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all atom molecular simulation toolkit

Software for evaluating the electrostatic properties of nanoscale biomolecular systems

Software for automated NOE assignment and NMR structure calculation.

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

A suite of automated docking tools

AutoDock Vina is a new program for drug discovery and molecular docking

Advanced molecular editor that uses Qt4 and OpenGL

A suite of programmes to process and view NMR data

Automated molecular replacement (MR) pipeline

Bist, the chemical drawing tool

A chemical drawing program

The Blue Obelisk Data Repository listing element and isotope properties.

Visualize multidimensional nuclear magnetic resonance (NMR) spectra

An application for the analysis of NMR spectra and Computer Aided Resonance Assignment

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

Library for parsing and interpreting the results of computational chemistry packages

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

Protein X-ray crystallography toolkit -- meta package

Protein X-ray crystallography toolkit

Protein X-ray crystallography toolkit -- graphical interface

The Collaborative Computing Project for NMR

chemical-mime-data

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

A GTK program for drawing organic molecules

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

Crystallography and NMR System

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

Combined assignment and dynamics algorithm for NMR applications

Low Resolution Structure Refinement

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

The protein secondary structure standard

convert dssp to pdb

Discovery Studio Visualizer

Chemical structure drawing program - focused on presentation.

A crystallographic real-space electron-density refinement and optimization program

periodic table of the elements

Crystallographic molecular replacement by evolutionary search

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

format-converter

GUI for computational chemistry packages

A powerful quantum chemistry package

Simple job manager for GAMESS-US

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

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

Chemical quantum mechanics and molecular mechanics

gnome-chemistry-utils

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

Periodic table application for Linux

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

The ultimate molecular dynamics simulation package

Programm for visualisation and processing of experimental and simulated NMR spectra

GTK-GAMESS is a graphical frontend for GAMESS

MolSoft LCC ICM Pro

MolSoft LCC ICM Browser

A new GUI for the Mosflm crystallographic data processing tool

the crystallographic computing system

a Java interface which allows links descriptions to be created

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

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

An interactive system for 3D graphics (primarily molecular)

ksdssp is an open source implementation of dssp

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

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

An application for processing and curation of macromolecular structure data

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

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

Macroscopic Electrostatics with Atomic Detail

Software to visualization and analysis of molecular structures

mgltools-autodocktools

mgltools plugin -- autodocktools

mgltools-bhtree

mgltools plugin -- bhtree

mgltools-cmolkit

mgltools plugin -- cMolKit

mgltools-dejavu

mgltools plugin -- dejavu

mgltools-geomutils

mgltools plugin -- geomutils

mgltools plugin -- gle

mgltools-mglutil

mgltools plugin -- mglutil

mgltools-molkit

mgltools plugin -- MolKit

mgltools-networkeditor

mgltools plugin -- NetworkEditor

mgltools-opengltk

mgltools plugin -- opengltk

mgltools plugin -- pmv

mgltools-pyautodock

mgltools plugin -- PyAutoDock

mgltools-pybabel

mgltools plugin -- PyBabel

mgltools plugin -- pyglf

mgltools-qslimlib

mgltools plugin -- qslimlib

mgltools-scenario

mgltools plugin -- scenario

mgltools-scenario2

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

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

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

Program for performing molecular dynamics simulations.

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

Publication-quality molecular visualization package

molecular replacement program

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

Powerful, fast semi-empirical package

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

Crystallographic structure or charge density refinement

A program for integrating single crystal diffraction data from area detectors

The Massively Parallel Quantum Chemistry Program

An automated scheme for Molecular Replacement

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

Converts CCP4 mtz-files containing anomalous data to Scalepack format

MUltiple STructural AligNment AlGorithm.

A powerful and highly parallelized molecular dynamics code

Spectral visualisation, analysis and Fourier processing

Visualisation and analysis of processed NMR data

A direct-method program for SAD/SIR phasing

interconverts file formats used in molecular modeling

Perl bindings for OpenBabel

openbabel-python

Python bindings for OpenBabel (including Pybel)

Ruby bindings for OpenBabel

Thermal ellipsoid plot program for crystal structure illustrations

Tools for extracting mmCIF data from structure determination applications

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

Phasing macromolecular crystal structures with maximum likelihood methods

Versatile, SHELX-97 compatible, multipurpose crystallographic tool

Automated structure refinement tools for CNS

Scores crystallographic Laue and space groups

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

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

Prepares molecular kinemages (input files for Mage & KiNG) from PDB-format coordinate files

Evaluates atomic packing within or between molecules

Checks the stereochemical quality of a protein structure

Designed to be the ultimate protein least squares fitting program

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

Multiple superposition of proteins, using a genetic algorithm for optimization

An NMR Extension for PyMOL, written in Python

GUI for Virtual Screening with AutoDock

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

Free program that displays molecular structure.

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

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

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

Macromolecular crystallographic refinement program

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

Additional scripts for rosetta

scale together multiple observations of reflections

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

Programs for crystal structure determination from single-crystal diffraction data

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

Simple Molecular Mechanics for Proteins

solve-resolve-bin

Automated crystallographic structure solution for MIR, SAD, and MAD

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

A program for generating standard InChI and InChIKeys

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

Maximum likelihood superpositioning and analysis of macromolecular structures

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.

The tools package from USF for macromolecular crystallography

The tools package from USF for macromolecular crystallography

Open-source graphical front end for computational chemistry programs

Visual Molecular Dynamics

Votca coarse-graining engine

votca-csg-tutorials

Web-based interface to computational chemistry packages

Chemical 3D graphics program with GAMESS input builder

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

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

An automated data reduction system for crystallography

Software for molecular modelling - computer-aided drug design