acpype

almost

all atom molecular simulation toolkit

ambertools

apbs

Software for evaluating the electrostatic properties of nanoscale biomolecular systems

aqua

aria

Software for automated NOE assignment and NMR structure calculation.

arp-warp-bin

ARP/wARP is a software for improvement and interpretation of crystallographic electron density maps

autodock

A suite of automated docking tools

autodock-vina

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

babel

balbes

Automated molecular replacement (MR) pipeline

ball

bist

Bist, the chemical drawing tool

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

cclib

Library for parsing and interpreting the results of computational chemistry packages

ccp1gui

A free, extensible Graphical User Interface (GUI) for community chemistry programs

ccp4

Protein X-ray crystallography toolkit -- meta package

ccp4-apps

Protein X-ray crystallography toolkit

ccp4i

Protein X-ray crystallography toolkit -- graphical interface

ccp4mg

ccpn

The Collaborative Computing Project for NMR

chemBuild

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

a program that will automatically determine values of the anomalous scattering factors

clashlist

cluster

cns

Crystallography and NMR System

cnsface

concoord

coot

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

cs-rosetta

curvefit

cyana

Combined assignment and dynamics algorithm for NMR applications

direx

Low Resolution Structure Refinement

dl_poly

drawxtl

This software can be used to produce crystal structure drawings from structural data

dssp

The protein secondary structure standard

dssp2pdb

convert dssp to pdb

dsv

Discovery Studio Visualizer

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

epmr

Crystallographic molecular replacement by evolutionary search

freeon

gabedit

GUI for computational chemistry packages

gamess

A powerful quantum chemistry package

gamessq

Simple job manager for GAMESS-US

gelemental

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

ghemical

Chemical quantum mechanics and molecular mechanics

gnome-chemistry-utils

gopenmol

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

gperiodic

Periodic table application for Linux

gridzilla

A GUI-based application designed to create grid screens for protein crystal optimization

gromacs

The ultimate molecular dynamics simulation package

GromacsWrapper

gsim

Programm for visualisation and processing of experimental and simulated NMR spectra

gtk-gamess

GTK-GAMESS is a graphical frontend for GAMESS

hollow

hoomd

hydronmr

icm

MolSoft LCC ICM Pro

icm-browser

MolSoft LCC ICM Browser

imosflm

A new GUI for the Mosflm crystallographic data processing tool

jana2000

the crystallographic computing system

jligand

a Java interface which allows links descriptions to be created

jmol

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

jmol-applet

kincontour

Read value/coordinate lists to produce contour maps in kinemage format

king

An interactive system for 3D graphics (primarily molecular)

ksdssp

ksdssp is an open source implementation of dssp

ligplot+

mage

Mage is a 3D vector display program which shows 'kinemage' graphics

makecif

mars

massxpert

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

mdanalysis

mddnmr

Program for processing of non-uniformly sampled (NUS) multidimensional NMR spectra

mdsctk

mead

Macroscopic Electrostatics with Atomic Detail

mgltools

Software to visualization and analysis of molecular structures

mgltools-autodocktools

mgltools plugin -- autodocktools

mgltools-bhtree

mgltools plugin -- bhtree

mgltools-cadd

mgltools-cmolkit

mgltools plugin -- cMolKit

mgltools-dejavu

mgltools plugin -- dejavu

mgltools-geomutils

mgltools plugin -- geomutils

mgltools-gle

mgltools plugin -- gle

mgltools-mglutil

mgltools plugin -- mglutil

mgltools-molkit

mgltools plugin -- MolKit

mgltools-networkeditor

mgltools plugin -- NetworkEditor

mgltools-opengltk

mgltools plugin -- opengltk

mgltools-pmv

mgltools plugin -- pmv

mgltools-pyautodock

mgltools plugin -- PyAutoDock

mgltools-pybabel

mgltools plugin -- PyBabel

mgltools-pyglf

mgltools plugin -- pyglf

mgltools-qslimlib

mgltools plugin -- qslimlib

mgltools-scenario2

mgltools-sff

mgltools plugin -- sff

mgltools-support

mgltools plugin -- support

mgltools-symserv

mgltools plugin -- symserv

mgltools-utpackages

mgltools plugin -- UTpackages

mgltools-viewer-framework

mgltools plugin -- Viewer-Framework

mgltools-vision

mgltools plugin -- vision

mgltools-visionlib

mgltools plugin -- visionlib

mgltools-volume

mgltools plugin -- volume

mgltools-webservices

mgltools plugin -- webservices

mics

mm-align

modelfree

modeller

MODELLER is used for homology or comparative modeling of protein three-dimensional structures

molden

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

moldy

Program for performing molecular dynamics simulations.

