apbs

Software for evaluating the electrostatic properties of nanoscale biomolecular systems

autodock

A suite of automated docking tools

avogadro

Advanced molecular editor that uses Qt4 and OpenGL

babel

Babel is a program to interconvert file formats used in molecular modeling.

bodr

The Blue Obelisk Data Repository listing element and isotope properties.

burrow-owl

Visualize multidimensional nuclear magnetic resonance (NMR) spectra

caver

Rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures

ccp4

Protein X-ray crystallography toolkit

chemical-mime-data

A collection of data files to add support for chemical MIME types.

chemtool

program for drawing organic molecules

cns

Crystallography and NMR System

coot

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

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

gamess

A powerful quantum chemistry package

gchempaint

2D chemical structures editor for the Gnome-2 desktop

gchemutils

C++ classes and Gtk+-2 widgets related to chemistry

gelemental

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

ghemical

Chemical quantum mechanics and molecular mechanics

gopenmol

gOpenMol is a tool for the visualization and analysis of molecular structures

gperiodic

Periodic table application for Linux

gromacs

The ultimate molecular dynamics simulation package

gtk-gamess

GTK-GAMESS is a graphical frontend for GAMESS, a General Atomic and Molecular Electronic Structure System

jmol

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

kemistry

Kemistry--a set of chemistry related tools for KDE.

maid

Automates the fitting of protein X-ray crystallographic electron density maps

massxpert

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

maxit

An application for processing and curation of macromolecular structure data

mead

Macroscopic Electrostatics with Atomic Detail

molden

Display molecular density from GAMESS-UK, GAMESS-US, GAUSSIAN and Mopac/Ampac.

moldy

Program for performing molecular dynamics simulations.

molmol

Publication-quality molecular visualization package

molscript

Display molecular 3D structures, such as proteins, in both schematic and detailed representations.

mopac7

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

mpqc

The Massively Parallel Quantum Chemistry Program

mustang

MUltiple STructural AligNment AlGorithm.

namd

A powerful and highly parallelized molecular dynamics code

nmrpipe

Spectral visualisation, analysis and Fourier processing

nmrview

Visualisation and analysis of processed NMR data

openbabel

Open Babel interconverts file formats used in molecular modeling.

ortep3

Thermal ellipsoid plot program for crystal structure illustrations

pdb-extract

Tools for extracting mmCIF data from structure determination applications

pdb2pqr

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

platon

Versatile, SHELX-97 compatible, multipurpose crystallographic tool

povscript+

Modified molscript that uses POV-Ray, does thermal ellipsoids, and more

probe

Evaluates atomic packing within or between molecules

psi

Suite of ab initio quantum chemistry programs to compute various molecular properties

pymol

A Python-extensible molecular graphics system.

pynmr

An NMR Extension for PyMOL, written in Python

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

shelx

Programs for crystal structure determination from single-crystal diffraction data

sparky

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

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.

validation

Set of tools used by the Protein Data Base (PDB) for processing and checking structure data

viewmol

Open-source graphical front end for computational chemistry programs

vmd

Visual Molecular Dynamics

webmo

Web-based interface to computational chemistry packages

xdrawchem

Molecular structure drawing program

apbs

gperiodic

ortep3

autodock

gromacs

pdb-extract

avogadro

gtk-gamess

pdb2pqr

babel

jmol

platon

bodr

kemistry

povscript+

burrow-owl

maid

probe

caver

massxpert

psi

ccp4

maxit

pymol

chemical-mime-data

mead

pynmr

chemtool

molden

rasmol

cns

moldy

raster3d

coot

molmol

reduce

easychem

molscript

shelx

eden

mopac7

sparky

elem

mpqc

tinker

gamess

mustang

validation

gchempaint

namd

viewmol

gchemutils

nmrpipe

vmd

gelemental

nmrview

webmo

ghemical

openbabel

xdrawchem

gopenmol