![]() Carbohydrates (in Haworth and other representations).Natural product structures (steroids, alkaloids, terpenes, and carotenes).Various functional groups, including acids, alcohols, aldehydes, ketones, ethers, peroxides, salts, and more.Generate names for organic, biochemical, inorganic, and organometallic structures, including:.Produce Index names in accordance with CAS nomenclature rules*.Generate accurate systematic names according to IUPAC recommendations.See the full list of supported data formats Although the initial proof of concept succeeds relatively well in assigning structures to arbitrary names and CAS Numbers, the underlying approach could be adapted to expose a number of other interesting cheminformatics services.Buy or Trial Select Software Browse Productsĭraw, copy/paste, or import molecular structures in various formats (including ChemDraw, MOL files, and SMILES) ConclusionsĬhemCell is a very small piece of software that exposes cheminformatics Web services through the familiar and ubiquitous interface of Microsoft Excel. The core system could be used for a number of purposes, including: generation of Standard InChI Key (currently supoported) returning structure images calculating logP, finding molecular weight, assigning IUPAC Name and a number of other capabilities.Īs more cheminformatics Web services like CSLS start to pop up, they could be integrated through Excel by making some very simple changes to the ChemCell code. Just the BeginningĬonverting names and CAS numbers to structures is but one possible use of the underlying ChemCell software. In other words, agreement between ChEBI and CSLS in terms of molecular atom connectivity was high. Most mismatches were due to unassigned stereochemistry in CSLS that was assigned in ChEBI. Rate of recall was found to be 70% (structures found) with 76% accuracy (exact matches). LimitationsĬhemCell's recall and accuracy were tested against a random sample of 1,000 name/structure pairings found in the ChEBI 3-star dataset. By invoking the getSMILES function, your spreadsheet is calling CSLS and parsing the result.Īlthough it's possible to use PubChem to perform one-off structure lookup based on CAS Number and/or name, the CSLS Web API is implemented in such a way so as to easily enable the exposure of this functionality through Excel. How it WorksĬhemCell uses Chemical Structure Lookup Service (CSLS), a web service created for the purpose of providing structural information based on chemical names. GetSMILES works just like any other Excel formula: it can be pasted down every row in a column, the resulting values can be sorted, and other calculations can be based off of it. To generate a SMILES string for a name contained in cell A4, click in any empty table cell and use this formula: =getSMILES(A4) A poster I gave at the 4th annual Collaborative Drug Discovery (CDD) Community Meeting describes ChemCell in more detail:Īfter downloading ChemCell, extract the archive, double-click on the file chemcell.xls, then open your spreadsheet containing trivial names, IUPAC names, or CAS Numbers. ChemCellĬhemCell is a macro that enables Microsoft Excel to convert columns of chemical names and CAS Numbers into SMILES strings. But what if there were an inexpensive, quick alternative? This article discusses one solution. Given the task of doing so for hundreds of structures, many organizations resort to manual data entry. Whether for the purpose of performing substructure search, generating structure images, clustering, or assigning molecular weight, generating chemical structures from common names and CAS Numbers can be a major problem. But as more and more expectations get placed on these ad hoc datasets, a point inevitably comes when the assignment of chemical structures becomes necessary. Note: the same functionality described in this article is now available on Google Spreadsheets.Ĭhemical databases often start as a list of names or Chemical Abstracts Service (CAS) Registry numbers contained in an Excel spreadsheet. ChemCell - Easily Convert Names and CAS Numbers to Chemical Structures in Excel
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