The Blue Obelisk—Interoperability in Chemical Informatics

By Rajarshi Guha, M. T. Howard, Geoffrey R. Hutchison, Peter Murray-Rust, H. Rzepa, Christoph Steinbeck, Jörg Kurt Wegner, Egon Willighagen. 2006

381 citations recorded by the source corpus.

The Blue Obelisk Movement (http://www.blueobelisk.org/) is the name used by a diverse Internet group promoting reusable chemistry via open source software development, consistent and complimentary chemoinformatics research, open data, and open standards. We outline recent examples of cooperation in the Blue Obelisk group: a shared dictionary of algorithms and implementations in chemoinformatics algorithms drawing from our various software projects; a shared repository of chemoinformatics data including elemental properties, atomic radii, isotopes, atom typing rules, and so forth; and Web services for the platform-independent use of chemoinformatics programs.

Subfields: Computational Theory and Mathematics, Physical and Theoretical Chemistry, Spectroscopy, Computational Chemistry & Drug Discovery

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Citations in the corpus

Machine learning of molecular electronic properties in chemical compound space (2013, methodology): “Based on the string representation (SMILES [16, 17]) of molecules in the database, we used the universal force field [18] to generate reasonable Cartesian molecular geometries, as implemented in OpenBabel [19].”
ChemMine tools: an online service for analyzing and clustering small molecules (2011, methodology): “The compound download function also serves as a format conversion tool to interconvert structure representations between SDF and SMILES formats using utilities from the Open Babel project (27,28).”
SwissDock, a protein-small molecule docking web service based on EADock DSS (2011, methodology): “The topology of the Mol2 files has to be correct, hence we recommend the use of the following software, working most of the time: UCSF Chimera, OpenBabel (33), MarvinSketch (http://www.”
Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information (2011, methodology): “For chemistry-related features we used the JME molecule editor [17], the CDK toolkits [81] and the ChemAxon (http://www.”
ChemmineR: a compound mining framework for R (2008, background): “∗ © 2008 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons which permits”
Learning Invariant Representations of Molecules for Atomization Energy Prediction (2012, methodology): “, 1992) as implemented in the software OpenBabel (Guha et al., 2006).”
ACPYPE - AnteChamber PYthon Parser interfacE (2012, methodology): “OpenBabel [22,23] installation is optional but required for reading molecule information from PDB-style files.”
Avogadro: an advanced semantic chemical editor, visualization, and analysis platform (2012, methodology): “The development team has also been members of the Blue Obelisk movement, following the three pillars outlined by the group: Open Data, Open Standards, and Open Source [48,49].”
The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching (2017, methodology): “Originally, Nightly integrated various tools (building, testing, JavaDoc, etc) [2].”
Computer-aided drug design platform using PyMOL (2011, methodology): “The following third-party programs are necessary for complete utilization of the described plugins: the Amber package [7, 10] (tested with Amber 9 and Amber 10) to perform molecular mechanics applications and MMPBSA calculations, changepdb and changecrd from U. Ryde to estimate entropic contribution”