Open Babel: An open chemical toolbox

Abstract

BackgroundA frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats.ResultsWe discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion.ConclusionsOpen Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org.

Genes associated with genotype-specific DNA methylation in squamous cell carcinoma as candidate drug targets

“…The smiles format was transformed to three dimensional structures by Babel [24]. The structures of 6510 of the compounds were obtained.…”

Molecular characterization, modeling, in silico analysis of equine pituitary gonadotropin alpha subunit and docking interaction studies with ganirelix

“…The 2D structure file was downloaded from the Pubchem open chemistry database available at NCBI in sdf/xml format. OpenBabelGUI (O'Boyle et al 2011) was used to create all the input files in.pdbqt format and saved. Before docking, PDB file of eCG alpha 3D model was energy-minimized and prepared by removal of water molecules, addition of polar hydrogens and Gasteiger charges.…”

OrCanome: a Comprehensive Resource for Oral Cancer

“…The one dimensional structure in the form of SMILES (http://www.daylight. com/smiles/) was generated using Open Babel software and the bioassay data were obtained from the chemical databases such as ChEMBL and BindingDB (Liu et al, 2007;O'Boyle et al, 2011). HTML toolkit from ChemDoodle was integrated for the visualization of chemical compounds (Burger, 2015).…”