Bioinformatics Links Directory : 3-D Structure Prediction

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

MODPROPEP - (Found June 24, 2008 )

MODPROPEP is a server for structural modeling of protein kinases and MHC proteins in complex with their substrate peptides.
http://www.nii.res.in/~narendra/PROT_PEP_INTERACTION/index.html

Modeller - (Found June 24, 2008 )

Homology or comparative modeling of 3D protein structures.
http://salilab.org/modeller/

Protinfo - (Found June 24, 2008 )

Protinfo takes a protein sequence as input and returns the atomic coordinates for a prediction of tertiary structure for that protein. Predictions can be made by comparative or de novo modelling.
http://protinfo.compbio.washington.edu/

RCI - (Found June 24, 2008 )

RCI (Random Coil Index) is a method for predicting protein flexibility using secondary chemical shifts.
http://wishart.biology.ualberta.ca/rci/cgi-bin/rci_cgi_1_d.py

VADAR - (Found June 24, 2008 )

Volume, Area, Dihedral Angle Reporter (VADAR) is a web server for qualitative evaluation of protein structure data.
http://redpoll.pharmacy.ualberta.ca/vadar/

Swiss-PdbViewer - (Found June 24, 2008 )

Excellent tool for comparing, colouring, annotating, mutating 3-D structures; a.k.a. Deep View; tutorial Molecular Modeling for Beginners is a must (listed on this page).
http://us.expasy.org/spdbv/

Swiss Model - (Found June 24, 2008 )

Automated protein modelling server.
http://www.expasy.ch/swissmod/SWISS-MODEL.html

Spritz - (Found June 24, 2008 )

Spritz is a tool for the prediction of disordered regions of proteins.
http://distill.ucd.ie/spritz/

SPACE - (Found June 24, 2008 )

SPACE (Structure Prediction and Analysis based on Complementarity with Environment) is a suite of tools for predicting and analyzing structures of biomolecules and their complexes.
http://ligin.weizmann.ac.il/space/

sgTarget - (Found June 24, 2008 )

sgTarget is a structural genomics resource that helps to select and prioritize good targets for structure determination from a list of sequences. Target selection is based on multiple factors including homology searches and a range of physiochemical properties.
http://www.ysbl.york.ac.uk/sgTarget/