autodock

A suite of automated docking tools

autodock_vina

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

avogadro2

bodr

The Blue Obelisk Data Repository listing element and isotope properties.

cara-bin

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

chemex

chemical-mime-data

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

chemtool

A GTK program for drawing organic molecules

clashlist

cluster

dssp

The protein secondary structure standard

easychem

Chemical structure drawing program - focused on presentation.

elem

periodic table of the elements

gelemental

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

gnome-chemistry-utils

gperiodic

Periodic table application for Linux

gromacs

The ultimate molecular dynamics simulation package

GromacsWrapper

ksdssp

ksdssp is an open source implementation of dssp

mdanalysis

mdtraj

moldy

Program for performing molecular dynamics simulations.

molmol

Publication-quality molecular visualization package

molsketch

mpqc

The Massively Parallel Quantum Chemistry Program

msms-bin

mustang

MUltiple STructural AligNment AlGorithm.

openbabel

interconverts file formats used in molecular modeling

ParmEd

pdbcat

pdbcns

pdbmat

probe

Evaluates atomic packing within or between molecules

propka

psi

pymol

A Python-extensible molecular graphics system.

raster3d

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

suitename

surf

theseus

Maximum likelihood superpositioning and analysis of macromolecular structures

threeV

tinker

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.

tm-align

vmd

Visual Molecular Dynamics

votca

wxmacmolplt

Chemical 3D graphics program with GAMESS input builder

xds-bin

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

autodock

gromacs

probe

autodock_vina

GromacsWrapper

propka

avogadro2

ksdssp

psi

bodr

mdanalysis

pymol

cara-bin

mdtraj

raster3d

chemex

moldy

suitename

chemical-mime-data

molmol

surf

chemtool

molsketch

theseus

clashlist

mpqc

threeV

cluster

msms-bin

tinker

dssp

mustang

tm-align

easychem

openbabel

vmd

elem

ParmEd

votca

gelemental

pdbcat

wxmacmolplt

gnome-chemistry-utils

pdbcns

xds-bin

gperiodic

pdbmat