mole-bin

A toolkit for automated location channels, tunnels and pores in molecular structures

molequeue

molmol

Publication-quality molecular visualization package

molrep

molecular replacement program

molscript

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

molsketch

mongochem

mopac2007-bin

Powerful, fast semi-empirical package

mopac7

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

mopro-bin

Crystallographic structure or charge density refinement

mosflm

A program for integrating single crystal diffraction data from area detectors

mpqc

The Massively Parallel Quantum Chemistry Program

mrbump

An automated scheme for Molecular Replacement

msms-bin

mtz2hkl

Intended to facilitate the transition from refmac5 refinement to shelxh or shelxl refinement

mtz2sca

Converts CCP4 mtz-files containing anomalous data to Scalepack format

mustang

MUltiple STructural AligNment AlGorithm.

namd

A powerful and highly parallelized molecular dynamics code

nMOLDYN

nmrglue

nmrpipe

Spectral visualisation, analysis and Fourier processing

nmrview

Visualisation and analysis of processed NMR data

numbat

nwchem

oasis

A direct-method program for SAD/SIR phasing

objcryst-fox

open3dqsar

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

Ruby bindings for OpenBabel

ortep3

Thermal ellipsoid plot program for crystal structure illustrations

p3d

panav

parassign

pdb-extract

Tools for extracting mmCIF data from structure determination applications

pdb-tools

pdb2pqr

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

pdbcat

pdbcns

pdbmat

pesto

phaser

Phasing macromolecular crystal structures with maximum likelihood methods

phenix-bin

pjnmr

platon

Versatile, SHELX-97 compatible, multipurpose crystallographic tool

pmb

Automated structure refinement tools for CNS

pointless

Scores crystallographic Laue and space groups

polygon

shows qualitatively if some models parameters are over- or under-refined

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

profit

Designed to be the ultimate protein least squares fitting program

psi

pyitc

PyMca

pymol

A Python-extensible molecular graphics system.

pymol-apbs-plugin

APBS plugin for pymol

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

assistance tool for the difficult to understand user interface of PyMOL

pymol-plugins-msms

pymol-plugins-promol

Fast and accurate regognition of active sites

pymol-plugins-psico

pymss

Multiple superposition of proteins, using a genetic algorithm for optimization

pyquante

pyrx

GUI for Virtual Screening with AutoDock

qutemol

High quality molecular visualization system that exploits GPU capabilites through OpenGL shaders

rasmol

Free program that displays molecular structure.

raster3d

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

rdkit

reduce

Adds hydrogens to a Protein Data Bank (PDB) molecule structure file

refmac

Macromolecular crystallographic refinement program

relax

rosetta

Prediction and design of protein structures, folding mechanisms, and protein-protein interactions

rosetta-tools

Additional scripts for rosetta

scala

scale together multiple observations of reflections

scicraft

sfcheck

Program for assessing the agreement between the atomic model and X-ray data or EM map

shakerr

shelx

Programs for crystal structure determination from single-crystal diffraction data

shiftx

With this form you can predict 1H, 13C and 15N chemical shifts for your favorite protein

shiftx2

simpson

smmp

Simple Molecular Mechanics for Proteins

solve-resolve-bin

Automated crystallographic structure solution for MIR, SAD, and MAD

sparky

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

specView

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.

