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.

browndye

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

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

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

ksdssp

ksdssp is an open source implementation of dssp

mdanalysis

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

MotionCor2

mpqc

The Massively Parallel Quantum Chemistry Program

msms-bin

mustang

MUltiple STructural AligNment AlGorithm.

nmrpipe

openbabel

interconverts file formats used in molecular modeling

ovito

pales-bin

panav

ParmEd

pdbcat

pdbcns

pdbmat

probe

Evaluates atomic packing within or between molecules

propka

psi

pymol

A Python-extensible molecular graphics system.

raster3d

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

relion

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

vesta-bin

vmd

Visual Molecular Dynamics

votca

wxmacmolplt

Chemical 3D graphics program with GAMESS input builder

xcrysden

xds-bin

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

autodock

gperiodic

pdbcns

autodock_vina

gromacs

pdbmat

avogadro2

GromacsWrapper

probe

bodr

ksdssp

propka

browndye

mdanalysis

psi

cara-bin

mics

pymol

chemex

modeller

raster3d

chemical-mime-data

molden

relion

chemtool

moldy

sage-jmol-bin

chimera

molequeue

ssp

clashlist

molmol

suitename

cluster

molsketch

surf

concoord

MotionCor2

theseus

ctffind

mpqc

threeV

dl_poly

msms-bin

tinker

drawxtl

mustang

tm-align

dssp

nmrpipe

vesta

easychem

openbabel

vesta-bin

elem

ovito

vmd

erkale

pales-bin

votca

gamess

panav

wxmacmolplt

gelemental

ParmEd

xcrysden

gnome-chemistry-utils

pdbcat

xds-bin