Structural Bioinformatics Software

ICM 3.4.4

Commercial modelling software installed on local computers in the graphics room and terminal room. Homology-based modelling, ligand-protein docking, protein-protein docking, virtual screening of ligand libraries into protein binding sites, alignment tools, visualization of molecules and molecular properties (e.g. Electrostatics).
Home page: http://www.molsoft.com


AMBER 8 (Assisted Model Building with Energy Refinement)

Commercial molecular mechanical and dynamics calculations of proteins, nucleic acids and ligands at the University.
Home page: http://amber.scripps.edu/

GAUSSIAN-98/03

Commercial software for quantum mechanical calculations at the University. Atomic point charges for small molecule ligands in the AMBER8 force fields are determined by GAUSSIAN.
Home page: http://www.gaussian.com


DOCK 5.3.0

Academic freeware for ligand-protein, protein-protein and protein-DNA docking
Home page: http://dock.compbio.ucsf.edu/


HEX 4e

Hex is an interactive protein docking and molecular superposition program. Free to academics.
Home page: http://www.csd.abdn.ac.uk/hex/


AUTODOCK 3.0 (Automated docking of flexible ligands to macromolecules)

Freeware for ligand-protein docking
Home Page: http://www.scripps.edu/mb/olson/doc/autodock/


MODELLER 8v1-1

Freeware for homology based modelling. MODELLER is available free of charge to academic non-profit institutions.
Home Page: http://salilab.org/modeller/