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

atnos-candid

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

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

caver

Calculation of pathways from buried cavities to outside solvent in protein structures

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

espresso

opEn-Source Package for Research in Electronic Structure, Simulation, and Optimization

format-converter

freeon

gabedit

GUI for computational chemistry packages

gamess

A powerful quantum chemistry package

gamessq

Simple job manager for GAMESS-US

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

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

hkl2map-bin

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.

maxit

An application for processing and curation of macromolecular structure data

mdanalysis

mddnmr

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

mdsctk

mdtools

Classes for the analysis and modification of protein structure and dynamics data.

mead

Macroscopic Electrostatics with Atomic Detail

mestrenova-bin

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-scenario

mgltools plugin -- scenario

mgltools-scenario2

mgltools-sff

mgltools plugin -- sff

mgltools-stride

mgltools plugin -- stride

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

mmtk

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

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

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

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-cealign

The CE algorithm is a fast and accurate protein structure alignment algorithm.

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

pynmr

An NMR Extension for PyMOL, written in Python

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

rci

Predicts protein flexibility by calculating the Random Coil Index from backbone CS

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

stdinchi

A program for generating standard InChI and InChIKeys

suitename

surf

talos+

A Hybrid method for predicting protein backbone torsion angles from NMR CS

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

validation

vasco

viewmol

Open-source graphical front end for computational chemistry programs

vmd

Visual Molecular Dynamics

votca-csg

Votca coarse-graining engine

votca-csg-tutorials

votca-csgapps

webmo

Web-based interface to computational chemistry packages

wxmacmolplt

Chemical 3D graphics program with GAMESS input builder

xcrysden

xdrfile

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

zodiac

Software for molecular modelling - computer-aided drug design

acpype

mars

phenix-bin

almost

massxpert

pjnmr

ambertools

maxit

platon

apbs

mdanalysis

pmb

aqua

mddnmr

pointless

aria

mdsctk

polygon

arp-warp-bin

mdtools

povscript+

atnos-candid

mead

prekin

autodock

mestrenova-bin

probe

autodock-vina

mgltools

procheck

autodock_vina

mgltools-autodocktools

prodecomp

avogadro

mgltools-bhtree

profit

azara

mgltools-cadd

psi

babel

mgltools-cmolkit

pyitc

balbes

mgltools-dejavu

PyMca

ball

mgltools-geomutils

pymol

bist

mgltools-gle

pymol-apbs-plugin

bkchem

mgltools-mglutil

pymol-plugins-bni-tools

bodr

mgltools-molkit

pymol-plugins-caver

burrow-owl

mgltools-networkeditor

pymol-plugins-cealign

camshift

mgltools-opengltk

pymol-plugins-dssp

cara-bin

mgltools-pmv

pymol-plugins-dynamics

caver

mgltools-pyautodock

pymol-plugins-emovie

cclib

mgltools-pybabel

pymol-plugins-ezviz

ccp1gui

mgltools-pyglf

pymol-plugins-msms

ccp4

mgltools-qslimlib

pymol-plugins-promol

ccp4-apps

mgltools-scenario

pymol-plugins-psico

ccp4i

mgltools-scenario2

pymss

ccp4mg

mgltools-sff

pynmr

ccpn

mgltools-stride

pyquante

chemBuild

mgltools-support

pyrx

chemical-mime-data

mgltools-symserv

qutemol

chemtool

mgltools-utpackages

rasmol

chimera-bin

mgltools-viewer-framework

raster3d

chooch

mgltools-vision

rci

clashlist

mgltools-visionlib

rdkit

cluster

mgltools-volume

reduce

cns

mgltools-webservices

refmac

cnsface

mics

relax

concoord

mm-align

rosetta

coot

mmtk

rosetta-tools

cs-rosetta

modelfree

scala

curvefit

modeller

scicraft

cyana

molden

sfcheck

direx

moldy

shakerr

dl_poly

mole-bin

shelx

drawxtl

molequeue

shiftx

dssp

molmol

shiftx2

dssp2pdb

molrep

simpson

dsv

molscript

smmp

easychem

molsketch

solve-resolve-bin

eden

mopac2007-bin

sparky

elem

mopac7

specView

epmr

mopro-bin

ssp

espresso

mosflm

stdinchi

format-converter

mpqc

suitename

freeon

mrbump

surf

gabedit

msms

talos+

gamess

msms-bin

talosn

gamessq

mtz2hkl

theseus

gchemutils

mtz2sca

threeV

gelemental

mustang

tinker

ghemical

namd

tisean

gnome-chemistry-utils

nMOLDYN

tm-align

gopenmol

nmrglue

trajng

gperiodic

nmrpipe

ucsf-tools

gridzilla

nmrview

unio

gromacs

numbat

usf-rave-bin

GromacsWrapper

nwchem

usf-tools

gsim

oasis

usf-voidoo-bin

gtk-gamess

objcryst-fox

validation

hkl2map-bin

open3dqsar

vasco

hollow

openbabel

viewmol

hoomd

openbabel-java

vmd

hydronmr

openbabel-perl

votca-csg

icm

openbabel-python

votca-csg-tutorials

icm-browser

openbabel-ruby

votca-csgapps

imosflm

ortep3

webmo

jana2000

p3d

wxmacmolplt

jligand

panav

xcrysden

jmol

parassign

xdrfile

jmol-applet

pdb-extract

xds-bin

kincontour

pdb-tools

xdsgui

king

pdb2pqr

xdsi

ksdssp

pdbcat

xdsstat-bin

ligplot+

pdbcns

xia2

mage

pdbmat

xyza2pipe

makecif

phaser

zodiac