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

modeller

molden

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

moldy

Program for performing molecular dynamics simulations.

molequeue

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

GromacsWrapper

pdbmat

autodock_vina

ksdssp

probe

avogadro2

mdanalysis

propka

bodr

modeller

psi

cara-bin

molden

pymol

chemex

moldy

raster3d

chemical-mime-data

molequeue

suitename

chemtool

molmol

surf

clashlist

molsketch

theseus

cluster

mpqc

threeV

dssp

msms-bin

tinker

easychem

mustang

tm-align

elem

openbabel

vmd

gelemental

ParmEd

votca

gnome-chemistry-utils

pdbcat

wxmacmolplt

gperiodic

pdbcns

xds-bin

gromacs