InChI - the worldwide chemical structure identifier standard

Heller, Stephen R.; Mcnaught, Alan D.; Stein, Stephen E.; Tchekhovskoi, Dmitrii V.; Pletnev, I. V.

doi:10.1186/1758-2946-5-7

Cited by 411 publications

(340 citation statements)

References 7 publications

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“…[238,239]), but, in brief, a similarity comparison is typically done as follows. The structure of the interrogating molecule, provided in the form of a SMILES [240] or InChI [241][242][243] string, is encoded therefrom as a string of 1s and 0s. Modern software suites such as RDKit [244] (www.rdkit.org/), CDK [245] or KNIME (which includes them both) [246][247][248] allow one to do this automatically.…”

Section: The Importance Of Qsars (Quantitative Structure-activity Relmentioning

confidence: 99%

Control of metabolite efflux in microbial cell factories: current advances and future prospects

Kell¹

2018

Preprint

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The yield and ease of purification of biotechnological products are typically greatly enhanced if they can be secreted into the external medium. Although not universally appreciated, however, small molecule biotechnological products do not ‘float across’ the phospholipid bilayer portion of biological membranes, and thus they need transporters to assist their passage into the extramembrane and extracellular spaces. Some of these transporters may be reversible, equilibrative transporters that might more normally be used for uptake, while others may have an efflux directionality imposed on them via suitable energy coupling mechanisms. Despite the energetic costs of small molecule synthesis, natural evolution does in fact provide a number of mechanisms by which the secretion of such products can actually enhance fitness. Where available these provide useful starting points, and assaying for such activities is crucial. In particular, in a systems biology approach, we first need to identify such/suitable activities before we can seek to increase them. They may then be improved through promoter engineering, via manipulation of control elements, or by directed evolution of the transporter proteins themselves. Modern methods of synthetic biology provide enormous opportunities for all kinds of efflux transporter engineering; they are just beginning to be realised.

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Section: The Importance Of Qsars (Quantitative Structure-activity Relmentioning

confidence: 99%

Control of metabolite efflux in microbial cell factories: current advances and future prospects

Kell¹

2018

Preprint

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“…The IUPAC International Chemical Identifier (InChI) [1,2] is a widely-used and computer-readable chem- ical identifier used in the electronic transmission of data. It represents the structure of a molecule using a slash-delimited string consisting of a well-defined series of fields or layers.…”

Section: Introductionmentioning

confidence: 99%

Data Formats for Elementary Gas-Phase Kinetics: Part 2. Unique Representations of Reactions

Burgess

Manion

Hayes

2015

Int. J. Chem. Kinet.

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A method of extending the IUPAC International Chemical Identifier (InChI) to describe and identify elementary reactions in a standard computer-readable notation is developed. Denoted InChI-ER, the method is based on the existing InChI formalism, with certain refinements for the better identification of molecular entities as proposed in Part 1 published previously in this journal. Using this base notation, an identifier for elementary reactions on a molecular level is created by adding additional layers in a conceptually similar and extensible manner. Two of the layers describe the atoms involved in the transition state and the connectivity changes that occur during the reaction. Additional layers classify the reactions on the basis of the connectivity changes, providing chemical information useful in organizing and searching kinetic data sets found in databases or used in detailed kinetic modeling. Important aspects of the method are that the proposed layers are optional, that they do not interfere with existing InChI specifications, and that they retain extensibility should further refinements be desired in the future. C 2015 Wiley Periodicals, Inc. Int J Chem Kinet 47: [334][335][336][337][338][339][340][341][342][343][344][345][346][347][348][349][350] 2015

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“…For instance, with Uta Frith's Twitter name 'utafrith', /scholia/twitter/utafrith will redirect to /scholia/Q8219, which in turn will redirect to /scholia/author/Q8219. Scholia implements similar functionality for DOI, ORCID, GitHub user identifier as well as for the InChIKey [8] and CAS chemical identifiers.…”

Section: Scholiamentioning

confidence: 99%

Scholia, Scientometrics and Wikidata

Nielsen

Mietchen²,

Willighagen

2017

Lecture Notes in Computer Science

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Abstract. Scholia is a tool to handle scientific bibliographic information through Wikidata. The Scholia Web service creates on-the-fly scholarly profiles for researchers, organizations, journals, publishers, individual scholarly works, and for research topics. To collect the data, it queries the SPARQL-based Wikidata Query Service. Among several display formats available in Scholia are lists of publications for individual researchers and organizations, plots of publications per year, employment timelines, as well as co-author and topic networks and citation graphs. The Python package implementing the Web service is also able to format Wikidata bibliographic entries for use in LaTeX/BIBTeX. Apart from detailing Scholia, we describe how Wikidata has been used for bibliographic information and we also provide some scientometric statistics on this information.

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InChI - the worldwide chemical structure identifier standard

Cited by 411 publications

References 7 publications

Control of metabolite efflux in microbial cell factories: current advances and future prospects

Control of metabolite efflux in microbial cell factories: current advances and future prospects

Data Formats for Elementary Gas-Phase Kinetics: Part 2. Unique Representations of Reactions

Scholia, Scientometrics and Wikidata

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