{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T03:34:18Z","timestamp":1767843258567,"version":"3.49.0"},"reference-count":35,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2018,4,21]],"date-time":"2018-04-21T00:00:00Z","timestamp":1524268800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Data"],"abstract":"<jats:p>Presently, software tools for retrosynthetic analysis are widely used by organic, medicinal, and computational chemists. Rule-based systems extensively use collections of retro-reactions (transforms). While there are many public datasets with reactions in synthetic direction (usually non-generic reactions), there are no publicly-available databases with generic reactions in computer-readable format which can be used for the purposes of retrosynthetic analysis. Here we present RetroTransformDB\u2014a dataset of transforms, compiled and coded in SMIRKS line notation by us. The collection is comprised of more than 100 records, with each one including the reaction name, SMIRKS linear notation, the functional group to be obtained, and the transform type classification. All SMIRKS transforms were tested syntactically, semantically, and from a chemical point of view in different software platforms. The overall dataset design and the retrosynthetic fitness were analyzed and curated by organic chemistry experts. The RetroTransformDB dataset may be used by open-source and commercial software packages, as well as chemoinformatics tools.<\/jats:p>","DOI":"10.3390\/data3020014","type":"journal-article","created":{"date-parts":[[2018,4,24]],"date-time":"2018-04-24T04:44:48Z","timestamp":1524545088000},"page":"14","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["RetroTransformDB: A Dataset of Generic Transforms for Retrosynthetic Analysis"],"prefix":"10.3390","volume":"3","author":[{"given":"Svetlana","family":"Avramova","sequence":"first","affiliation":[{"name":"Faculty of Chemistry, University of Plovidv \u201cP. Hilendarski\u201d, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria"}]},{"given":"Nikolay","family":"Kochev","sequence":"additional","affiliation":[{"name":"Faculty of Chemistry, University of Plovidv \u201cP. Hilendarski\u201d, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3625-9933","authenticated-orcid":false,"given":"Plamen","family":"Angelov","sequence":"additional","affiliation":[{"name":"Faculty of Chemistry, University of Plovidv \u201cP. Hilendarski\u201d, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria"}]}],"member":"1968","published-online":{"date-parts":[[2018,4,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1127","DOI":"10.1070\/RCR4746","article-title":"Artificial intelligence in synthetic chemistry: Achievements and prospects","volume":"86","author":"Baskin","year":"2017","journal-title":"Russ. Chem. Rev."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1021\/acscentsci.7b00303","article-title":"Retrosynthetic Reaction Prediction Using Neural Sequence-to-Sequence Models","volume":"3","author":"Liu","year":"2017","journal-title":"ACS Cent. Sci."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"5966","DOI":"10.1002\/chem.201605499","article-title":"Neural-Symbolic Machine Learning for Retrosynthesis and Reaction Prediction","volume":"23","author":"Segler","year":"2017","journal-title":"Chem. A Eur. J."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1021\/ci800228y","article-title":"Route Designer: A retrosynthetic analysis tool utilizing automated retrosynthetic rule generation","volume":"49","author":"Law","year":"2009","journal-title":"J. Chem. Inf. Model."},{"key":"ref_5","unstructured":"(2018, February 02). CMBI\u2014LHASA. Available online: http:\/\/cheminf.cmbi.ru.nl\/cheminf\/olp\/history.shtml."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Wipke, W.T., Braun, H., Smith, G., Choplin, F., and Sieber, W. (1977). SECS-Simulation and Evaluation of Chemical Synthesis: Strategy and Planning. Computer-Assisted Organic Synthesis, ACS Publications.","DOI":"10.1021\/bk-1977-0061.ch005"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1021\/ci970115v","article-title":"Distributed heuristic synthesis search","volume":"38","author":"Krebsbach","year":"1998","journal-title":"J. Chem. Inf. Comput. Sci."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1021\/ci9004332","article-title":"Construction of Functional Group Reactivity Database under Various Reaction Conditions Automatically Extracted from Reaction Database in a Synthesis Design System","volume":"50","author":"Tanaka","year":"2010","journal-title":"J. Chem. Inf. Model."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2768","DOI":"10.1021\/ci100216g","article-title":"RASA: A rapid retrosynthesis-based scoring method for the assessment of synthetic accessibility of drug-like molecules","volume":"51","author":"Huang","year":"2011","journal-title":"J. Chem. Inf. Model."},{"key":"ref_10","first-page":"316","article-title":"A Novel Approach to Retrosynthetic Analysis Using Knowledge Bases Derived from Reaction Databases","volume":"39","author":"Satoh","year":"1999","journal-title":"J. Chem. Inf. Model."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"2034","DOI":"10.1021\/ci900157k","article-title":"No Electron Left Behind: A Rule-Based Expert System To Predict Chemical Reactions and Reaction Mechanisms","volume":"49","author":"Chen","year":"2009","journal-title":"J. Chem. Inf. Model."},{"key":"ref_12","unstructured":"(2018, February 11). Elsevier, Reaxys Syntheis Planner. Available online: https:\/\/www.elsevier.com\/solutions\/reaxys\/how-reaxys-works\/synthesis-planner."