aqua

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.

gmxapi

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

mars

mdanalysis

mdtraj

mm-align

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

molscript

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

molsketch

mopac7

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

mpqc

The Massively Parallel Quantum Chemistry Program

msms-bin

mustang

MUltiple STructural AligNment AlGorithm.

namd

A powerful and highly parallelized molecular dynamics code

nmrglue

numbat

openbabel

interconverts file formats used in molecular modeling

openbabel-perl

Perl bindings for OpenBabel

pdbcat

pdbcns

pdbmat

povscript+

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

prekin

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

probe

Evaluates atomic packing within or between molecules

procheck

Checks the stereochemical quality of a protein structure

propka

psi

pymol

A Python-extensible molecular graphics system.

rasmol

Free program that displays molecular structure.

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-csg

Votca coarse-graining engine

votca-csgapps

votca-ctp

votca-xtp

wxmacmolplt

Chemical 3D graphics program with GAMESS input builder

xds-bin

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

xyza2pipe

aqua

mdtraj

prekin

autodock

mm-align

probe

autodock_vina

modeller

procheck

avogadro2

molden

propka

bodr

moldy

psi

cara-bin

molequeue

pymol

chemex

molmol

rasmol

chemical-mime-data

molscript

raster3d

chemtool

molsketch

suitename

clashlist

mopac7

surf

cluster

mpqc

theseus

dssp

msms-bin

threeV

easychem

mustang

tinker

elem

namd

tm-align

gelemental

nmrglue

vmd

gmxapi

numbat

votca-csg

gnome-chemistry-utils

openbabel

votca-csgapps

gperiodic

openbabel-perl

votca-ctp

gromacs

pdbcat

votca-xtp

GromacsWrapper

pdbcns

wxmacmolplt

ksdssp

pdbmat

xds-bin

mars

povscript+

xyza2pipe

mdanalysis