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 […]
Abstract 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 been especially valuable as the internet has exploded in terms of the amount of chemistry related information available online. This thematic issue […]
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 enhance crawling of their websites by the Googlebot and consequent IK indexing. Searchers who use Google as an adjunct to database access may be […]
Abstract UniChem is a low-maintenance, fast and freely available compound identifier mapping service, recently made available on the Internet. Until now, the criterion of molecular equivalence within UniChem has been on the basis of complete identity between Standard InChIs. However, a limitation of this approach is that stereoisomers, isotopes and salts of otherwise identical molecules […]
Abstract Background: There are many databases of small molecules focused on different aspects of research and its applications. Some tasks may require integration of information from various databases. However, determining which entries from different databases represent the same compound is not straightforward. Integration can be based, for example, on automatically generated cross-reference links between entries. […]
Abstract IUPAC Standards Online is a database built from IUPAC’s (The International Union of Pure and Applied Chemistry) standards and recommendations, which are extracted from the journal Pure and Applied Chemistry (PAC). The International Union of Pure and Applied Chemistry (IUPAC) is the organization responsible for setting the standards in chemistry that are internationally binding […]
Abstract Background The InChI algorithms are written in C++ and not available as Java library. Integration into software written in Java therefore requires a bridge between C and Java libraries, provided by the Java Native Interface (JNI) technology. Results We here describe how the InChI library is used in the Bioclipse workbench and the Chemistry […]
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 Bank (PDB). Efficient annotation, indexing, […]
Abstract Optimal descriptors calculated with International Chemical Identifier (InChI) have been used to construct one-variable model of the solubility of fullerene C60 in organic solvents . Attempts to calculate the model for three splits into training and test sets gave stable results.
This presentation is a part of Google Tech Talks which was added to the GoogleTalksArchive on August 22, 2006. The original presentation date took place on November 2, 2006. ABSTRACT (Imported From YouTube Source) The central token of information in Chemistry is a chemical substance, an entity that can often be represented as a well-defined […]
Capturing mixture composition: an open machine-readable format for representing mixed substances Alex M. Clark, Leah R. McEwen, Peter Gedeck & Barry A. Bunin Journal of Cheminformatics volume 11, Article number: 33 (2019) Abstract: We describe a file format that is designed to represent mixtures of compounds in a way that is fully machine readable. This […]
This RDKit InChI Calculation with Jupyter Notebook tutorial is useful to teach the basics of how to interact with InChI using a cheminformatics toolkit in a Jupyter Notebook. The notebook has the following learning objectives: Setup RDKit with a Jupyter Notebook Construct a molecule (RDKit molecular object) from a SMILES string Display molecule images Calculate […]
Web and high-resolution formats of an InChI infographic. Nov 2018 [pdf-embedder url=”https://www.inchi-trust.org/wp/wp-content/uploads/2018/11/Web_A55856_InChi-trust_infographic.pdf”] HRM_A55856_InChi-trust_infographic Web_A55856_InChi-trust_infographic HR_A55856_InChi-trust_infographic
This is a collection of Matlab scripts for working with InChIKeys: IKextract, IKfreqFH, IKstring, and IKmusic IKextract, InChIKey Extract, can extract InChIKeys from chemical Structure data files (SDFs). This script was successfully used to extract over 90 million InChIKeys (unique chemical identifiers) from over 5000 PubChem SD files. Users can also extract other data from SDFs […]