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

mdtraj

mics

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

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

pdbmat

autodock_vina

gromacs

probe

avogadro2

GromacsWrapper

propka

bodr

ksdssp

psi

browndye

mdanalysis

pymol

cara-bin

mdtraj

raster3d

chemex

mics

relion

chemical-mime-data

moldy

sage-jmol-bin

chemtool

molequeue

ssp

chimera

molmol

suitename

clashlist

molsketch

surf

cluster

MotionCor2

theseus

concoord

mpqc

threeV

ctffind

msms-bin

tinker

dl_poly

mustang

tm-align

drawxtl

nmrpipe

vesta

dssp

openbabel

vesta-bin

easychem

pales-bin

vmd

elem

panav

votca

erkale

ParmEd

wxmacmolplt

gamess

pdbcat

xcrysden

gelemental

pdbcns

xds-bin

gnome-chemistry-utils