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Table 1 Software applications and libraries that use Open Babel
| 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/ |
