acpype

AnteChamber PYthon Parser interfacE

ambertools

A suite for carrying out complete molecular mechanics investigations

apbs

Software for evaluating the electrostatic properties of nanoscale biomolecular systems

aqua

Program suite in this distribution calculates restraint violations

aria

Automated NOE assignment and NMR structure calculation

arp-warp-bin

Software for improvement and interpretation of crystallographic electron density maps

autodock

A suite of automated docking tools

autodock_vina

Program for drug discovery, molecular docking and virtual screening

avogadro

Advanced molecular editor that uses Qt4 and OpenGL

azara

A suite of programmes to process and view NMR data

babel

Interconvert file formats used in molecular modeling

balbes

Automated molecular replacement (MR) pipeline

ball

Biochemical Algorithms Library

bkchem

Chemical drawing program

bodr

The Blue Obelisk Data Repository listing element and isotope properties.

burrow-owl

Visualize multidimensional nuclear magnetic resonance (NMR) spectra

cara-bin

Analysis of NMR spectra and Computer Aided Resonance Assignment

ccp4

Protein X-ray crystallography toolkit -- meta package

ccp4-apps

Protein X-ray crystallography toolkit

ccp4i

Protein X-ray crystallography toolkit -- graphical interface

ccpn

The Collaborative Computing Project for NMR

chemical-mime-data

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

chemtool

GTK program for drawing organic molecules

clashlist

Build lists of van der Waals clashes from an input PDB file

cluster

Build lists of collections of interacting items

cns

Crystallography and NMR System

coot

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

cyana

Combined assignment and dynamics algorithm for NMR applications

dssp

The protein secondary structure standard

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

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

gopenmol

Tool for the visualization and analysis of molecular structures

gperiodic

Periodic table application for Linux

gromacs

The ultimate molecular dynamics simulation package

gsim

Programm for visualisation and processing of experimental and simulated NMR spectra

gtk-gamess

GUI for GAMESS, a General Atomic and Molecular Electronic Structure System

hollow

Production of surface images of proteins

icm

MolSoft LCC ICM Pro

icm-browser

MolSoft LCC ICM Browser

imosflm

A new GUI for the Mosflm crystallographic data processing tool

jmol

Java molecular viever for 3-D chemical structures

ksdssp

ksdssp is an open source implementation of dssp

makecif

PDB --> CIF convertor

mars

Robust automatic backbone assignment of proteins

massxpert

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

mead

Macroscopic Electrostatics with Atomic Detail

mm-align

Protein Complex Structural Alignment

mmtk

The Molecular Modelling Toolkit

molden

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

moldy

Molecular dynamics simulations platform

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

A drawing tool for 2D molecular structures

mopac7

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

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

MSMS allows to compute very efficiently triangulations of Solvent Excluded Surfaces

mustang

MUltiple STructural AligNment AlGorithm

namd

A powerful and highly parallelized molecular dynamics code

oasis

A direct-method program for SAD/SIR phasing

openbabel

Interconverts file formats used in molecular modeling

openbabel-perl

Perl bindings for OpenBabel

openbabel-python

Python bindings for OpenBabel (including Pybel)

ortep3

Thermal ellipsoid plot program for crystal structure illustrations

p3d

Python module for structural bioinformatics

pdb-extract

Tools for extracting mmCIF data from structure determination applications

pdb-tools

Tools for manipulating and doing calculations on wwPDB macromolecule structure files

pdb2pqr

An automated pipeline for performing Poisson-Boltzmann electrostatics calculations

pdbcns

Convert atom names for common amino acids and nucleic acid bases from PDB format to CNS or back

pdbmat

Calculate Tirion's model from pdb structures

phaser

A program for phasing macromolecular crystal structures

platon

Versatile, SHELX-97 compatible, multipurpose crystallographic tool

pointless

Scores crystallographic Laue and space groups

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

Decomposition-based analysis of NMR projections

psi

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

PyMca

X-ray Fluorescence Toolkit

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

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

pymol-plugins-dssp

DSSP Plugin for PyMOL

pymol-plugins-emovie

eMovie is a plug-in tool for the molecular visualization program PyMOL

pymol-plugins-msms

GUI for MSMS and displaying its results in PyMOL

pymol-plugins-promol

Fast and accurate regognition of active sites

pymol-plugins-psico

Pymol ScrIpt COllection

rasmol

Molecular Graphics Visualisation Tool

raster3d

Generation high quality raster images of proteins or other molecules

reduce

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

refmac

Macromolecular crystallographic refinement program

scala

Scale together multiple observations of reflections

sfcheck

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

shelx

Programs for crystal structure determination from single-crystal diffraction data

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

suitename

The ROC RNA Ontology Consortium consensus RNA backbone nomenclature and conformer-list development

surf

Solvent accesible Surface calculator

talos+

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

theseus

maximum likelihood superpositioning and analysis of macromolecular structures

threeV

3V: Voss Volume Voxelator

tinker

Molecular modeling package that includes force fields, such as AMBER and CHARMM

tm-align

Quick & Accurate Structural Alignment

viewmol

Open-source graphical front end for computational chemistry programs

vmd

Visual Molecular Dynamics

votca-csg

Votca coarse-graining engine

votca-csgapps

Extra applications for votca-csg

webmo

Web-based interface to computational chemistry packages

wxmacmolplt

Chemical 3D graphics program with GAMESS input builder

xds-bin

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

xdsi

A crude interface for running the XDS

xia2

An automated data reduction system for crystallography

xyza2pipe

Cross conversion environment of NMR spectra

acpype

gtk-gamess

prekin

ambertools

hollow

probe

apbs

icm

procheck

aqua

icm-browser

prodecomp

aria

imosflm

psi

arp-warp-bin

jmol

PyMca

autodock

ksdssp

pymol

autodock_vina

makecif

pymol-apbs-plugin

avogadro

mars

pymol-plugins-bni-tools

azara

massxpert

pymol-plugins-caver

babel

mead

pymol-plugins-dssp

balbes

mm-align

pymol-plugins-emovie

ball

mmtk

pymol-plugins-msms

bkchem

molden

pymol-plugins-promol

bodr

moldy

pymol-plugins-psico

burrow-owl

molmol

rasmol

cara-bin

molrep

raster3d

ccp4

molscript

reduce

ccp4-apps

molsketch

refmac

ccp4i

mopac7

scala

ccpn

mosflm

sfcheck

chemical-mime-data

mpqc

shelx

chemtool

mrbump

solve-resolve-bin

clashlist

msms-bin

sparky

cluster

mustang

suitename

cns

namd

surf

coot

oasis

talos+

cyana

openbabel

theseus

dssp

openbabel-perl

threeV

easychem

openbabel-python

tinker

eden

ortep3

tm-align

elem

p3d

viewmol

gabedit

pdb-extract

vmd

gamess

pdb-tools

votca-csg

gamessq

pdb2pqr

votca-csgapps

gchemutils

pdbcns

webmo

gelemental

pdbmat

wxmacmolplt

ghemical

phaser

xds-bin

gopenmol

platon

xdsi

gperiodic

pointless

xia2

gromacs

povscript+

xyza2pipe

gsim