International chemical identifier for reactions (RInChI) Guenter Grethe, Gerd Blanke, Hans Kraut & Jonathan M. Goodman Journal of Cheminformatics volume 10, Article number: 22 (2018) Abstract: The Reaction InChI (RInChI) extends the idea of the InChI, which provides a unique descriptor of molecular structures, towards reactions. Prototype versions of the […]
InChI Tag: InChI Applications
89 posts
Reaction InChI (RInChI) – What’s next Gerd Blanke, March 22, 2021 Powerpoint presentation at NIH InChI workshop, March 22-24, 2021 https://cactus.nci.nih.gov/presentations/NIHInChI_2021-03/NIHInChI.html
InChI Markush and Variability Jonathan M. Goodman, Gerd Blanke, Istvan Ori & Anthony Baston Presentation given during NIH Virtual Workshop on InChI by Jonathan Goodman March 22, 2021. The direct link allows you to play this in full screen mode. This could be of use to organic chemistry education as […]
Tautomers in InChI NIH InChI Workshop, March 22, 2021 ? https://cactus.nci.nih.gov/presentations/NIHInChI_2021-03/Day_1_Nicklaus_Tautomerism_2021-03-21A.pdf Presentation by Marc C. Nicklaus Redesign of Handling of Tautomerism for InChI V2 IUPAC Project 2012-023-2-800
Tautomerizer – Predict tautomers based on 80+ rules https://cactus.nci.nih.gov/tautomerizer/ Introduction from Web Service (11/24/2022): Experimental service that allows you to test a set of tautomeric transforms with your own molecules. The predefined set of transforms comprises both the current 24 standard rules used by the chemoinformatics toolkit CACTVS and 55+ additional […]
Enumeration of Ring – Chain Tautomers Based on SMIRKS Rules Laura Guasch, Markus Sitzmann, and Marc C. Nicklaus https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4170818/ J Chem Inf Model. 2014 Sep 22; 54(9): 2423 – 2432. Abstract: A compound exhibits (prototropic) tautomerism if it can be represented by two or more structures that are related by […]
Tautomerism of Warfarin: Combined Chemoinformatics, Quantum Chemical, and NMR Investigation Laura Guasch, Megan L. Peach, and Marc C. Nicklaus https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7724503/ J Org Chem. 2015 Oct 16; 80(20): 9900-9909. Abstract: Warfarin, an important anticoagulant drug, can exist in solution in 40 distinct tautomeric forms through both prototropic tautomerism and ring chain […]
Experimental and Chemoinformatics Study of Tautomerism in a Database of Commercially Available Screening Samples Laura Guasch, Waruna Yapamudiyansel, Megan L. Peach, James A. Kelley, Joseph J. Barchi, Jr., and Marc C. Nicklaus https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5129033/ J Chem Inf Model. 2016 Nov 28; 56(11): 2149 – 2161. Abstract: We investigated how many cases […]
Tautomerism in large databases Markus Sitzmann, Wolf-Dietrich Ihlenfeldt, and Marc C. Nicklaus https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2886898/ Journal of Computer-Aided Molecular Design volume 24, pages 521-551 (2010) https://link.springer.com/article/10.1007/s10822-010-9346-4 Abstract: We have used the Chemical Structure DataBase (CSDB) of the NCI CADD Group, an aggregated collection of over 150 small-molecule databases totaling 103.5 million […]
Tautomer Database: A Comprehensive Resource for Tautomerism Analyses Devendra K. Dhaked, Laura Guasch, and Marc C. Nicklaus https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8456363/ Abstract: We report a database of tautomeric structures that contains 2819 tautomeric tuples extracted from 171 publications. Each tautomeric entry has been annotated with experimental conditions reported in the respective publication, […]
Toward a Comprehensive Treatment of Tautomerism in Chemoinformatics Including in InChI V2 Devendra K. Dhaked, Wolf-Dietrich Ihlenfeldt, Hitesh Patel, Victorien Delannée, and Marc C. Nicklaus* https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8459712/ Abstract: We have collected 86 different transforms of tautomeric interconversions. Out of those, 54 are for prototropic (non-ring–chain) tautomerism, 21 for ring–chain tautomerism, and 11 […]
Crowdsourced Evaluation of InChI-based Tautomer Identification precisionFDA Challenge https://precision.fda.gov/challenges/29 Challenge Time Period November 1, 2022 – March 1, 2023 This challenge focuses on the International Chemical Identifier (InChI), which was developed and is maintained under the auspices of the International Union of Pure and Applied Chemistry (IUPAC) and the InChI Trust. […]
Why is Isotopic Labeling Useful in Metabolomics? 2019-06-24 Metabolomics Workshop Introduction Slide Show
Isotope Enumerator Web GUI isoenum-webgui provides Flask-based web user interface that uses isoenum package to generate accurate InChI (International Chemical Identifier) for NMR metabolite features based on standard NMR experimental descriptions (currently 1D-1H and 1D-CHSQC) in order to improve data reusability of metabolomics data Andrey Smelter, Hunter N.B. Moseley Revision isoenum […]
Figshare repository of the InChI Isotopologue and Isotopomer Development Team lead by Hunter Moseley. Provides some definitions that could be of value to educators who wish to expound upon the nuances of isotopologues and isotopomers.
