Skip to main content

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
cclib Parse computational chemistry output files [72]
CCP1GUI GUI for computational chemistry Jens Thomas
ChemAzTech Manage a chemical laboratory database Rémy Dernat
ChemSpotlight Chemistry file indexer for MacOSX G. Hutchison
ChemT GUI for generating combinatorial libraries Rui Abreu
ChemTool 2D molecular drawing [73]
CMDF Library for handling and preparing multi-scale multi-paradigm simulations [74]
Confab Systematically generate conformers [36]
DockoMatic Automate the preparation and analysis of AutoDock runs [75]
DOVIS 2.0 Automate the preparation and analysis of AutoDock runs [76]
FAF-Drugs2 ADMET filtering of molecular datasets [77]
FMiner2 Large-scale chemical graph mining based on backbone refinement classes [78, 79]
Ghemical GUI for computational chemistry Tommi Hassinen
Gnome Chemistry Utils 2D chemical editor, 3D viewer, chemical calculator and periodic table for Linux Jean Bréfort
iBabel MacOSX interface to Open Babel and other Open chemistry tools Chris Swain
Kalzium GUI showing information on the periodic table of the elements Carsten Niehaus
Lazar Lazy Structure-Activity Relationships for toxicity prediction [80]
Molekel GUI for computational chemistry Ugo Varetto
molsKetch 2D chemical editor Harm van Eersel
MyChem Chemistry extension to the MySQL database J. Pansanel
NanoEngineer-1 Computer-aided design for the nanoscale Nanorex, Inc.
NanoHive-1 Simulator for the study, experimentation, and development of nanotech entities Brian Helfrich
OpenMD Open Source molecular dynamics engine [81]
Open3DQSAR High-throughput
chemometric analysis of molecular interaction fields
[82, 83]
OSRA Extracts chemical structures from images [84]
PgChem Chemistry extension to the PostgreSQL database Ernst-Georg Schmidt
Pharao Pharmacophore discovery and searching Silicos NV
Pharmer Pharmacophore searching [85]
Piramid Shape-based alignment of molecules Silicos NV
PyADF Library for handling and preparing quantum mechanical multi-scale simulations [86]
PyRx GUI for virtual screening with protein-ligand docking Sargis Dallakyan
QMForge GUI for analysing results of quantum chemistry calculations [72]
RMG Reaction Mechanism Generator [87]
Sci3D Interactive visualization of 3D models of scientific data, such as molecular structures and surfaces T.J. O'Donnell
Sieve Filter molecules from datasets Silicos NV
SMIREP Generation of fragment-based structure-activity relationships [88]
Stripper Extract molecular scaffolds Silicos NV
Toxtree Toxic hazard estimation using decision trees Ideaconsult Ltd.
V_Sim Visualize atomic structures such as crystals and grain boundaries Damien Caliste
WebBabel Web application for file format conversion T.J. O'Donnell
XDrawChem 2D molecular editor Bryan Herger
XtalOpt Extension to Avogadro for crystal-structure prediction [89]
YASARA GUI for molecular graphics, modeling and simulation Elmar Krieger
ZODIAC GUI for molecular modelling and docking [90]