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.

browndye

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

chimera

clashlist

cluster

concoord

ctffind

dl_poly

drawxtl

dssp

The protein secondary structure standard

easychem

Chemical structure drawing program - focused on presentation.

elem

periodic table of the elements

erkale

gamess

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

jligand

ksdssp

ksdssp is an open source implementation of dssp

mdanalysis

mdtraj

mics

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

mopac7

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

MotionCor2

mpqc

The Massively Parallel Quantum Chemistry Program

msms-bin

mustang

MUltiple STructural AligNment AlGorithm.

namd

A powerful and highly parallelized molecular dynamics code

nmrglue

nmrpipe

openbabel

interconverts file formats used in molecular modeling

ovito

pales-bin

panav

ParmEd

pdbcat

pdbcns

pdbmat

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.

raster3d

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

relion

sage-jmol-bin

ssp

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

vesta

vesta-bin

vmd

Visual Molecular Dynamics

votca

wxmacmolplt

Chemical 3D graphics program with GAMESS input builder

xcrysden

xds-bin

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

xyza2pipe

aqua

GromacsWrapper

pdbcns

autodock

jligand

pdbmat

autodock_vina

ksdssp

probe

avogadro2

mdanalysis

procheck

bodr

mdtraj

propka

browndye

mics

psi

cara-bin

modeller

pymol

chemex

molden

raster3d

chemical-mime-data

moldy

relion

chemtool

molequeue

sage-jmol-bin

chimera

molmol

ssp

clashlist

molsketch

suitename

cluster

mopac7

surf

concoord

MotionCor2

theseus

ctffind

mpqc

threeV

dl_poly

msms-bin

tinker

drawxtl

mustang

tm-align

dssp

namd

vesta

easychem

nmrglue

vesta-bin

elem

nmrpipe

vmd

erkale

openbabel

votca

gamess

ovito

wxmacmolplt

gelemental

pales-bin

xcrysden

gnome-chemistry-utils

panav

xds-bin

gperiodic

ParmEd

xyza2pipe

gromacs

pdbcat