Bioinformatics Links Directory : 3-D Structure Prediction

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

DisEMBL - (Found June 24, 2008 )

A computational tool for prediction of disorderedunstructured regions within a protein sequence.
http://dis.embl.de/

Institute of Enzymology Servers - (Found June 24, 2008 )

A set of severs developed by the Institute of Enzymology that includes tools for transmembrane protein structure prediction and structural analyses.
http://www.enzim.hu/servers.html

ICGEBnet Protein Tools - (Found June 24, 2008 )

ICGEBnet Protein Tools is a resource for analysis of 3D protein structures including domain predictors, a protein fold similiarity server (PRIDE), and tools for calculating atom protusion (CX) andor depth (DPX) indexes in 3D models.
http://www.icgeb.org/protein/

I-Mutant2.0 - (Found June 24, 2008 )

I-Mutant2.0 is a tool that can predict the effect of a single point mutation on protein stability from protein sequences or protein structures.
http://gpcr2.biocomp.unibo.it/cgi/predictors/I-Mutant2.0/I-Mutant2.0.cgi

HHpred - (Found June 24, 2008 )

Based on the comparison of profile HMMs, HHpred takes a protein sequence or multiple sequence alignment as input and searches for remote homologues in an assortment of databases such as PDB, SMART and Pfam. The user can select either a local or global alignment method, and the search results can be used to generate 3D structural models.
http://protevo.eb.tuebingen.mpg.de/hhpred

Harmony - (Found June 24, 2008 )

Harmony is a server to assess the compatibility of an amino acid sequence with a proposed three-dimensional structure.
http://caps.ncbs.res.in/harmony/

GeneSilico - (Found June 24, 2008 )

GeneSilico is a protein structure prediction meta-server that gives access to various fold-recognition servers.
http://genesilico.pl/meta

FRalanyzer - (Found June 24, 2008 )

FRalanyzer (Fold Recognition alignment analyzer) takes as input a sequence-structure alignment, automatically searches annotated databases, and highlights the functionally important positions that are identical in the alignment.
http://fralanyzer.cse.buffalo.edu/

FoldX - (Found June 24, 2008 )

FOLD-X is a program for calculating the folding energies of proteins and for calculating the effect of a point mutation on the stability of a protein.
http://foldx.embl.de/

FFAS03 - (Found June 24, 2008 )

The Fold & Function Assignment System (FFAS03) takes an amino-acid sequence as input and generates a profile which is compared to several sets of sequence profiles including PDB, SCOP, and PFAM.
http://ffas.burnham.org/