{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,3]],"date-time":"2025-07-03T18:40:06Z","timestamp":1751568006496,"version":"3.41.0"},"reference-count":68,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2018,4,16]],"date-time":"2018-04-16T00:00:00Z","timestamp":1523836800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2018,4,16]],"date-time":"2018-04-16T00:00:00Z","timestamp":1523836800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006147","name":"Office of Nuclear Energy","doi-asserted-by":"publisher","award":["DE-AC07-05ID14517"],"award-info":[{"award-number":["DE-AC07-05ID14517"]}],"id":[{"id":"10.13039\/100006147","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P20GM103408"],"award-info":[{"award-number":["P20GM103408"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["P20GM109095"],"award-info":[{"award-number":["P20GM109095"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001309","name":"Research Corporation for Science Advancement","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001309","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008982","name":"National Science Foundation","doi-asserted-by":"publisher","award":["0619793","0923535"],"award-info":[{"award-number":["0619793","0923535"]}],"id":[{"id":"10.13039\/501100008982","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000937","name":"M.J. Murdock Charitable Trust","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000937","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2018,12]]},"DOI":"10.1186\/s12859-018-2153-y","type":"journal-article","created":{"date-parts":[[2018,4,16]],"date-time":"2018-04-16T12:07:09Z","timestamp":1523880429000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["SPIDR: small-molecule peptide-influenced drug repurposing"],"prefix":"10.1186","volume":"19","author":[{"given":"Matthew D.","family":"King","sequence":"first","affiliation":[]},{"given":"Thomas","family":"Long","sequence":"additional","affiliation":[]},{"given":"Daniel L.","family":"Pfalmer","sequence":"additional","affiliation":[]},{"given":"Timothy L.","family":"Andersen","sequence":"additional","affiliation":[]},{"given":"Owen M.","family":"McDougal","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2018,4,16]]},"reference":[{"key":"2153_CR1","doi-asserted-by":"publisher","first-page":"428","DOI":"10.1038\/nrd3405","volume":"10","author":"F Pammolli","year":"2011","unstructured":"Pammolli F, Magazzini L, Riccaboni M. The productivity crisis in pharmaceutical R&D. Nat Rev Drug Discov. 2011;10:428\u201338.","journal-title":"Nat Rev Drug Discov"},{"key":"2153_CR2","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1016\/j.jhealeco.2016.01.012","volume":"47","author":"JA DiMasi","year":"2016","unstructured":"DiMasi JA, Grabowski HG, Hansen RW. Innovation in the pharmaceutical industry: new estimates of R&D costs. J Health Econ. 2016;47:20\u201333.","journal-title":"J Health Econ"},{"key":"2153_CR3","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1038\/nrd1468","volume":"3","author":"TT Ashburn","year":"2004","unstructured":"Ashburn TT, Thor KB. Drug repositioning: identifying and developing new uses for existing drugs. Nat Rev Drug Discov. 2004;3:673\u201383.","journal-title":"Nat Rev Drug Discov"},{"key":"2153_CR4","first-page":"51","volume":"4","author":"PP Deotarse","year":"2015","unstructured":"Deotarse PP, Jain AS, Baile MB, Kolhe NS, Kulkarni AA. Drug repositioning: a review. Int. J. Pharma. Res Rev. 2015;4:51\u20138.","journal-title":"Int. J. Pharma. Res Rev"},{"key":"2153_CR5","doi-asserted-by":"publisher","first-page":"759","DOI":"10.1208\/s12248-012-9390-1","volume":"14","author":"TI Oprea","year":"2012","unstructured":"Oprea TI, Mestres J. Drug repurposing: far beyond new targets for old drugs. AAPS J. 2012;14:759\u201363.","journal-title":"AAPS J"},{"key":"2153_CR6","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1016\/j.drudis.2013.11.005","volume":"19","author":"G Jin","year":"2014","unstructured":"Jin G, Wong TC. Toward better drug repositioning: prioritizing and integrating existing methods into efficient pipelines. Drug Discov Today. 2014;19:637\u201344.","journal-title":"Drug Discov Today"},{"key":"2153_CR7","doi-asserted-by":"publisher","first-page":"D1202","DOI":"10.1093\/nar\/gkv951","volume":"44","author":"S Kim","year":"2016","unstructured":"Kim S, Thiessen PA, Bolton EE, Chen J, Gu G, Gindulyte A, Han L, He J, He S, Shoemaker BA, Wang J, Yu B, Zhang J, Bryant SH. PubChem substance and compound databases. Nucleic Acids Res. 2016;44:D1202\u201313.","journal-title":"Nucleic Acids Res"},{"key":"2153_CR8","doi-asserted-by":"publisher","first-page":"2347","DOI":"10.1002\/jcc.20756","volume":"28","author":"Z Hu","year":"2007","unstructured":"Hu Z, Southerland W. WinDock: structure-based drug discovery on Windowsbased PCs. J Comput Chem. 2007;28:2347\u201351.","journal-title":"J Comput Chem"},{"key":"2153_CR9","doi-asserted-by":"publisher","first-page":"1803","DOI":"10.1093\/bioinformatics\/btl197","volume":"22","author":"M Vaqu","year":"2006","unstructured":"Vaqu M, Arola A, Aliagas C, Pujadas G. BDT: an easy-to-use frontend application for automation of massive docking tasks and complex docking strategies with AutoDock. Bioinformatics. 