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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/