{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T12:28:03Z","timestamp":1675254483495},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1568,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The MolClass toolkit and data portal generate computational models from user-defined small molecule datasets based on structural features identified in hit and non-hit molecules in different screens. Each new model is applied to all datasets in the database to classify compound specificity. MolClass thus defines a likelihood value for each compound entry and creates an activity fingerprint across diverse sets of screens. MolClass uses a variety of machine-learning methods to find molecular patterns and can therefore also assign a priori predictions of bioactivities for previously untested molecules. The power of the MolClass resource will grow as a function of the number of screens deposited in the database.<\/jats:p>\n               <jats:p>Availability and implementation: The MolClass webportal, software package and source code are freely available for non-commercial use at http:\/\/tyerslab.bio.ed.ac.uk\/molclass. A MolClass tutorial and a guide on how to build models from datasets can also be found on the web site. MolClass uses the chemistry development kit (CDK), WEKA and MySQL for its core functionality. A REST service is available at http:\/\/tyerslab.bio.ed.ac.uk\/molclass\/api based on the OpenTox API 1.2.<\/jats:p>\n               <jats:p>Contact: \u00a0jan.wildenhain@ed.ac.uk or md.tyers@umontreal.ca<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts349","type":"journal-article","created":{"date-parts":[[2012,6,19]],"date-time":"2012-06-19T00:19:39Z","timestamp":1340065179000},"page":"2200-2201","source":"Crossref","is-referenced-by-count":8,"title":["MolClass: a web portal to interrogate diverse small molecule screen datasets with different computational models"],"prefix":"10.1093","volume":"28","author":[{"given":"Jan","family":"Wildenhain","sequence":"first","affiliation":[{"name":"1, \u00a01Wellcome Trust Centre for Cell Biology and School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, UK, 2Department of Computer Science and Engineering, University of Washington, Seattle, WA 98122, USA and 3Institute for Research in Immunology and Cancer, Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada H3T 1J4"}]},{"given":"Nicholas","family":"FitzGerald","sequence":"additional","affiliation":[{"name":"1, \u00a01Wellcome Trust Centre for Cell Biology and School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, UK, 2Department of Computer Science and Engineering, University of Washington, Seattle, WA 98122, USA and 3Institute for Research in Immunology and Cancer, Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada H3T 1J4"}]},{"given":"Mike","family":"Tyers","sequence":"additional","affiliation":[{"name":"1, \u00a01Wellcome Trust Centre for Cell Biology and School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, UK, 2Department of Computer Science and Engineering, University of Washington, Seattle, WA 98122, USA and 3Institute for Research in Immunology and Cancer, Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada H3T 1J4"}]}],"member":"286","published-online":{"date-parts":[[2012,6,17]]},"reference":[{"key":"2023012512560495400_B1","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1038\/nchembio.380","article-title":"A predictive model for drug bioaccumulation and bioactivity in Caenorhabditis elegans","volume":"6","author":"Burns","year":"2010","journal-title":"Nat. Chem. Biol."},{"key":"2023012512560495400_B2","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1038\/nchembio873","article-title":"Chemical genetics reveals a complex functional ground state of neural stem cells","volume":"3","author":"Diamandis","year":"2007","journal-title":"Nat. Chem. Biol."},{"key":"2023012512560495400_B3","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1038\/nature03192","article-title":"Chemical space and biology","volume":"432","author":"Dobson","year":"2004","journal-title":"Nature"},{"key":"2023012512560495400_B4","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1145\/1656274.1656278","article-title":"The WEKA data mining software: an update","volume":"11","author":"Hall","year":"2009","journal-title":"SIGKDD Explorations"},{"key":"2023012512560495400_B5","doi-asserted-by":"crossref","first-page":"5079","DOI":"10.3390\/molecules15085079","article-title":"Functionality pattern matching as an efficient complemntary structure\/reaction search tool: an open-source approach","volume":"15","author":"Haider","year":"2010","journal-title":"Molecules"},{"issue":"9","key":"2023012512560495400_B6","doi-asserted-by":"crossref","first-page":"2077","DOI":"10.1021\/ci900161g","article-title":"Benchmark data set for in silico prediction of Ames mutagenicity","volume":"49","author":"Hansen","year":"2009","journal-title":"J. Chem. Inf. Model."},{"key":"2023012512560495400_B7","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1038\/nchembio.118","article-title":"Network pharmacology: the next paradigm in drug discovery","volume":"4","author":"Hopkins","year":"2008","journal-title":"Nat. Chem. Biol."},{"key":"2023012512560495400_B8","doi-asserted-by":"crossref","first-page":"1585","DOI":"10.1021\/ci049884m","article-title":"ADME evaluation in drug discovery. 5. Correlation of Caco-2 permeation with simple molecular properties","volume":"44","author":"Hou","year":"2004","journal-title":"J. Chem. Inf. Comput. Sci."},{"key":"2023012512560495400_B9","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1021\/jm040835a","article-title":"Derivation and validation of toxicophores for mutagenicity prediction","volume":"48","author":"Kazius","year":"2005","journal-title":"J. Med. Chem."},{"key":"2023012512560495400_B10","doi-asserted-by":"crossref","first-page":"1376","DOI":"10.1021\/ci050135u","article-title":"Effect of selection of molecular descriptors on the prediction of blood\u2013brain barrier penetrating and nonpenetrating agents by statistical learning methods","volume":"45","author":"Li","year":"2005","journal-title":"J. Chem. Inf. Model."},{"key":"2023012512560495400_B11","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1613\/jair.953","article-title":"SMOTE: synthetic minority over-sampling technique","volume":"16","author":"Nitesh","year":"2002","journal-title":"J. Artif. Intell. Res."},{"key":"2023012512560495400_B12","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/msb.2011.31","article-title":"Cross-species discovery of syncretic drug combinations that potentiate the antifungal flucanozole","volume":"7","author":"Spitzer","year":"2011","journal-title":"Mol. Syst. Biol."},{"key":"2023012512560495400_B13","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1021\/ci025584y","article-title":"The Chemistry Development Kit (CDK): an open-source java library for chemo- and bioinformatics","volume":"43","author":"Steinbeck","year":"2003","journal-title":"J. Chem. Inf. Comput. Sci."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/16\/2200\/48871762\/bioinformatics_28_16_2200.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/16\/2200\/48871762\/bioinformatics_28_16_2200.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T18:13:38Z","timestamp":1674670418000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/16\/2200\/324662"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,6,17]]},"references-count":13,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2012,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts349","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,8,15]]},"published":{"date-parts":[[2012,6,17]]}}}