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

erkale

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

jspecview

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

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

ligplot+

pdbcns

almost

mage

pdbmat

ambertools

makecif

pesto

apbs

mars

phaser

aqua

massxpert

phenix-bin

aria

mdanalysis

pjnmr

arp-warp-bin

mddnmr

platon

autodock

mdsctk

pmb

autodock-vina

mead

pointless

autodock_vina

mgltools

polygon

avogadro

mgltools-autodocktools

povscript+

avogadro2

mgltools-bhtree

prekin

azara

mgltools-cadd

probe

babel

mgltools-cmolkit

procheck

balbes

mgltools-dejavu

prodecomp

ball

mgltools-geomutils

profit

bist

mgltools-gle

psi

bkchem

mgltools-mglutil

pyitc

bodr

mgltools-molkit

PyMca

burrow-owl

mgltools-networkeditor

pymol

camshift

mgltools-opengltk

pymol-apbs-plugin

cara-bin

mgltools-pmv

pymol-plugins-bni-tools

cclib

mgltools-pyautodock

pymol-plugins-caver

ccp1gui

mgltools-pybabel

pymol-plugins-dssp

ccp4

mgltools-pyglf

pymol-plugins-dynamics

ccp4-apps

mgltools-qslimlib

pymol-plugins-emovie

ccp4i

mgltools-scenario2

pymol-plugins-ezviz

ccp4mg

mgltools-sff

pymol-plugins-msms

ccpn

mgltools-support

pymol-plugins-promol

chemBuild

mgltools-symserv

pymol-plugins-psico

chemical-mime-data

mgltools-utpackages

pymss

chemtool

mgltools-viewer-framework

pyquante

chimera-bin

mgltools-vision

pyrx

chooch

mgltools-visionlib

qutemol

clashlist

mgltools-volume

rasmol

cluster

mgltools-webservices

raster3d

cns

mics

rdkit

cnsface

mm-align

reduce

concoord

modelfree

refmac

coot

modeller

relax

cs-rosetta

molden

rosetta

curvefit

moldy

rosetta-tools

cyana

mole-bin

scala

direx

molequeue

scicraft

dl_poly

molmol

sfcheck

drawxtl

molrep

shakerr

dssp

molscript

shelx

dssp2pdb

molsketch

shiftx

dsv

mongochem

shiftx2

easychem

mopac2007-bin

simpson

eden

mopac7

smmp

elem

mopro-bin

solve-resolve-bin

epmr

mosflm

sparky

erkale

mpqc

specView

freeon

mrbump

ssp

gabedit

msms-bin

suitename

gamess

mtz2hkl

surf

gamessq

mtz2sca

talosn

gelemental

mustang

theseus

ghemical

namd

threeV

gnome-chemistry-utils

nMOLDYN

tinker

gopenmol

nmrglue

tisean

gperiodic

nmrpipe

tm-align

gridzilla

nmrview

trajng

gromacs

numbat

unio

GromacsWrapper

nwchem

usf-rave-bin

gsim

oasis

usf-tools

gtk-gamess

objcryst-fox

usf-voidoo-bin

hollow

open3dqsar

vasco

hoomd

openbabel

viewmol

hydronmr

openbabel-java

vmd

icm

openbabel-perl

votca-csg

icm-browser

openbabel-python

votca-csgapps

imosflm

openbabel-ruby

webmo

jana2000

ortep3

wxmacmolplt

jligand

p3d

xcrysden

jmol

panav

xds-bin

jmol-applet

parassign

xdsgui

jspecview

pdb-extract

xdsi

kincontour

pdb-tools

xdsstat-bin

king

pdb2pqr

xia2

ksdssp

pdbcat

xyza2pipe