acpype

ambertools

apbs

Software for evaluating the electrostatic properties of nanoscale biomolecular systems

aqua

aria

Software for automated NOE assignment and NMR structure calculation.

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

azara

A suite of programmes to process and view NMR data

ball

bkchem

A chemical drawing program

bodr

The Blue Obelisk Data Repository listing element and isotope properties.

burrow-owl

Visualize multidimensional nuclear magnetic resonance (NMR) spectra

camshift

cara-bin

An application for the analysis of NMR spectra and Computer Aided Resonance Assignment

ccpn

The Collaborative Computing Project for NMR

chemBuild

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

cns

Crystallography and NMR System

cnsface

concoord

coot

Crystallographic Object-Oriented Toolkit for model building, completion and validation

cp2k

cpmgfit

cs-rosetta

curvefit

cyana

Combined assignment and dynamics algorithm for NMR applications

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

A powerful quantum chemistry package

gamessq

Simple job manager for GAMESS-US

gelemental

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

ghemical

Chemical quantum mechanics and molecular mechanics

gnome-chemistry-utils

gperiodic

Periodic table application for Linux

gromacs

The ultimate molecular dynamics simulation package

GromacsWrapper

gsim

Programm for visualisation and processing of experimental and simulated NMR spectra

gtk-gamess

GTK-GAMESS is a graphical frontend for GAMESS

hollow

hoomd

hydronmr

icm

MolSoft LCC ICM Pro

jana2000

jligand

jmol

Jmol is a java molecular viever for 3-D chemical structures.

jmol-applet

jspecview

ksdssp

ksdssp is an open source implementation of dssp

ligplot+

mage

Mage is a 3D vector display program which shows 'kinemage' graphics

mars

massxpert

A software suite to predict/analyze mass spectrometric data on (bio)polymers.

mdanalysis

mddnmr

mdsctk

mead

Macroscopic Electrostatics with Atomic Detail

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

mongochem

mopac7

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

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

NMRdyn

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)

openbabel-ruby

ortep3

Thermal ellipsoid plot program for crystal structure illustrations

p3d

pales-bin

panav

parassign

pdb-tools

pdb2pqr

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

pdbcat

pdbcns

pdbmat

pesto

phenix-bin

platon

Versatile, SHELX-97 compatible, multipurpose crystallographic tool

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

prody

propka

psi

PyMca

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-dynamics

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

redcat

reduce

Adds hydrogens to a Protein Data Bank (PDB) molecule structure file

relax

rosetta

rosetta-tools

sage-jmol-bin

scicraft

shelx

Programs for crystal structure determination from single-crystal diffraction data

shiftx

shiftx2

simpson

smmp

sparky

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

specView

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-xtp

wxmacmolplt

Chemical 3D graphics program with GAMESS input builder

xcrysden

xds-bin

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

xdsgui

xdsstat-bin

prints various statistics (that are not available from XDS itself)

xplor-nih

xyza2pipe

acpype

mddnmr

pdb2pqr

ambertools

mdsctk

pdbcat

apbs

mead

pdbcns

aqua

mgltools

pdbmat

aria

mgltools-autodocktools

pesto

autodock

mgltools-bhtree

phenix-bin

autodock_vina

mgltools-cadd

platon

avogadro

mgltools-cmolkit

polygon

avogadro2

mgltools-dejavu

povscript+

azara

mgltools-geomutils

prekin

ball

mgltools-gle

probe

bkchem

mgltools-mglutil

procheck

bodr

mgltools-molkit

prodecomp

burrow-owl

mgltools-networkeditor

prody

camshift

mgltools-opengltk

propka

cara-bin

mgltools-pmv

psi

ccpn

mgltools-pyautodock

PyMca

chemBuild

mgltools-pybabel

pymol

chemical-mime-data

mgltools-pyglf

pymol-plugins-bni-tools

chemtool

mgltools-qslimlib

pymol-plugins-caver

chimera-bin

mgltools-scenario2

pymol-plugins-dssp

chooch

mgltools-sff

pymol-plugins-dynamics

clashlist

mgltools-support

pymol-plugins-emovie

cluster

mgltools-symserv

pymol-plugins-ezviz

cns

mgltools-utpackages

pymol-plugins-msms

cnsface

mgltools-viewer-framework

pymol-plugins-promol

concoord

mgltools-vision

pymol-plugins-psico

coot

mgltools-visionlib

pyquante

cp2k

mgltools-volume

rasmol

cpmgfit

mgltools-webservices

raster3d

cs-rosetta

mics

redcat

curvefit

mm-align

reduce

cyana

modelfree

relax

dl_poly

modeller

rosetta

drawxtl

module2

rosetta-tools

dssp

molden

sage-jmol-bin

dssp2pdb

moldy

scicraft

easychem

molequeue

shelx

eden

molmol

shiftx

elem

molscript

shiftx2

erkale

molsketch

simpson

freeon

mongochem

smmp

gabedit

mopac7

sparky

gamess

mpqc

specView

gamessq

msms-bin

ssp

gelemental

mtz2hkl

suitename

ghemical

mtz2sca

surf

gnome-chemistry-utils

mustang

talosn

gperiodic

namd

theseus

gromacs

nMOLDYN

threeV

GromacsWrapper

NMRdyn

tinker

gsim

nmrglue

tm-align

gtk-gamess

nmrpipe

trajng

hollow

nmrview

unio

hoomd

numbat

usf-tools

hydronmr

nwchem

viewmol

icm

openbabel

vmd

jana2000

openbabel-java

votca-csg

jligand

openbabel-perl

votca-csgapps

jmol

openbabel-python

votca-xtp

jmol-applet

openbabel-ruby

wxmacmolplt

jspecview

ortep3

xcrysden

ksdssp

p3d

xds-bin

ligplot+

pales-bin

xdsgui

mage

panav

xdsstat-bin

mars

parassign

xplor-nih

massxpert

pdb-tools

xyza2pipe

mdanalysis