{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,30]],"date-time":"2026-04-30T23:27:51Z","timestamp":1777591671927,"version":"3.51.4"},"reference-count":69,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2015,3,31]],"date-time":"2015-03-31T00:00:00Z","timestamp":1427760000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1004153","type":"journal-article","created":{"date-parts":[[2015,4,1]],"date-time":"2015-04-01T17:30:46Z","timestamp":1427909446000},"page":"e1004153","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":70,"title":["Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens"],"prefix":"10.1371","volume":"11","author":[{"given":"Yu-Chen","family":"Lo","sequence":"first","affiliation":[]},{"given":"Silvia","family":"Senese","sequence":"additional","affiliation":[]},{"given":"Chien-Ming","family":"Li","sequence":"additional","affiliation":[]},{"given":"Qiyang","family":"Hu","sequence":"additional","affiliation":[]},{"given":"Yong","family":"Huang","sequence":"additional","affiliation":[]},{"given":"Robert","family":"Damoiseaux","sequence":"additional","affiliation":[]},{"given":"Jorge Z.","family":"Torres","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2015,3,31]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1038\/nrd2410","article-title":"Target deconvolution strategies in drug discovery","volume":"6","author":"GC Terstappen","year":"2007","journal-title":"Nat Rev Drug Discov"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1038\/nchembio.1199","article-title":"Target identification and mechanism of action in chemical biology and drug discovery","volume":"9","author":"M Schenone","year":"2013","journal-title":"Nat Chem Biol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1039\/c2mb25468a","article-title":"Target identification of small molecules based on chemical biology approaches","volume":"9","author":"Y Futamura","year":"2013","journal-title":"Mol Biosyst"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1038\/nchembio.216","article-title":"Target profiling of small molecules by chemical proteomics","volume":"5","author":"U Rix","year":"2009","journal-title":"Nat Chem Biol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1021\/cb100294v","article-title":"Identification of direct protein targets of small molecules","volume":"6","author":"B Lomenick","year":"2011","journal-title":"ACS Chem Biol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1038\/nbt1284","article-title":"Relating protein pharmacology by ligand chemistry","volume":"25","author":"MJ Keiser","year":"2007","journal-title":"Nat Biotechnol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"W55","DOI":"10.1093\/nar\/gkn307","article-title":"SuperPred: drug classification and target prediction","volume":"36","author":"M Dunkel","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1208\/s12248-012-9449-z","article-title":"TargetHunter: an in silico target identification tool for predicting therapeutic potential of small organic molecules based on chemogenomic database","volume":"15","author":"L Wang","year":"2013","journal-title":"AAPS J"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1827","DOI":"10.1093\/bioinformatics\/btt270","article-title":"ChemMapper: a versatile web server for exploring pharmacology and chemical structure association based on molecular 3D similarity method","volume":"29","author":"J Gong","year":"2013","journal-title":"Bioinformatics"},{"key":"ref10","doi-asserted-by":"crossref","unstructured":"Cereto-Massague A, Ojeda MJ, Valls C, Mulero M, Pujadas G, et al. (2014) Tools for in silico target fishing. Methods.","DOI":"10.1016\/j.ymeth.2014.09.006"},{"key":"ref11","volume":"xix","author":"MA Johnson","year":"1990"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"3186","DOI":"10.1021\/jm401411z","article-title":"Molecular similarity in medicinal chemistry","volume":"57","author":"G Maggiora","year":"2014","journal-title":"J Med Chem"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"D1100","DOI":"10.1093\/nar\/gkr777","article-title":"ChEMBL: a large-scale bioactivity database for drug discovery","volume":"40","author":"A Gaulton","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"1052","DOI":"10.1016\/j.drudis.2010.10.003","article-title":"PubChem as a public resource for drug discovery","volume":"15","author":"Q Li","year":"2010","journal-title":"Drug Discov Today"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"2921","DOI":"10.1021\/jm051139t","article-title":"Robust ligand-based modeling of the biological targets of known