acpype

ambertools

apbs

Software for evaluating the electrostatic properties of nanoscale biomolecular systems

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

bkchem

A chemical drawing program

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.

eden

A crystallographic real-space electron-density refinement and optimization program

elem

periodic table of the elements

erkale

freeon

gabedit

GUI for computational chemistry packages

gamess

gelemental

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

ghemical

Chemical quantum mechanics and molecular mechanics

gmxapi

gnome-chemistry-utils

gperiodic

Periodic table application for Linux

gromacs

The ultimate molecular dynamics simulation package

GromacsWrapper

hollow

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

nmrdepaker

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

p3d

pales-bin

panav

ParmEd

pdb-tools

pdb2pqr

pdb2pqr is an automated pipeline for performing Poisson-Boltzmann electrostatics calculations

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

prodecomp

propka

psi

pymol

A Python-extensible molecular graphics system.

pymol-plugins-bni-tools

Gives Pymol additional functionalities and presets to the PyMOL GUI

pymol-plugins-caver

pymol-plugins-dssp

pymol-plugins-emovie

eMovie is a plug-in tool for the molecular visualization program PyMOL

pymol-plugins-ezviz

pymol-plugins-msms

pymol-plugins-promol

Fast and accurate regognition of active sites

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

relax

relion

rosetta

rosetta-tools

sage-jmol-bin

scicraft

shelx

Programs for crystal structure determination from single-crystal diffraction data

shiftx

shiftx2

smmp

sparky

Graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers

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

viewmol

Open-source graphical front end for computational chemistry programs

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-cadd

pdb-tools

ambertools

mgltools-cmolkit

pdb2pqr

apbs

mgltools-dejavu

pdbcat

aqua

mgltools-geomutils

pdbcns

autodock

mgltools-gle

pdbmat

autodock_vina

mgltools-mglutil

pesto

avogadro

mgltools-molkit

polygon

avogadro2

mgltools-networkeditor

povscript+

bkchem

mgltools-opengltk

prekin

bodr

mgltools-pmv

probe

burrow-owl

mgltools-pyautodock

procheck

camshift

mgltools-pybabel

prodecomp

cara-bin

mgltools-pyglf

propka

chemex

mgltools-qslimlib

psi

chemical-mime-data

mgltools-scenario2

pymol

chemtool

mgltools-sff

pymol-plugins-bni-tools

chimera-bin

mgltools-support

pymol-plugins-caver

chooch

mgltools-symserv

pymol-plugins-dssp

clashlist

mgltools-utpackages

pymol-plugins-emovie

cluster

mgltools-viewer-framework

pymol-plugins-ezviz

concoord

mgltools-vision

pymol-plugins-msms

coot

mgltools-visionlib

pymol-plugins-promol

cpmgfit

mgltools-volume

pymol-plugins-psico

cs-rosetta

mgltools-webservices

pyquante

ctffind

mics

rasmol

curvefit

mm-align

raster3d

dl_poly

modelfree

relax

drawxtl

modeller

relion

dssp

module2

rosetta

dssp2pdb

molden

rosetta-tools

easychem

moldy

sage-jmol-bin

eden

molequeue

scicraft

elem

molmol

shelx

erkale

molscript

shiftx

freeon

molsketch

shiftx2

gabedit

mopac7

smmp

gamess

MotionCor2

sparky

gelemental

mpqc

ssp

ghemical

msms-bin

suitename

gmxapi

mtz2hkl

surf

gnome-chemistry-utils

mtz2sca

talosn

gperiodic

mustang

theseus

gromacs

namd

threeV

GromacsWrapper

nMOLDYN

tinker

hollow

nmrdepaker

tm-align

hydronmr

nmrglue

trajng

jligand

nmrpipe

unio

ksdssp

nmrview

usf-tools

ligplot+

numbat

viewmol

mage

nwchem

vmd

mars

openbabel

votca-csg

marvin

openbabel-java

votca-csgapps

mdanalysis

openbabel-perl

votca-ctp

mddnmr

openbabel-python

votca-xtp

mdsctk

ortep3

wxmacmolplt

mdtraj

p3d

xds-bin

mgltools

pales-bin

xplor-nih

mgltools-autodocktools

panav

xyza2pipe

mgltools-bhtree

ParmEd