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.

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

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

freeon

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

ligplot+

mage

marvin

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

nmrview

numbat

openbabel

interconverts file formats used in molecular modeling

pales-bin

panav

ParmEd

pdbcat

pdbcns

pdbmat

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-psico

raster3d

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

relion

rosetta-tools

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

vmd

Visual Molecular Dynamics

votca

votca-csg

Votca coarse-graining engine

votca-csgapps

votca-xtp

wxmacmolplt

Chemical 3D graphics program with GAMESS input builder

xds-bin

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

xyza2pipe

aqua

ligplot+

pdbmat

autodock

mage

prekin

autodock_vina

marvin

probe

avogadro2

mdanalysis

procheck

bodr

mdtraj

propka

cara-bin

mics

psi

chemex

modeller

pymol

chemical-mime-data

molden

pymol-plugins-psico

chemtool

moldy

raster3d

chimera-bin

molequeue

relion

clashlist

molmol

rosetta-tools

cluster

molsketch

sage-jmol-bin

concoord

mopac7

ssp

ctffind

MotionCor2

suitename

dl_poly

mpqc

surf

drawxtl

msms-bin

theseus

dssp

mustang

threeV

easychem

namd

tinker

elem

nmrglue

tm-align

erkale

nmrpipe

vesta

freeon

nmrview

vmd

gamess

numbat

votca

gelemental

openbabel

votca-csg

gnome-chemistry-utils

pales-bin

votca-csgapps

gperiodic

panav

votca-xtp

gromacs

ParmEd

wxmacmolplt

GromacsWrapper

pdbcat

xds-bin

jligand

pdbcns

xyza2pipe

ksdssp