tisean

tm-align

trajng

ucsf-tools

unio

usf-rave-bin

The tools package from USF for macromolecular crystallography

usf-tools

usf-voidoo-bin

The tools package from USF for macromolecular crystallography

vasco

viewmol

Open-source graphical front end for computational chemistry programs

vmd

Visual Molecular Dynamics

votca-csg

Votca coarse-graining engine

votca-csgapps

webmo

Web-based interface to computational chemistry packages

wxmacmolplt

Chemical 3D graphics program with GAMESS input builder

xcrysden

xds-bin

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

xdsgui

xdsi

xdsstat-bin

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

xia2

An automated data reduction system for crystallography

xyza2pipe

acpype

makecif

pesto

almost

mars

phaser

ambertools

massxpert

phenix-bin

apbs

mdanalysis

pjnmr

aqua

mddnmr

platon

aria

mdsctk

pmb

arp-warp-bin

mead

pointless

autodock

mgltools

polygon

autodock-vina

mgltools-autodocktools

povscript+

autodock_vina

mgltools-bhtree

prekin

avogadro

mgltools-cadd

probe

avogadro2

mgltools-cmolkit

procheck

azara

mgltools-dejavu

prodecomp

babel

mgltools-geomutils

profit

balbes

mgltools-gle

psi

ball

mgltools-mglutil

pyitc

bist

mgltools-molkit

PyMca

bkchem

mgltools-networkeditor

pymol

bodr

mgltools-opengltk

pymol-apbs-plugin

burrow-owl

mgltools-pmv

pymol-plugins-bni-tools

camshift

mgltools-pyautodock

pymol-plugins-caver

cara-bin

mgltools-pybabel

pymol-plugins-dssp

cclib

mgltools-pyglf

pymol-plugins-dynamics

ccp1gui

mgltools-qslimlib

pymol-plugins-emovie

ccp4

mgltools-scenario2

pymol-plugins-ezviz

ccp4-apps

mgltools-sff

pymol-plugins-msms

ccp4i

mgltools-support

pymol-plugins-promol

ccp4mg

mgltools-symserv

pymol-plugins-psico

ccpn

mgltools-utpackages

pymss

chemBuild

mgltools-viewer-framework

pyquante

chemical-mime-data

mgltools-vision

pyrx

chemtool

mgltools-visionlib

qutemol

chimera-bin

mgltools-volume

rasmol

chooch

mgltools-webservices

raster3d

clashlist

mics

rdkit

cluster

mm-align

reduce

cns

modelfree

refmac

cnsface

modeller

relax

concoord

molden

rosetta

coot

moldy

rosetta-tools

cs-rosetta

mole-bin

scala

curvefit

molequeue

scicraft

cyana

molmol

sfcheck

direx

molrep

shakerr

dl_poly

molscript

shelx

drawxtl

molsketch

shiftx

dssp

mongochem

shiftx2

dssp2pdb

mopac2007-bin

simpson

dsv

mopac7

smmp

easychem

mopro-bin

solve-resolve-bin

eden

mosflm

sparky

elem

mpqc

specView

epmr

mrbump

ssp

freeon

msms-bin

suitename

gabedit

mtz2hkl

surf

gamess

mtz2sca

talosn

gamessq

mustang

theseus

gelemental

namd

threeV

ghemical

nMOLDYN

tinker

gnome-chemistry-utils

nmrglue

tisean

gopenmol

nmrpipe

tm-align

gperiodic

nmrview

trajng

gridzilla

numbat

ucsf-tools

gromacs

nwchem

unio

GromacsWrapper

oasis

usf-rave-bin

gsim

objcryst-fox

usf-tools

gtk-gamess

open3dqsar

usf-voidoo-bin

hollow

openbabel

vasco

hoomd

openbabel-java

viewmol

hydronmr

openbabel-perl

vmd

icm

openbabel-python

votca-csg

icm-browser

openbabel-ruby

votca-csgapps

imosflm

ortep3

webmo

jana2000

p3d

wxmacmolplt

jligand

panav

xcrysden

jmol

parassign

xds-bin

jmol-applet

pdb-extract

xdsgui

kincontour

pdb-tools

xdsi

king

pdb2pqr

xdsstat-bin

ksdssp

pdbcat

xia2

ligplot+

pdbcns

xyza2pipe

mage

pdbmat