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

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

cns

Crystallography and NMR System

cnsface

concoord

coot

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

cpmgfit

cs-rosetta

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

eperiodique

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

gnome-chemistry-utils

gperiodic

Periodic table application for Linux

gromacs

The ultimate molecular dynamics simulation package

GromacsWrapper

hollow

hydronmr

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

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

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

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

ParmEd

pdb-tools

pdb2pqr

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

pdbcat

pdbcns

pdbmat

pesto

phenix-bin

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

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

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

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.

xdsstat-bin

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

xplor-nih

xyza2pipe

acpype

mgltools

ParmEd

ambertools

mgltools-autodocktools

pdb-tools

apbs

mgltools-bhtree

pdb2pqr

aqua

mgltools-cadd

pdbcat

aria

mgltools-cmolkit

pdbcns

autodock

mgltools-dejavu

pdbmat

autodock_vina

mgltools-geomutils

pesto

avogadro

mgltools-gle

phenix-bin

avogadro2

mgltools-mglutil

polygon

azara

mgltools-molkit

povscript+

ball

mgltools-networkeditor

prekin

bkchem

mgltools-opengltk

probe

bodr

mgltools-pmv

procheck

burrow-owl

mgltools-pyautodock

prodecomp

camshift

mgltools-pybabel

prody

cara-bin

mgltools-pyglf

propka

ccpn

mgltools-qslimlib

psi

chemex

mgltools-scenario2

pymol

chemical-mime-data

mgltools-sff

pymol-plugins-bni-tools

chemtool

mgltools-support

pymol-plugins-caver

chimera-bin

mgltools-symserv

pymol-plugins-dssp

chooch

mgltools-utpackages

pymol-plugins-dynamics

clashlist

mgltools-viewer-framework

pymol-plugins-emovie

cluster

mgltools-vision

pymol-plugins-ezviz

cns

mgltools-visionlib

pymol-plugins-msms

cnsface

mgltools-volume

pymol-plugins-promol

concoord

mgltools-webservices

pymol-plugins-psico

coot

mics

pyquante

cpmgfit

mm-align

rasmol

cs-rosetta

modelfree

raster3d

curvefit

modeller

reduce

dl_poly

module2

relax

drawxtl

molden

rosetta

dssp

moldy

rosetta-tools

dssp2pdb

molequeue

sage-jmol-bin

easychem

molmol

scicraft

eden

molscript

shelx

elem

molsketch

shiftx

eperiodique

mopac7

shiftx2

erkale

mpqc

smmp

freeon

msms-bin

sparky

gabedit

mtz2hkl

ssp

gamess

mtz2sca

suitename

gelemental

mustang

surf

ghemical

namd

talosn

gnome-chemistry-utils

nMOLDYN

theseus

gperiodic

nmrdepaker

threeV

gromacs

NMRdyn

tinker

GromacsWrapper

nmrglue

tm-align

hollow

nmrpipe

trajng

hydronmr

nmrview

unio

jligand

numbat

usf-tools

jmol

nwchem

viewmol

jmol-applet

openbabel

vmd

jspecview

openbabel-java

votca-csg

ksdssp

openbabel-perl

votca-csgapps

ligplot+

openbabel-python

votca-ctp

mage

openbabel-ruby

votca-xtp

mars

ortep3

wxmacmolplt

marvin

p3d

xds-bin

mdanalysis

pales-bin

xdsstat-bin

mddnmr

panav

xplor-nih

mdsctk

parassign

xyza2pipe

mdtraj