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Table 1 Software applications and libraries that use Open Babel

From: Open Babel: An open chemical toolbox

Name

Description

Reference

Web page

Avogadro

GUI for molecular modelling and computational chemistry

G. Hutchison M. Hanwell

http://avogadro.openmolecules.net/

cclib

Parse computational chemistry output files

[72]

http://cclib.sf.net/

CCP1GUI

GUI for computational chemistry

Jens Thomas

http://www.cse.scitech.ac.uk/ccg/software/ccp1gui

ChemAzTech

Manage a chemical laboratory database

Rémy Dernat

http://chemaztech.sf.net/

ChemSpotlight

Chemistry file indexer for MacOSX

G. Hutchison

http://chemspotlight.openmolecules.net/

ChemT

GUI for generating combinatorial libraries

Rui Abreu

http://www.esa.ipb.pt/~ruiabreu/chemt

ChemTool

2D molecular drawing

[73]

http://ruby.chemie.uni-freiburg.de/~martin/chemtool

CMDF

Library for handling and preparing multi-scale multi-paradigm simulations

[74]

http://web.mit.edu/mbuehler/www/research/CMDF/CMDF.htm

Confab

Systematically generate conformers

[36]

http://confab.googlecode.com/

DockoMatic

Automate the preparation and analysis of AutoDock runs

[75]

http://sf.net/projects/dockomatic/

DOVIS 2.0

Automate the preparation and analysis of AutoDock runs

[76]

http://www.bhsai.org/dovis.html

FAF-Drugs2

ADMET filtering of molecular datasets

[77]

http://www.mti.univ-paris-diderot.fr/fr/downloads.html

FMiner2

Large-scale chemical graph mining based on backbone refinement classes

[78, 79]

http://www.maunz.de/wordpress/bbrc

Ghemical

GUI for computational chemistry

Tommi Hassinen

http://www.uku.fi/~thassine/projects/ghemical

Gnome Chemistry Utils

2D chemical editor, 3D viewer, chemical calculator and periodic table for Linux

Jean Bréfort

http://gchemutils.nongnu.org/

iBabel

MacOSX interface to Open Babel and other Open chemistry tools

Chris Swain

http://homepage.mac.com/swain/Sites/Macinchem/page65/ibabel3.html

Kalzium

GUI showing information on the periodic table of the elements

Carsten Niehaus

http://edu.kde.org/kalzium/

Lazar

Lazy Structure-Activity Relationships for toxicity prediction

[80]

http://www.in-silico.de/software/

Molekel

GUI for computational chemistry

Ugo Varetto

http://molekel.cscs.ch/

molsKetch

2D chemical editor

Harm van Eersel

http://molsketch.sf.net/

MyChem

Chemistry extension to the MySQL database

J. Pansanel

http://mychem.sf.net/

NanoEngineer-1

Computer-aided design for the nanoscale

Nanorex, Inc.

http://nanoengineer-1.net/

NanoHive-1

Simulator for the study, experimentation, and development of nanotech entities

Brian Helfrich

http://www.nanohive-1.org/

OpenMD

Open Source molecular dynamics engine

[81]

http://openmd.net/

Open3DQSAR

High-throughput

chemometric analysis of molecular interaction fields

[82, 83]

http://www.open3dqsar.org/

OSRA

Extracts chemical structures from images

[84]

http://osra.sf.net/

PgChem

Chemistry extension to the PostgreSQL database

Ernst-Georg Schmidt

http://pgfoundry.org/projects/pgchem

Pharao

Pharmacophore discovery and searching

Silicos NV

http://www.silicos.be/

Pharmer

Pharmacophore searching

[85]

http://smoothdock.ccbb.pitt.edu/pharmer

Piramid

Shape-based alignment of molecules

Silicos NV

http://www.silicos.be/

PyADF

Library for handling and preparing quantum mechanical multi-scale simulations

[86]

http://www.ipc.kit.edu/cfn-ysg/158.php

PyRx

GUI for virtual screening with protein-ligand docking

Sargis Dallakyan

http://pyrx.scripps.edu/

QMForge

GUI for analysing results of quantum chemistry calculations

[72]

http://qmforge.sf.net/

RMG

Reaction Mechanism Generator

[87]

http://rmg.sf.net/

Sci3D

Interactive visualization of 3D models of scientific data, such as molecular structures and surfaces

T.J. O'Donnell

http://sci3d.sf.net/

Sieve

Filter molecules from datasets

Silicos NV

http://www.silicos.be/

SMIREP

Generation of fragment-based structure-activity relationships

[88]

http://www.karwath.org/systems/smirep.html

Stripper

Extract molecular scaffolds

Silicos NV

http://www.silicos.be/

Toxtree

Toxic hazard estimation using decision trees

Ideaconsult Ltd.

http://toxtree.sf.net/

V_Sim

Visualize atomic structures such as crystals and grain boundaries

Damien Caliste

http://inac.cea.fr/L_Sim/V_Sim/index.en.html

WebBabel

Web application for file format conversion

T.J. O'Donnell

http://webbabel.sf.net/

XDrawChem

2D molecular editor

Bryan Herger

http://xdrawchem.sf.net/

XtalOpt

Extension to Avogadro for crystal-structure prediction

[89]

http://xtalopt.openmolecules.net/

YASARA

GUI for molecular graphics, modeling and simulation

Elmar Krieger

http://www.yasara.org/

ZODIAC

GUI for molecular modelling and docking

[90]

http://www.zeden.org/