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A suite of automated docking tools

AutoDock Vina is a new program for drug discovery and molecular docking

Advanced molecular editor that uses Qt4 and OpenGL

The Blue Obelisk Data Repository listing element and isotope properties.

An application for the analysis of NMR spectra and Computer Aided Resonance Assignment

chemical-mime-data

A collection of data files to add support for chemical MIME types.

A GTK program for drawing organic molecules

The protein secondary structure standard

Chemical structure drawing program - focused on presentation.

periodic table of the elements

a periodic table viewer that provides detailed information on the chemical elements.

gnome-chemistry-utils

Periodic table application for Linux

The ultimate molecular dynamics simulation package

ksdssp is an open source implementation of dssp

Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac.

Program for performing molecular dynamics simulations.

Publication-quality molecular visualization package

Display molecular 3D structures, such as proteins, in both schematic and detailed representations.

Autotooled, updated version of a powerful, fast semi-empirical package

The Massively Parallel Quantum Chemistry Program

MUltiple STructural AligNment AlGorithm.

A powerful and highly parallelized molecular dynamics code

interconverts file formats used in molecular modeling

Perl bindings for OpenBabel

openbabel-python

Python bindings for OpenBabel (including Pybel)

Modified molscript that uses POV-Ray, does thermal ellipsoids, and more

Prepares molecular kinemages (input files for Mage & KiNG) from PDB-format coordinate files

Evaluates atomic packing within or between molecules

Checks the stereochemical quality of a protein structure

A Python-extensible molecular graphics system.

pymol-plugins-psico

Free program that displays molecular structure.

a set of tools for generating high quality raster images of proteins or other molecules

Maximum likelihood superpositioning and analysis of macromolecular structures

TINKER is a molecular modeling package that includes force fields for handing large molecules and large systems, such as AMBER and CHARMM. A Java based visualization front end is included.

Visual Molecular Dynamics

Votca coarse-graining engine

Chemical 3D graphics program with GAMESS input builder

X-ray Detector Software for processing single-crystal monochromatic diffraction data.