InChI: Measuring the Molecules 2020 AIS3D Summer seminar series presentation by Jonathan Goodman, University of Cambridge
Enhanced recognition and encoding of stereoconfiguration by InChI tools https://iupac.org/project/2019-017-2-800/ Chair: Andrey Yerin InChI tools are widely used as substance identifiers in various sources of chemical information. However, the current support of stereochemical information is limited to tetrahedral, double bond and short allene stereoisomerism. Among the unsupported stereo types are […]
Identifying International Chemical Identifier (InChI) Enhancements—QR Codes and Industry Applications IUPAC Project 2015-019-2-800 Chair: Richard M Hartshorn Objective: The International Chemical Identifier (InChI) is a text string that encodes chemical structure and provides a means to search databases for the structure. The InChI Trust <www.inchi-trust.org> is examining development of a […]
Implementation of InChI for chemically modified large biomolecules IUPAC Project 2013-010-1-800 Project chair: Evan Bolton & Keith T. Taylor Objective: To establish requirements and guidelines for the generation of a unique name for biological sequences including chemically modified. The intended outcome is the world-wide adoption of the a standard with […]
InChI’ng forward: Community Engagement in IUPAC’s Digital Chemical identifier Leah McEwen Chemistry International https://doi.org/10.1515/ci-2018-0109 Chemistry International overview of IUPAC projects related to InChI.
The RInChI Project The aim of the RInChI Project is to create a unique, canonical, text string to describe a reaction. Different researchers working on the same reaction should be able to generate the same RInChI without needing to confer with each other https://www-rinchi.ch.cam.ac.uk/ International chemical identifier for chemical reactions 8th German […]
How can the International Chemical Identifier (InChI) be extended to non-trivial chemicals? Slideshow uploaded to Figshare
CAPTURING MIXTURES ” BRINGING INFORMATICS TO THE WORLD OF PRACTICAL CHEMISTRY” Recorded live December 19, 2019 Hosted and presented by the Collaborative Drug Discovery (CDD) Vault Watch our webinar featuring Dr. Chris Jakober (Johns Hopkins), Leah McEwen (Cornell), and Dr. Alex Clark (CDD) to hear about our work toward new […]
PubChem chemical structure standardization Volker D. Hähnke, Sunghwan Kim & Evan E. Bolton Journal of Cheminformatics volume 10, Article number: 36 (2018) Background: PubChem is a chemical information repository, consisting of three primary databases: Substance, Compound, and BioAssay. When individual data contributors submit chemical substance descriptions to Substance, the unique […]
UniChem: a unified chemical structure cross-referencing and identifier tracking system Jon Chambers, Mark Davies, Anna Gaulton, Anne Hersey, Sameer Velankar, Robert Petryszak, Janna Hastings, Louisa Bellis, Shaun McGlinchey & John P Overington Journal of Cheminformatics volume 5, Article number: 3 (2013) Abstract: UniChem is a freely available compound identifier mapping […]
Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2 Hulda S Haraldsdóttir, Ines Thiele & Ronan MT Fleming Journal of Cheminformatics volume 6, Article number: 2 (2014) Abstract Background: An important step in the reconstruction of a metabolic network is annotation of metabolites. Metabolites are generally annotated […]
Consistency of systematic chemical identifiers within and between small-molecule databases Saber A Akhondi, Jan A Kors & Sorel Muresan Journal of Cheminformatics volume 4, Article number: 35 (2012) Abstract Background: Correctness of structures and associated metadata within public and commercial chemical databases greatly impacts drug discovery research activities such as […]
Enhancement of the chemical semantic web through the use of InChI identifiers Simon J. Coles,a Nick E. Day,b Peter Murray-Rust,b Henry S. Rzepac and Yong Zhang Org. Biomol. Chem., 2005,3, 1832-1834 Abstract: Molecules, as defined by connectivity specified via the International Chemical Identifier (InChI), are precisely indexed by major web search engines […]