drugs","volume":"49","author":"AE Cleves","year":"2006","journal-title":"J Med Chem"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1021\/ci2003544","article-title":"Exploring polypharmacology using a ROCS-based target fishing approach","volume":"52","author":"MD AbdulHameed","year":"2012","journal-title":"J Chem Inf Model"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"W609","DOI":"10.1093\/nar\/gkq300","article-title":"PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach","volume":"38","author":"X Liu","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"2455","DOI":"10.1021\/ci2002704","article-title":"Rapid shape-based ligand alignment and virtual screening method based on atom\/feature-pair similarities and volume overlap scoring","volume":"51","author":"GM Sastry","year":"2011","journal-title":"J Chem Inf Model"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"6802","DOI":"10.1021\/jm060902w","article-title":"Bridging chemical and biological space: &quot;target fishing&quot; using 2D and 3D molecular descriptors","volume":"49","author":"JH Nettles","year":"2006","journal-title":"J Med Chem"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"W219","DOI":"10.1093\/nar\/gkl114","article-title":"TarFisDock: a web server for identifying drug targets with docking approach","volume":"34","author":"H Li","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1021\/ci990308d","article-title":"Database searching for compounds with similar biological activity using short binary bit string representations of molecules","volume":"39","author":"L Xue","year":"1999","journal-title":"J Chem Inf Comput Sci"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1483","DOI":"10.1016\/j.chembiol.2012.09.014","article-title":"Development of antibiotic activity profile screening for the classification and discovery of natural product antibiotics","volume":"19","author":"WR Wong","year":"2012","journal-title":"Chem Biol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1126\/science.1250217","article-title":"Mapping the cellular response to small molecules using chemogenomic fitness signatures","volume":"344","author":"AY Lee","year":"2014","journal-title":"Science"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1021\/ci3004489","article-title":"Virtual affinity fingerprints for target fishing: a new application of Drug Profile Matching","volume":"53","author":"A Peragovics","year":"2013","journal-title":"J Chem Inf Model"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1038\/nbt1338","article-title":"Drug-target network","volume":"25","author":"MA Yildirim","year":"2007","journal-title":"Nat Biotechnol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"W39","DOI":"10.1093\/nar\/gku337","article-title":"DINIES: drug-target interaction network inference engine based on supervised analysis","volume":"42","author":"Y Yamanishi","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"2313","DOI":"10.1021\/ci800079x","article-title":"Ligand-target prediction using Winnow and naive Bayesian algorithms and the implications of overall performance statistics","volume":"48","author":"F Nigsch","year":"2008","journal-title":"J Chem Inf Model"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"2190","DOI":"10.1021\/ci9000376","article-title":"Target fishing for chemical compounds using target-ligand activity data and ranking based methods","volume":"49","author":"N Wale","year":"2009","journal-title":"J Chem Inf Model"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"2440","DOI":"10.1021\/ci200192v","article-title":"Identifying compound-target associations by combining bioactivity profile similarity search and public databases mining","volume":"51","author":"T Cheng","year":"2011","journal-title":"J Chem Inf Model"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"6075","DOI":"10.1021\/jm800867g","article-title":"Structure-activity relationship anatomy by network-like similarity graphs and local structure-activity relationship indices","volume":"51","author":"M Wawer","year":"2008","journal-title":"J Med Chem"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1186\/1471-2105-13-99","article-title":"MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity","volume":"13","author":"DK Barupal","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"2429","DOI":"10.1021\/ci9001102","article-title":"Finding key members in compound libraries by analyzing networks of molecules assembled by structural similarity","volume":"49","author":"Z Lepp","year":"2009","journal-title":"J Chem Inf