Bioinformatics Links Directory : 3-D Structure Prediction

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

Wurst - (Found June 24, 2008 )

Wurst is a protein structure prediction tool that uses threading, aligning submitted sequences to thousands of PDB template structures.
http://www.zbh.uni-hamburg.de/wurst/

ProTarget - (Found June 24, 2008 )

ProTarget offers a method for the prediction of novel structural superfamilies by assessing the relationship of input protein sequences to previously solved 3D structures.
http://www.protarget.cs.huji.ac.il/index.php

PROSPECT-PSPP - (Found June 24, 2008 )

An automated Protein Structure Prediction Pipeline (PSPP) based on multiple structure prediction tools. A key component of the pipeline is the fold recognition program, PROSPECT. Server supports genome scale analyses.
http://csbl.bmb.uga.edu/protein_pipeline

ProSA-web - (Found June 24, 2008 )

ProSA-web (Protein Structure Analysis) is an extension of the classic ProSA program used for the refinement and validation of experimental protein structures and in structure prediction and modeling.
https://prosa.services.came.sbg.ac.at/prosa.php

PREDITOR - (Found June 24, 2008 )

PREDITOR predicts torsion angles in proteins from NMR chemical shift data and sequence homology. PREDITOR combines sequence alignment methods with advanced chemical shift analysis techniques to generate its torsion angle predictions.
http://wishart.biology.ualberta.ca/shiftor/cgi-bin/preditor_current.py

PrDOS - (Found June 24, 2008 )

PrDOS (Protein Disorder Prediction Server) is a server to predict the disordered regions of a protein from its amino acid sequence.
http://prdos.hgc.jp/cgi-bin/top.cgi

Pcons.net - (Found June 24, 2008 )

Pcons.net is a protein structure prediction meta server that provides automated tools for protein structure prediction and analysis using a consensus approach.
http://pcons.net/

NQ-Flipper - (Found June 24, 2008 )

NQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures.
https://flipper.services.came.sbg.ac.at/cgi-bin/flipper.php

NORSp - (Found June 24, 2008 )

NORSp (predictor of NOn-Regular Secondary Structure) is a tool for predicting disordered regions in proteins.
http://cubic.bioc.columbia.edu/services/NORSp/

Molecular Modeling for Beginners - (Found June 24, 2008 )

Excellent hands-on Swiss-PdbViewerDeep View tutorial; a must-do before attempting to use Swiss-PdbViewer.
http://www.usm.maine.edu/~rhodes/SPVTut/index.html