{"title":"Tautomeric Conflicts in Forty Small-Molecule Databases.","authors":"Devendra K Dhaked, Marc C Nicklaus","doi":"10.1021/acs.jcim.4c00700","DOIUrl":null,"url":null,"abstract":"<p><p>We have analyzed 40 different databases ranging in size from a few thousand to nearly 100 million molecules, comprising a total of over 210 million structures, for their tautomeric conflicts. A tautomeric conflict is defined as an occurrence of two or more structures within a data set identified by the tautomeric rules applied as being tautomers of each other. We tested a total of 119 detailed tautomeric transform rules expressed as SMIRKS, out of which 79 yielded at least one conflict. These transformations include three types of tautomerism: prototropic, ring-chain, and valence tautomerism. The databases analyzed spanned a wide variety of types including large aggregating databases, drug collections, and structure collections based on experimental data. All databases analyzed showed intra-database tautomeric conflicts. The conflict rates as percentage of the database were typically in the few tenths of a percent range, which for the largest databases amounts to >100,000 cases per database.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":null,"pages":null},"PeriodicalIF":5.6000,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chemical Information and Modeling ","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1021/acs.jcim.4c00700","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, MEDICINAL","Score":null,"Total":0}
引用次数: 0
Abstract
We have analyzed 40 different databases ranging in size from a few thousand to nearly 100 million molecules, comprising a total of over 210 million structures, for their tautomeric conflicts. A tautomeric conflict is defined as an occurrence of two or more structures within a data set identified by the tautomeric rules applied as being tautomers of each other. We tested a total of 119 detailed tautomeric transform rules expressed as SMIRKS, out of which 79 yielded at least one conflict. These transformations include three types of tautomerism: prototropic, ring-chain, and valence tautomerism. The databases analyzed spanned a wide variety of types including large aggregating databases, drug collections, and structure collections based on experimental data. All databases analyzed showed intra-database tautomeric conflicts. The conflict rates as percentage of the database were typically in the few tenths of a percent range, which for the largest databases amounts to >100,000 cases per database.
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The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery.
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