},{"key":"ref_13","unstructured":"(2018, January 14). Reactions\u2014CASREACT. Available online: http:\/\/support.cas.org\/content\/reactions."},{"key":"ref_14","unstructured":"(2018, January 14). InfoChem\u2014SPRESI\u2014Storage and Retrieval of Chemical Structure and Reaction Information. Available online: http:\/\/www.infochem.de\/products\/databases\/spresi.shtml."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1296","DOI":"10.1021\/ci020023s","article-title":"Over 20 Years of Reaction Access Systems from MDL: A Novel Reaction Substructure Search Algorithm","volume":"42","author":"Chen","year":"2002","journal-title":"J. Chem. Inf. Comput. Sci."},{"key":"ref_16","unstructured":"(2018, April 12). Daniel Lowe, Chemical Reactions from US Patents (1976\u2013Sep 2016). Available online: https:\/\/figshare.com\/articles\/Chemical_reactions_from_US_patents_1976-Sep2016_\/5104873."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1021\/ml2000609","article-title":"Chemical Transformations That Yield Compounds with Distinct Activity Profiles","volume":"2","author":"Hu","year":"2011","journal-title":"ACS Med. Chem. Lett."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1002\/minf.201600092","article-title":"Hierarchical Analysis of Bioactive Matched Molecular Pairs, Encoded Chemical Transformations, and Associated Substructures","volume":"35","author":"Hu","year":"2016","journal-title":"Mol. Inform."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1002\/wcms.1140","article-title":"Automatic reaction mapping and reaction center detection","volume":"3","author":"Chen","year":"2013","journal-title":"Wiley Interdiscip. Rev. Comput. Mol. Sci."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"5904","DOI":"10.1002\/anie.201506101","article-title":"Computer-Assisted Synthetic Planning: The End of the Beginning","volume":"55","author":"Gajewska","year":"2016","journal-title":"Angew. Chem. Int. Ed."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1016\/j.chempr.2018.02.002","article-title":"Efficient Syntheses of Diverse, Medicinally Relevant Targets Planned by Computer and Executed in the Laboratory","volume":"4","author":"Klucznik","year":"2018","journal-title":"Chem"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"3093","DOI":"10.1021\/ci200379p","article-title":"A Collection of Robust Organic Synthesis Reactions for In Silico Molecule Design","volume":"51","author":"Hartenfeller","year":"2011","journal-title":"J. Chem. Inf. Model."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Hartenfeller, M., Zettl, H., Walter, M., Rupp, M., Reisen, F., Proschak, E., Weggen, S., Stark, H., and Schneider, G. (2012). Dogs: Reaction-driven de novo design of bioactive compounds. PLoS Comput. Biol., 8.","DOI":"10.1371\/journal.pcbi.1002380"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1021\/acs.jcim.5b00697","article-title":"Multistep Reaction Based de Novo Drug Design: Generating Synthetically Feasible Design Ideas","volume":"56","author":"Masek","year":"2016","journal-title":"J. Chem. Inf. Model."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1021\/ci0496853","article-title":"Prospective exploration of synthetically feasible, medicinally relevant chemical space","volume":"45","author":"Tyagi","year":"2005","journal-title":"J. Chem. Inf. Model."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1351\/pac198961040725","article-title":"Nomenclature for organic chemical transformations (Recommendations 1988)","volume":"61","author":"Jones","year":"1989","journal-title":"Pure Appl. Chem."},{"key":"ref_27","unstructured":"Corey, E.J. (1989). The Logic of Chemical Synthesis, John Wiley & Sons."},{"key":"ref_28","unstructured":"Jeliazkova, N., Kochev, N., and Jeliazkov, V. (2017, December 19). ambitcli-3.0.2. Available online: https:\/\/zenodo.org\/record\/173560#.WjlcRyvfHVq."},{"key":"ref_29","unstructured":"(2017, December 19). Ideaconsult Ltd., AMBIT. Available online: http:\/\/ambit.sourceforge.net\/."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/1758-2946-3-18","article-title":"AMBIT RESTful web services: An implementation of the OpenTox application programming interface","volume":"3","author":"Jeliazkova","year":"2011","journal-title":"J. Cheminform."},{"key":"ref_31","unstructured":"(2017, December 20). Daylight, SMIRKS: A Reaction Transform Language. Available online: http:\/\/www.daylight.com\/dayhtml\/doc\/theory\/theory.smirks.html."},{"key":"ref_32","unstructured":"(2017, September 20). Daylight, Reaction Toolkit. Available online: http:\/\/www.daylight.com\/products\/reaction_kit.html."},{"key":"ref_33","unstructured":"(2017, September 19). Daylight, SMARTS: A Language for Describing Molecular Patterns. Available online: http:\/\/www.daylight.com\/dayhtml\/doc\/theory\/theory.smarts.html."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Angelo, J.D., and Smith, M.B. (2015). Hybrid Retrosynthesis, Elsevier.","DOI":"10.1016\/B978-0-12-411498-2.00004-8"},{"key":"ref_35","unstructured":"Ideaconsult Ltd. (2018, April 20). Ambit-SMIRKS. Available online: http:\/\/ambit.sourceforge.net\/smirks.html."}],"container-title":["Data"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2306-5729\/3\/2\/14\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T15:01:38Z","timestamp":1760194898000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2306-5729\/3\/2\/14"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,4,21]]},"references-count":35,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2018,6]]}},"alternative-id":["data3020014"],"URL":"https:\/\/doi.org\/10.3390\/data3020014","relation":{},"ISSN":["2306-5729"],"issn-type":[{"value":"2306-5729","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,4,21]]}}}