Model"},{"key":"ref33","volume":"xii","author":"ED Kolaczyk","year":"2009"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1038\/msb4100129","article-title":"Network-based prediction of protein function","volume":"3","author":"R Sharan","year":"2007","journal-title":"Mol Syst Biol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"W623","DOI":"10.1093\/nar\/gkp456","article-title":"PubChem: a public information system for analyzing bioactivities of small molecules","volume":"37","author":"Y Wang","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1016\/j.cbpa.2010.02.018","article-title":"Privileged scaffolds for library design and drug discovery","volume":"14","author":"ME Welsch","year":"2010","journal-title":"Curr Opin Chem Biol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1758-2946-3-33","article-title":"Open Babel: An open chemical toolbox","volume":"3","author":"NM O'Boyle","year":"2011","journal-title":"J Cheminform"},{"key":"ref38","volume":"xii","author":"J-L Faulon","year":"2010"},{"key":"ref39","volume":"xxx","author":"J Gasteiger","year":"2003"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"i357","DOI":"10.1093\/bioinformatics\/btn187","article-title":"BLASTing small molecules\u2014statistics and extreme statistics of chemical similarity scores","volume":"24","author":"P Baldi","year":"2008","journal-title":"Bioinformatics"},{"key":"ref41","volume":"xix","author":"D Jungnickel","year":"2008"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1038\/35015694","article-title":"Protein function in the post-genomic era","volume":"405","author":"D Eisenberg","year":"2000","journal-title":"Nature"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"1257","DOI":"10.1038\/82360","article-title":"A network of protein-protein interactions in yeast","volume":"18","author":"B Schwikowski","year":"2000","journal-title":"Nat Biotechnol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1038\/nbt825","article-title":"Global protein function prediction from protein-protein interaction networks","volume":"21","author":"A Vazquez","year":"2003","journal-title":"Nat Biotechnol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1038\/nbt1196","article-title":"Modeling cellular machinery through biological network comparison","volume":"24","author":"R Sharan","year":"2006","journal-title":"Nat Biotechnol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1002\/yea.706","article-title":"Assessment of prediction accuracy of protein function from protein\u2014protein interaction data","volume":"18","author":"H Hishigaki","year":"2001","journal-title":"Yeast"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/1758-2946-1-14","article-title":"Optimal assignment methods for ligand-based virtual screening","volume":"1","author":"A Jahn","year":"2009","journal-title":"J Cheminform"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"669","DOI":"10.2174\/138620708785739952","article-title":"A ligand-based approach to mining the chemogenomic space of drugs","volume":"11","author":"E Gregori-Puigjane","year":"2008","journal-title":"Comb Chem High Throughput Screen"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1038\/sj.jhh.1002018","article-title":"Dual ACE\/NEP inhibitors\u2014more than playing the ACE card","volume":"20","author":"KA Jandeleit-Dahm","year":"2006","journal-title":"J Hum Hypertens"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"4299","DOI":"10.1158\/0008-5472.CAN-05-2507","article-title":"Discovery and evaluation of dual CDK1 and CDK2 inhibitors","volume":"66","author":"M Payton","year":"2006","journal-title":"Cancer Res"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1038\/nchembio.732","article-title":"Chemical informatics and target identification in a zebrafish phenotypic screen","volume":"8","author":"C Laggner","year":"2012","journal-title":"Nat Chem Biol"},{"key":"ref52","volume":"xv","author":"C Avendan\u0303o","year":"2008"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1038\/nrd3253","article-title":"Microtubule-binding agents: a dynamic field of cancer therapeutics","volume":"9","author":"C Dumontet","year":"2010","journal-title":"Nat Rev Drug Discov"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"4151","DOI":"10.1016\/j.bmcl.2009.05.119","article-title":"Novel and potent inhibitors of stearoyl-CoA desaturase-1. Part I: Discovery of 3-(2-hydroxyethoxy)-4-methoxy-N-[5-(3-trifluoromethylbenzyl)thiazol-2-yl]benzamid e","volume":"19","author":"Y Uto","year":"2009","journal-title":"Bioorg Med Chem