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Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies? Nanomaterials 2020, 10(12), 2493; https://doi.org/10.3390/nano10122493 by Iseult Lynch, Antreas Afantitis, Thomas Exner, Martin Himly, Vladimir Lobaskin, Philip Doganis, Dieter Maier, Natasha Sanabria, Anastasios G. Papadiamantis, Anna Rybinska-Fryca, Maciej Gromelski, Tomasz Puzyn, Egon Willighagen, Blair D. Johnston, Mary Gulumian, […]

A possible extension to the RInChI as a means of providing machine readable process data Philipp-Maximilian Jacob, Tian Lan, Jonathan M. Goodman & Alexei A. Lapkin Journal of Cheminformatics volume 9, Article number: 23 (2017) Abstract: The algorithmic, large-scale use and analysis of reaction databases such as Reaxys is currently hindered by the absence of […]

Analysing a billion reactions with the RInChI Jonathan M. Goodman, Gerd Blanke and Hans Kraut From the journal Pure and Applied Chemistry Abstract: The RInChI is a canonical identifier for reactions which is widely used in reaction databases. It can be used to handle large collections of reactions and to link information from diverse data […]

International chemical identifier for reactions (RInChI) Guenter Grethe, Jonathan M Goodman & Chad HG Allen Journal of Cheminformatics volume 5, Article number: 45 (2013) Abstract: The IUPAC International Chemical Identifier (InChI) provides a method to generate a unique text descriptor of molecular structures. Building on this work, we report a process to generate a unique […]

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 […]

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 […]

Abstract Background: The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and […]

Abstract UniChem is a freely available compound identifier mapping service on the internet, designed to optimize the efficiency with which structure-based hyperlinks may be built and maintained between chemistry-based resources. In the past, the creation and maintenance of such links at EMBL-EBI, where several chemistry-based resources exist, has required independent efforts by each of the […]

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 frst ofcial release (RInChIV1.00), funded by the InChI Trust, is now available for download (https://www.inchi-trust.org/wp/downloads/). This release defnes the format and generates hashed […]

Abstract Background: An important step in the reconstruction of a metabolic network is annotation of metabolites. Metabolites are generally annotated with various database or structure based identifiers. Metabolite annotations in metabolic reconstructions may be incorrect or incomplete and thus need to be updated prior to their use. Genome-scale metabolic reconstructions generally include hundreds of metabolites. […]

Abstract Background: Correctness of structures and associated metadata within public and commercial chemical databases greatly impacts drug discovery research activities such as quantitative structure–property relationships modelling and compound novelty checking. MOL files, SMILES notations, IUPAC names, and InChI strings are ubiquitous file formats and systematic identifiers for chemical structures. While interchangeable for many cheminformatics purposes […]

Abstract Background: There are two line notations of chemical structures that have established themselves in the field: the SMILES string and the InChI string. The InChI aims to provide a unique, or canonical, identifier for chemical structures, while SMILES strings are widely used for storage and interchange of chemical structures, but no standard exists to […]