the reconstruction of complete protein structures from their alpha-carbon descriptions.
http://bioserv.rpbs.jussieu.fr/cgi-bin/SABBAC

Robetta - (Found June 24, 2008 )

The Robetta server provides protein structure prediction tools and interface alanine scanning. The structure prediction is accomplished by either comparative modelling or the de novo Rosetta fragment insertion method. Interface alanine scanning is employed to predict how protein-protein interactions could be affected by mutations.
http://robetta.bakerlab.org/

MIGenAS Toolkit - (Found June 24, 2008 )

Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure "meta"-tools as a pipeline of individual tools and intermediate filters.
http://www.migenas.org/

M4T - (Found June 24, 2008 )

M4T (Multiple Mapping Method with Multiple Templates) is a comparative protein structure modeling server that uses a combination of multiple templates and iterative optimization of alternative alignments.
http://manaslu.aecom.yu.edu/M4T/

iPDA - (Found June 24, 2008 )

iPDA (Integrated Protein Disorder Analyzer) predicts disordered regions of a query protein sequence.
http://biominer.bime.ntu.edu.tw/ipda/

CrysTwiV - (Found June 24, 2008 )

CrysTwiV (Crystal Twin Variables) is an automated approach for phase extension and refinement in X-ray crystallography; free registration is required for use.
http://btweb.aua.gr:8080/crystwiv/

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

COLORADO-3D allows you to color your protein structures to indicate the presence of potential errors in protein structure (detected by ANOLEA, PROSAII, PROVE or VERIFY3D), buried residues, and sequence conservation. The server returns a PDB-formatted file which can be displayed in RASMOL.
http://asia.genesilico.pl/colorado3d/