Detection of IUPAC and IUPAC-like chemical names Roman Klinger, Corinna Kolá?ik, Juliane Fluck, Martin Hofmann-Apitius, Christoph M. Friedrich Bioinformatics, Volume 24, Issue 13, July 2008, Pages i268–i276, https://doi.org/10.1093/bioinformatics/btn181 Motivation: Chemical compounds like small signal molecules or other biological active chemical substances are an important entity class in life science publications and patents. Several representations and nomenclatures […]
Tautomer Identification and Tautomer Structure Generation Based on the InChI Code Torsten Thalheim, Armin Vollmer, Ralf-Uwe Ebert, Ralph Kühne, and Gerrit Schüürmann Abstract: An algorithm is introduced that enables a fast generation of all possible prototropic tautomers resulting from the mobile H atoms and associated heteroatoms as defined in the […]
How Many Miles Have We Gone, InChI by InChI? by Alex Tropsha and Antony Williams Chemistry International — Newsmagazine for IUPAC https://doi.org/10.1515/ci.2012.34.5.33
Abstract A modified InChI (International Chemical Identifier) string scheme, yaInChI (yet another InChI), is suggested as a method for including the structural information of a given molecule, making it straightforward and more easily readable. The yaInChI theme is applicable for checking the structural identity with higher sensitivity and generating three-dimensional […]
InChI: connecting and navigating chemistry Antony J Williams Journal of Cheminformatics volume 4, Article number: 33 (2012) Abstracrt: The International Chemical Identifier (InChI) has had a dramatic impact on providing a means by which to deduplicate, validate and link together chemical compounds and related information across databases. Its influence has […]
MMsDusty: an Alternative InChI-Based Tool to Minimize Chemical Redundancy Molecular Informatics, Volume32, Issue8, August 2013, Pages 681-684 Marco Fanton, Matteo Floris, Andrea Cristiani, Stefania Olla, Ricardo Medda, Davide Sabbadin, Alessandro Bulfone, Stefano Moro MMsDusty is an alternative web-oriented InChI-based normalization tool developed with the specific aim to efficiently analyze and remove chemical redundancy, […]
InChI in the wild: an assessment of InChIKey searching in Google Christopher Southan Journal of Cheminformatics 2013, 5:10 http://www.jcheminf.com/content/5/1/10 Abstract: While chemical databases can be queried using the InChI string and InChIKey (IK) the latter was designed for open-web searching. It is becoming increasingly effective for this since more sources […]
InChI, the IUPAC International Chemical Identifier Stephen R Heller1, Alan McNaught2, Igor Pletnev, Stephen Stein and Dmitrii Tchekhovskoi Heller et al. Journal of Cheminformatics (2015) 7:23 DOI 10.1186/s13321-015-0068-4 Abstract: This paper documents the design, layout and algorithms of the IUPAC International Chemical Identifier, InChI.
Webinar: Solving the issues in standardisation of stereochemical representations from Chemistry World on Vimeo. Sponsored by Bio-Rad Laboratories Abstract: Learn about technology that solves the issue of interpreting 3D stereochemical information implied in 2D structure representations.
Abstract The HIV structural database (HIVSDB) is a comprehensive collection of the structures of HIV protease, both of unliganded enzyme and of its inhibitor complexes. It contains abstracts and crystallographic data such as inhibitor and protein coordinates for 248 data sets, of which only 141 are from the Protein Data […]
Additive InChI-based optimal descriptors: QSPR modeling of fullerene C 60 solubility in organic solvents Journal of Mathematical Chemistry volume 46, pages1232–1251 (2009) Abstract: Optimal descriptors calculated with International Chemical Identifier (InChI) have been used to construct one-variable model of the solubility of fullerene C 60 in organic solvents . Attempts to calculate the model for three splits into […]
Isotopic (iso) enumerator (enum) – enumerates isotopically resolved InChI (International Chemical Identifier) for metabolites. The isoenum Python package provides command-line interface that allows you to enumerate the possible isotopically-resolved InChI from one of the Chemical Table file (CTfile) formats (i.e. molfile, SDfile) used to describe chemical molecules and reactions as […]