acpype

ambertools

aqua

autodock

A suite of automated docking tools

autodock_vina

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

avogadro

Advanced molecular editor that uses Qt4 and OpenGL

avogadro2

bodr

The Blue Obelisk Data Repository listing element and isotope properties.

burrow-owl

camshift

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-bin

chooch

clashlist

cluster

concoord

coot

cpmgfit

cs-rosetta

ctffind

curvefit

dl_poly

drawxtl

dssp

The protein secondary structure standard

dssp2pdb

easychem

Chemical structure drawing program - focused on presentation.

elem

periodic table of the elements

erkale

freeon

gamess

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

hydronmr

jligand

ksdssp

ksdssp is an open source implementation of dssp

ligplot+

mage

mars

marvin

mdanalysis

mddnmr

mdsctk

mdtraj

mgltools

mgltools-autodocktools

mgltools-bhtree

mgltools-cadd

mgltools-cmolkit

mgltools-dejavu

mgltools-geomutils

mgltools-gle

mgltools-mglutil

mgltools-molkit

mgltools-networkeditor

mgltools-opengltk

mgltools-pmv

mgltools-pyautodock

mgltools-pybabel

mgltools-pyglf

mgltools-qslimlib

mgltools-scenario2

mgltools-sff

mgltools-support

mgltools-symserv

mgltools-utpackages

mgltools-viewer-framework

mgltools-vision

mgltools-visionlib

mgltools-volume

mgltools-webservices

mics

mm-align

modelfree

modeller

module2

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

MotionCor2

mpqc

The Massively Parallel Quantum Chemistry Program

msms-bin

mtz2hkl

mtz2sca

mustang

MUltiple STructural AligNment AlGorithm.

namd

A powerful and highly parallelized molecular dynamics code

nMOLDYN

nmrglue

nmrpipe

nmrview

numbat

nwchem

openbabel

interconverts file formats used in molecular modeling

openbabel-java

openbabel-perl

Perl bindings for OpenBabel

openbabel-python

Python bindings for OpenBabel (including Pybel)

ortep3

Thermal ellipsoid plot program for crystal structure illustrations

pales-bin

panav

ParmEd

pdbcat

pdbcns

pdbmat

pesto

polygon

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.

pymol-plugins-ezviz

pymol-plugins-psico

pyquante

rasmol

Free program that displays molecular structure.

raster3d

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

relion

rosetta

rosetta-tools

sage-jmol-bin

scicraft

shiftx

shiftx2

smmp

ssp

suitename

surf

talosn

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

trajng

unio

usf-tools

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.

xplor-nih

xyza2pipe

acpype

mgltools-bhtree

openbabel-perl

ambertools

mgltools-cadd

openbabel-python

aqua

mgltools-cmolkit

ortep3

autodock

mgltools-dejavu

pales-bin

autodock_vina

mgltools-geomutils

panav

avogadro

mgltools-gle

ParmEd

avogadro2

mgltools-mglutil

pdbcat

bodr

mgltools-molkit

pdbcns

burrow-owl

mgltools-networkeditor

pdbmat

camshift

mgltools-opengltk

pesto

cara-bin

mgltools-pmv

polygon

chemex

mgltools-pyautodock

povscript+

chemical-mime-data

mgltools-pybabel

prekin

chemtool

mgltools-pyglf

probe

chimera-bin

mgltools-qslimlib

procheck

chooch

mgltools-scenario2

propka

clashlist

mgltools-sff

psi

cluster

mgltools-support

pymol

concoord

mgltools-symserv

pymol-plugins-ezviz

coot

mgltools-utpackages

pymol-plugins-psico

cpmgfit

mgltools-viewer-framework

pyquante

cs-rosetta

mgltools-vision

rasmol

ctffind

mgltools-visionlib

raster3d

curvefit

mgltools-volume

relion

dl_poly

mgltools-webservices

rosetta

drawxtl

mics

rosetta-tools

dssp

mm-align

sage-jmol-bin

dssp2pdb

modelfree

scicraft

easychem

modeller

shiftx

elem

module2

shiftx2

erkale

molden

smmp

freeon

moldy

ssp

gamess

molequeue

suitename

gelemental

molmol

surf

gmxapi

molscript

talosn

gnome-chemistry-utils

molsketch

theseus

gperiodic

mopac7

threeV

gromacs

MotionCor2

tinker

GromacsWrapper

mpqc

tm-align

hydronmr

msms-bin

trajng

jligand

mtz2hkl

unio

ksdssp

mtz2sca

usf-tools

ligplot+

mustang

vmd

mage

namd

votca-csg

mars

nMOLDYN

votca-csgapps

marvin

nmrglue

votca-ctp

mdanalysis

nmrpipe

votca-xtp

mddnmr

nmrview

wxmacmolplt

mdsctk

numbat

xds-bin

mdtraj

nwchem

xplor-nih

mgltools

openbabel

xyza2pipe

mgltools-autodocktools

openbabel-java