Chemical Name to Structure: OPSIN, an Open Source Solution

Lowe, Daniel M.; Corbett, Peter; Murray‐Rust, Peter; Glen, Robert C.

doi:10.1021/ci100384d

Cited by 181 publications

(152 citation statements)

References 23 publications

Supporting

Mentioning

150

Contrasting

Unclassified

Order By: Relevance

“…SMILES, SDF, and InChI strings are common structural representation formats for chemical entities, which can be directly used for structure search operations or the generation of physico-chemical properties. In contrast, each IUPAC name is converted to the corresponding structure using the OPSIN library [39], before any chemical object is created and subsequently preprocessed. If the chemical (protein, DNA or RNA molecule) input is submitted in FASTA format, every sequence is either identified as a nucleotide or peptide sequence type.…”

Section: The Classification Processmentioning

confidence: 99%

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

Eisner²,

et al. 2016

View full text Add to dashboard Cite

BackgroundScientists have long been driven by the desire to describe, organize, classify, and compare objects using taxonomies and/or ontologies. In contrast to biology, geology, and many other scientific disciplines, the world of chemistry still lacks a standardized chemical ontology or taxonomy. Several attempts at chemical classification have been made; but they have mostly been limited to either manual, or semi-automated proof-of-principle applications. This is regrettable as comprehensive chemical classification and description tools could not only improve our understanding of chemistry but also improve the linkage between chemistry and many other fields. For instance, the chemical classification of a compound could help predict its metabolic fate in humans, its druggability or potential hazards associated with it, among others. However, the sheer number (tens of millions of compounds) and complexity of chemical structures is such that any manual classification effort would prove to be near impossible.ResultsWe have developed a comprehensive, flexible, and computable, purely structure-based chemical taxonomy (ChemOnt), along with a computer program (ClassyFire) that uses only chemical structures and structural features to automatically assign all known chemical compounds to a taxonomy consisting of >4800 different categories. This new chemical taxonomy consists of up to 11 different levels (Kingdom, SuperClass, Class, SubClass, etc.) with each of the categories defined by unambiguous, computable structural rules. Furthermore each category is named using a consensus-based nomenclature and described (in English) based on the characteristic common structural properties of the compounds it contains. The ClassyFire webserver is freely accessible at http://classyfire.wishartlab.com/. Moreover, a Ruby API version is available at https://bitbucket.org/wishartlab/classyfire_api, which provides programmatic access to the ClassyFire server and database. ClassyFire has been used to annotate over 77 million compounds and has already been integrated into other software packages to automatically generate textual descriptions for, and/or infer biological properties of over 100,000 compounds. Additional examples and applications are provided in this paper.ConclusionClassyFire, in combination with ChemOnt (ClassyFire’s comprehensive chemical taxonomy), now allows chemists and cheminformaticians to perform large-scale, rapid and automated chemical classification. Moreover, a freely accessible API allows easy access to more than 77 million “ClassyFire” classified compounds. The results can be used to help annotate well studied, as well as lesser-known compounds. In addition, these chemical classifications can be used as input for data integration, and many other cheminformatics-related tasks.Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-016-0174-y) contains supplementary material, which is available to authorized users.

show abstract

Section: The Classification Processmentioning

confidence: 99%

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

Eisner²,

et al. 2016

View full text Add to dashboard Cite

show abstract

“…OPSIN [23], the Open Parser for Systematic IUPAC nomenclature, converts plain-text chemical nomenclature to machine readable CML or InChi formats.…”

Section: Cheminformaticsmentioning

confidence: 99%

Open source molecular modeling

Pirhadi

Sunseri

2016

Journal of Molecular Graphics and Modelling

View full text Add to dashboard Cite

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.

show abstract

“…Besides this basic cheminformatics functionality, Bioclipse also supports chemical names. There is search functionality to find chemicals in ChemSpider and PubChem, and with the OPSIN [29] plugin handling IUPAC names is trivial. Further support is provided by a plugin for the Chemical Resolver Identifier (cactus.nci.nih.gov/chemical/structure).…”

Section: Cheminformaticsmentioning

confidence: 99%

Open Source Drug Discovery with Bioclipse

Spjuth¹,

Carlsson²,

Alvarsson³

et al. 2012

Current Topics in Medicinal Chemistry

View full text Add to dashboard Cite

Abstract.We present the open source components for drug discovery that has been developed and integrated into the graphical workbench Bioclipse. Building on a solid open source cheminformatics core, Bioclipse has advanced functionality for managing and visualizing chemical structures and related information. The features presented here include QSAR/QSPR modeling, various predictive solutions such as decision support for chemical liability assessment, site-of-metabolism prediction, virtual screening, and knowledge discovery and integration. We demonstrate the utility of the described tools with examples from computational pharmacology, toxicology, and ADME. Bioclipse is used in both academia and industry, and is a good example of open source leading to new solutions for drug discovery.

show abstract

Chemical Name to Structure: OPSIN, an Open Source Solution

Cited by 181 publications

References 23 publications

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

Open source molecular modeling

Open Source Drug Discovery with Bioclipse

Contact Info

Product

Resources

About