Murray Lab
Murray Lab
Web Resources

bioinformatics tools

Here is an exercise to introduce some useful bioinformatics websites.

Webtools And Software used in our research:

PIPELINE: High-throughput comparative modeling

PrISM: A protein informatics system for modeling

Modeller: Program for comparative protein structure modeling by satisfaction of spatial restraints

jackal: Programs for comparative modeling, side chain prediction/packing and loop prediction

CHARMM: Chemistry at Harvard Molecular Mechanics

CE: Structure alignment using the Combinatorial Extension method

PSIPRED, SSPRO, SAM-T02, PHD: Secondary structure prediction

FUGUE, 123-D, 3D-PSSM/PHYRE: Protein threading and detection of structural templates for modeling

GRASP: Graphical Representation and Analysis of Structural Properties

MolProbity:  Protein structure analysis

The European Bioinformatics Institute: Assorted webtools

PSI-BLAST: Detecting remote sequence homologues

Verify3D: Structure Evaluation Server

CMS: Molecular Biology Resource

LPC: Ligand-Protein Contacts and Contacts of Structural Units

VOIDOO: a program for detection of cavities in macromolecular structures

PHYLIP, MrBayes: programs for modeling phylogenies