Lett"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"4328","DOI":"10.1016\/j.bmcl.2008.06.082","article-title":"N-(thiazol-2-yl)-2-thiophene carboxamide derivatives as Abl inhibitors identified by a pharmacophore-based database screening of commercially available compounds","volume":"18","author":"F Manetti","year":"2008","journal-title":"Bioorg Med Chem Lett"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"1640","DOI":"10.1021\/jm101202j","article-title":"Discovery of a novel series of inhibitors of lymphoid tyrosine phosphatase with activity in human T cells","volume":"54","author":"SM Stanford","year":"2011","journal-title":"J Med Chem"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1016\/S1367-5931(98)80095-1","article-title":"Protein tyrosine phosphatases: mechanisms of catalysis and regulation","volume":"2","author":"JM Denu","year":"1998","journal-title":"Curr Opin Chem Biol"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"e33823","DOI":"10.1371\/journal.pone.0033823","article-title":"SCD1 inhibition causes cancer cell death by depleting mono-unsaturated fatty acids","volume":"7","author":"P Mason","year":"2012","journal-title":"PLoS One"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"2465","DOI":"10.1007\/s00018-003-3123-7","article-title":"Receptor and nonreceptor protein tyrosine phosphatases in the nervous system","volume":"60","author":"S Paul","year":"2003","journal-title":"Cell Mol Life Sci"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1038\/ncomms1634","article-title":"ABL1 regulates spindle orientation in adherent cells and mammalian skin","volume":"3","author":"S Matsumura","year":"2012","journal-title":"Nat Commun"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"e379","DOI":"10.1371\/journal.pbio.0020379","article-title":"Parallel chemical genetic and genome-wide RNAi screens identify cytokinesis inhibitors and targets","volume":"2","author":"US Eggert","year":"2004","journal-title":"PLoS Biol"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1038\/nature08869","article-title":"Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes","volume":"464","author":"B Neumann","year":"2010","journal-title":"Nature"},{"key":"ref63","first-page":"775","article-title":"A high-throughput model for screening anti-tumor agents capable of promoting polymerization of tubulin in vitro","volume":"25","author":"W Hu","year":"2004","journal-title":"Acta Pharmacol Sin"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"6107","DOI":"10.1021\/jm050502t","article-title":"A common pharmacophore for a diverse set of colchicine site inhibitors using a structure-based approach","volume":"48","author":"TL Nguyen","year":"2005","journal-title":"J Med Chem"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1002\/jms.1804","article-title":"Competitive mass spectrometry binding assay for characterization of three binding sites of tubulin","volume":"45","author":"CM Li","year":"2010","journal-title":"J Mass Spectrom"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1038\/nrd2876","article-title":"Multi-parameter phenotypic profiling: using cellular effects to characterize small-molecule compounds","volume":"8","author":"Y Feng","year":"2009","journal-title":"Nat Rev Drug Discov"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"1623","DOI":"10.1093\/bioinformatics\/btl145","article-title":"Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions","volume":"22","author":"HN Chua","year":"2006","journal-title":"Bioinformatics"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"1309","DOI":"10.1016\/j.cell.2011.11.020","article-title":"The STARD9\/Kif16a kinesin associates with mitotic microtubules and regulates spindle pole assembly","volume":"147","author":"JZ Torres","year":"2011","journal-title":"Cell"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1038\/nature02393","article-title":"Insight into tubulin regulation from a complex with colchicine and a stathmin-like domain","volume":"428","author":"RB Ravelli","year":"2004","journal-title":"Nature"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004153","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,22]],"date-time":"2019-08-22T19:00:27Z","timestamp":1566500427000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004153"}},"subtitle":[],"editor":[{"given":"Christos A.","family":"Ouzounis","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2015,3,31]]},"references-count":69,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2015,3,31]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1004153","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,3,31]]}}}