Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on

O’Boyle, Noel M.; Guha, Rajarshi; Willighagen, Egon; Adams, Sam; Alvarsson, Jonathan; Bradley, Jean‐Claude; Filippov, Igor V.; Hanson, Robert M.; Hanwell, Marcus D.; Hutchison, Geoffrey; James, Craig A.; Jeliazkova, Nina; Lang, Andrew S.; Langner, Karol M.; Lonie, David; Lowe, Daniel M.; Pansanel, Jérôme; Павлов, Д. С.; Spjuth, Ola; Steinbeck, Christoph; Tenderholt, Adam L.; Theisen, Kevin J.; Murray‐Rust, Peter

doi:10.1186/1758-2946-3-37

Cited by 78 publications

(48 citation statements)

References 41 publications

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“…Other applications such as preparing input for MD simulations and visualizing periodic structures will also be presented, demonstrating the flexibility of the Avogadro platform. 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]. …”

Section: Methodsmentioning

confidence: 99%

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

et al. 2012

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BackgroundThe Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types.ResultsThe work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here.ConclusionsAvogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net.

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Section: Methodsmentioning

confidence: 99%

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

et al. 2012

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“…The Chemistry Development Kit (CDK) is one of the tools developed under the aegis of the Blue Obelisk, a movement promoting Open Data, Open Source, and Open Standards in chemistry [1, 2]. The CDK providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them.…”

Section: Introductionmentioning

confidence: 99%

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Mayfield²,

et al. 2017

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Background The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them. The library implements a wide variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. It is used in drug discovery, metabolomics, and toxicology. Over the last 10 years, the code base has grown significantly, however, resulting in many complex interdependencies among components and poor performance of many algorithms.Results We report improvements to the CDK v2.0 since the v1.2 release series, specifically addressing the increased functional complexity and poor performance. We first summarize the addition of new functionality, such atom typing and molecular formula handling, and improvement to existing functionality that has led to significantly better performance for substructure searching, molecular fingerprints, and rendering of molecules. Second, we outline how the CDK has evolved with respect to quality control and the approaches we have adopted to ensure stability, including a code review mechanism.ConclusionsThis paper highlights our continued efforts to provide a community driven, open source cheminformatics library, and shows that such collaborative projects can thrive over extended periods of time, resulting in a high-quality and performant library. By taking advantage of community support and contributions, we show that an open source cheminformatics project can act as a peer reviewed publishing platform for scientific computing software.Graphical abstractCDK 2.0 provides new features and improved performance Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-017-0220-4) contains supplementary material, which is available to authorized users.

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“…For example, there are several forks of AutoDock Vina that improve it’s performance on computing clusters and there are an array of tools in several categories that effiectively perform the same task. This underscores the importance of efforts like Blue Obelisk [187, 188] and Open Chemistry (http://www.openchemistry.org) which foster collaboration among open source cheminformatics projects.…”

Section: Discussionmentioning

confidence: 99%

Open source molecular modeling

Pirhadi

Sunseri

2016

Journal of Molecular Graphics and Modelling

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The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry.

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Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on

Cited by 78 publications

References 41 publications

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Open source molecular modeling

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