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Category bioinformatik.de / Software / Unix / Molecular Modeling /

BRAGI is a interactive protein-modelling program. It was developed for the special purpose to modell unknown proteins from the structure of a known one.
http://www.uni-koeln.de/math-nat-fak/biochemie/ds/dsbrag_e.htm

DomainFinder is an interactive program for the determination and characterization of dynamical domains in proteins.
http://dirac.cnrs-orleans.fr/DomainFinder/

GROMOS is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems.
http://igc.ethz.ch/gromos/

Mc-Sym (Macromolecular Conformations by SYMbolic programming) is the result of a joint effort between the computer science and biochemistry departments of the Université de Montréal to develop a tool for three-dimentional determination of RNA structures.
http://www-lbit.iro.umontreal.ca/mcsym/

Molecular Simulations Inc. (MSI)- is a leading provider of molecular modeling and simulation software for both life and materials science research.
http://www.msi.com/

Molegro Virtual Docker (MVD) - MVD is an integrated platform for predicting protein-ligand interactions.
http://www.molegro.com

MOLMOL - MOLecule analysis and MOLecule display.
http://www.mol.biol.ethz.ch/wuthrich/software/molmol/

RasMol & Chime: Molecular Visualization Freeware
http://www.umass.edu/microbio/rasmol/

Raster3D Version 2.4 s a set of tools for generating high quality raster images of proteins or other molecules.
http://www.bmsc.washington.edu/raster3d/raster3d.html

Swiss-PdbViewer
http://www.expasy.ch/spdbv/mainpage.htm

WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc.
http://swift.embl-heidelberg.de/whatif/