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Open Babel specifications


Unique identifier OMICS_12101
Name Open Babel
Alternative name OpenBabel
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C#, C++, Java, Perl, Python, Ruby
License GNU General Public License version 2.0
Computer skills Medium
Version 2.3.1
Stability Stable
Maintained Yes




No version available


  • person_outline Noel O'Boyle

Publication for Open Babel

Open Babel citations


Discovery of small molecules through pharmacophore modeling, docking and molecular dynamics simulation against Plasmodium vivax Vivapain 3 (VP 3)

PMCID: 5944417
PMID: 29756074
DOI: 10.1016/j.heliyon.2018.e00612

[…] in a SDF (Structure data format) from a PubChem database (, an unwrap storehouse for small compounds. All the compounds were initially energy minimization done by the Open Babel in PyRx Virtual Screening Tool (). Once consider the pharmacophore query, virtual screening was passed out by the LS next to the PubChem database. The known hits, were docked into the recep […]


Targeting matrix metalloproteinases with novel diazepine substituted cinnamic acid derivatives: design, synthesis, in vitro and in silico studies

Chem Cent J
PMCID: 5910448
PMID: 29679218
DOI: 10.1186/s13065-018-0411-8

[…] BQT file for the proteins was generated with the help of AutoDock tools by addition of all polar hydrogen atoms charge assignment to the macromolecule. The geometries of the ligands were optimized by Open Babel using force field []. The ligands were prepared for docking by using AutoDock tools by assigning the charges to all the atoms and storing them as PDBQT file. The calculations of grid parame […]


The Mu.Ta.Lig. Chemotheca: A Community Populated Molecular Database for Multi Target Ligands Identification and Compound Repurposing

PMCID: 5917039
PMID: 29725591
DOI: 10.3389/fchem.2018.00130
call_split See protocol

[…] , ). All Chemotheca data are stored in a MySQL database ( An ad hoc developed Python ( code (CDC) computes molecular descriptors for each uploaded compound, by using the OpenBabel library (O'Boyle et al., ) and its wrapper Pybel (O'Boyle et al., ).The molecule upload process uses the isomeric SMILES code produced by the JSME applet. The CDC converts SMILES into a fing […]


Homology modelling, molecular docking, and molecular dynamics simulations reveal the inhibition of Leishmania donovani dihydrofolate reductase thymidylate synthase enzyme by Withaferin A

BMC Res Notes
PMCID: 5902840
PMID: 29661206
DOI: 10.1186/s13104-018-3354-1

[…] The structures of WA, MTX and DHFA (PubChem CID 265237, 126941, 98792, respectively) were obtained from PubChem ( (Additional file : Fig. S1). Open Babel ( was used to obtain. pdbqt files. Molecular docking studies were carried out in Auto Dock Vina []. Initially, blind docking, was performed, followed by […]


Prediction of Cell Penetrating Potential of Modified Peptides Containing Natural and Chemically Modified Residues

Front Microbiol
PMCID: 5906597
PMID: 29706944
DOI: 10.3389/fmicb.2018.00725

[…] Atom composition is computed from CPPs and non-CPPs by converting peptide structures in SMILES format using openbabel (O'Boyle et al., ). These SMILES were further used to compute atom composition of following atoms C, H, O, N, S, Cl, Br, and F. The atomic composition provided the fixed length of 8 vectors. […]


The Alexandria library, a quantum chemical database of molecular properties for force field development

Sci Data
PMCID: 5892371
PMID: 29633987
DOI: 10.1038/sdata.2018.62
call_split See protocol

[…] mann family of methods was used on a subset of about 600 compounds only, due to computational cost. The procedure of thermochemistry calculations has been explained in detail in our previous work.The OpenBabel program (version 2.4.1) was used to determine the number of rotatable bonds based on the optimized geometry for each molecule. The results, wherever possible, were compared to the PubChem da […]


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Open Babel institution(s)
Analytical and Biological Chemistry Research Facility, Cavanagh Pharmacy Building, University College Cork, Co. Cork, Ireland; Department of Chemistry, Technische Universität München, Garching, Germany; eMolecules, Inc., Solana Beach, CA, USA; Open Babel development team; University of Pittsburgh, Department of Chemistry, Pittsburgh, PA, USA

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