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Progress towards “Large Molecule” support with InChI Evan Bolton,Ph.D. NCI NIH Virtual Workshop on InChI 2021-03-22 Direct Link (Alows you to activate “Full Screen mode” and open as a single slide show)  

PubChem: Advancing chemical information through InChI Evan Bolton InChI in the Wild: Celebrating Over 20 years of InChI Development in Memory of InChI Developer Igor PletnevFall 2022 ACS National Meeting2022-08-21 Abstract: The PubChem project (https://pubchem.ncbi.nlm.nih.gov) has been a long time user and contributor to the InChI project. The impact of the InChI project on chemical information and chemical informatics cannot […]

Mixtures InChI: A story of how stadards drive upstream products Alex M. Clark & Leah R. McEwen NCI Virtual Workshop on international Chemical Identifiers, March 22, 2021   Video Presentation Presentation  

Mixtures as first class citizens in the realms of informatics Alex M. Clark, Collaborative Drug Discovery Cambridge Cheminformatics Network Meeting February 10, 2021   YouTube recording (starts at 1:06) Slideshare Slides

Mixtures: Informatics for formulations and consumer products Leah R. McEwen &  Alex M. Clark Presentation to the Royal Society of Chemistry Formulation 4.1 https://www.formulation.org.uk/f4p1programme/253-past/2020/form4p1/783-form4p1-clark.html (Video)   Slides: https://www.slideshare.net/aclarkxyz/mixtures-informatics-for-formulations-and-consumer-products

Capturing Mixtures — Bringing Informatics to the World of Practical Chemistry Recorded live December 19, 2019 CDD Bault Webinar https://www.collaborativedrug.com/recorded-cdd-webinar-capturing-mixtures-bringing-informatics-world-practical-chemistry/ Chris Jakober, Leah McEwen and Alex Clark Slides and Video Available at CDD VAULT   Webinar Summary Our industry has been using cheminformatics to support drug discovery for decades, leveraging formats for describing organic molecules, […]

The RInChI Project https://www-rinchi.ch.cam.ac.uk/ https://www-rinchi.ch.cam.ac.uk/rinchi.php   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

International chemical identifier for reactions (RInChI) Guenter Grethe, Gerd Blanke, Hans Kraut & Jonathan M. Goodman Journal of Cheminformatics volume 10, Article number: 22 (2018) May 9, 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 RInChI have been available since 2011. The […]

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, István Öri & Anthony Baston PDF of Presentation given during NIH Virtual Workshop on InChI, March 22, 2021

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 rules compiled in the context of […]

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 a formal intramolecular movement of a hydrogen atom from […]

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 tautomerism. We have investigated all warfarin […]

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 of the same chemical sold as different products […]

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, pages521–551 (2010) https://link.springer.com/article/10.1007/s10822-010-9346-4#Ack1   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 structure records, to conduct tautomerism analyses on one of […]

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, plus bibliographic details, structural identifiers […]

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 for valence tautomerism. The majority […]

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. The InChI Trust, the IUPAC […]

InChI Isotopologue and Isotopomer Proposal Figshare deposit of a draft 2018 proposal and acompanying slide show that resulted in an InChI Trust working group on isotopologues.  

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 isoenum @ GitHub isoenum @ PyPI isoenum @ ReadTheDocs

Isotope Enumerator 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 well as from […]

Andrew P. Cornell, Robert E. Belford Chemistry Department, University of Arkansas at Little Rock, Little Rock, Arkansas 72204   Abstract Many individual chemicals have a specific page on Wikipedia that will give information about the use, manufacture and properties of that chemical. The properties that are displayed off to the side include the relevant chemical […]

Andrew P. Cornell, Robert E. Belford Chemistry Department, University of Arkansas at Little Rock, Little Rock, Arkansas 72204   Abstract In this tutorial, a program written in Python will take a user specified chemical name and retrieve the associated chemical identifier or basic property using an online chemical database. This program can be used as […]

Abstract 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 chemical structures are extracted and stored into Compound through an automated process called structure standardization. The present study describes the PubChem standardization approaches and analyzes them […]

Abstract Background: Over the past several centuries, chemistry has permeated virtually every facet of human lifestyle, enriching fields as diverse as medicine, agriculture, manufacturing, warfare, and electronics, among numerous others. Unfortunately, application-specific, incompatible chemical information formats and representation strategies have emerged as a result of such diverse adoption of chemistry. Although a number of efforts […]