2006;22:1803\u20134.","journal-title":"Bioinformatics"},{"key":"2153_CR10","doi-asserted-by":"publisher","first-page":"1739","DOI":"10.1021\/jm0306430","volume":"47","author":"RA Friesner","year":"2004","unstructured":"Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PSG. A new approach for rapid, accurate docking and scoring method and assessment of docking accuracy. J Med Chem. 2004;47:1739\u201349.","journal-title":"J Med Chem"},{"key":"2153_CR11","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1186\/1756-0500-3-289","volume":"3","author":"CW Bullock","year":"2003","unstructured":"Bullock CW, Jacob RB, McDougal OM, Hampikian G, Andersen T. Dockomatic - automated ligand creation and docking. BMC Res Notes. 2003;3:289.","journal-title":"BMC Res Notes"},{"key":"2153_CR12","doi-asserted-by":"crossref","unstructured":"Jacob RB, Bullock CW, Andersen T, McDougal OM. DockoMatic: automated peptide analog creation for high throughput virtual screening. J Comput Chem. 2001, 32:2936\u201341.","DOI":"10.1002\/jcc.21864"},{"key":"2153_CR13","doi-asserted-by":"publisher","first-page":"1639","DOI":"10.1002\/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B","volume":"19","author":"GM Morris","year":"1998","unstructured":"Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function. J Comput Chem. 1998;19:1639\u201362.","journal-title":"J Comput Chem"},{"key":"2153_CR14","doi-asserted-by":"publisher","first-page":"1145","DOI":"10.1002\/jcc.20634","volume":"28","author":"R Huey","year":"2007","unstructured":"Huey R, Morris GM, Olson AJ, Goodsell DS. A semi-empirical free energy force field with charge-based desolvation. J Comput Chem. 2007;28:1145\u201352.","journal-title":"J Comput Chem"},{"key":"2153_CR15","unstructured":"The Open Babel Package, Version 2.2.3, 2011. Available: http:\/\/www.openbabel.org ."},{"key":"2153_CR16","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1007\/11415770_32","volume-title":"Research in computational molecular biology","author":"J Xu","year":"2005","unstructured":"Xu, J. Research in computational molecular biology. Eds. Miyano, S.; Mesirov, J.; Kasif, S.; Istrail, S.; Pevzner, P.; Waterman, M. Springer. Berlin: 2005. pp. 423\u2013439."},{"key":"2153_CR17","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1145\/1162349.1162350","volume":"53","author":"J Xu","year":"2006","unstructured":"Xu J, Berger B. Fast and accurate algorithms for protein side-chain packing. JACM. 2006;53:533\u201357.","journal-title":"JACM"},{"key":"2153_CR18","doi-asserted-by":"publisher","unstructured":"Robinson SD, Undheim EAB, Ueberheide B, King GF. Venom peptides as therapeutics: advances, challenges and the future of venom-peptide discovery. Expert Rev Proteomics. 2017:1\u20139. https:\/\/doi.org\/10.1080\/14789450.2017.1377613 .","DOI":"10.1080\/14789450.2017.1377613"},{"key":"2153_CR19","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1016\/j.cbpa.2017.03.004","volume":"38","author":"C Netirojjanakul","year":"2017","unstructured":"Netirojjanakul C, Miranda LP. Progress and challenges in the optimization of toxin peptides for development as pain therapeutics. Curr Opin Chem Biol. 2017;38:70\u20139. https:\/\/doi.org\/10.1016\/j.cbpa.2017.03.004 .","journal-title":"Curr Opin Chem Biol"},{"key":"2153_CR20","doi-asserted-by":"crossref","unstructured":"Shaw C. Advancing drug discovery with reptile and amphibian venom peptides - venom-based medicines. Biochem Evol. 2009:34\u20137. www.biochemist.org\/bio\/03105\/0034\/031050034.pdf","DOI":"10.1042\/BIO03105034"},{"key":"2153_CR21","first-page":"10441050","volume":"46","author":"DM Morens","year":"1996","unstructured":"Morens DM, Davis JW, Grandinetti A, Ross GW, Popper JS, White LR. Epidemiologic observations on Parkinson\u2019s disease: incidence and mortality in a prospective study of middle-aged men. Neurology. 1996;46:10441050.","journal-title":"Neurology"},{"key":"2153_CR22","doi-asserted-by":"publisher","first-page":"614","DOI":"10.1002\/mds.20029","volume":"19","author":"MF Allam","year":"2004","unstructured":"Allam MF, Campbell MJ, Hofman A, Del Castillo AS, Fernandez-Crehuet Navajas R. Smoking and Parkinson\u2019s disease: systematic review of prospective studies. Movement Disord. 2004;19:614\u201321.","journal-title":"Movement Disord"},{"key":"2153_CR23","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1016\/S0741-8329(01)00130-6","volume":"24","author":"EK Perry","year":"2001","unstructured":"Perry EK, Martin-Ruiz CM, Court JA. Nicotinic receptor subtypes in human brain related to aging and dementia. Alcohol. 2001;24:63\u20138.","journal-title":"Alcohol"},{"key":"2153_CR24","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1007\/s00213-005-0164-7","volume":"184","author":"ED Levin","year":"2006","unstructured":"Levin ED, McClernon FJ, Rezvani AH. Nicotinic effects on cognitive function: behavioral characterization, pharmacological specification, and anatomic localization. Psychopharmacology. 2006;184:523\u201339.","journal-title":"Psychopharmacology"},{"key":"2153_CR25","doi-asserted-by":"publisher","first-page":"492","DOI":"10.2741\/2695","volume":"13","author":"MR Picciotto","year":"2008","unstructured":"Picciotto MR, Zoli M. Neuroprotection via nAChRs: the role of nAChRs in neurodegenerative disorders such as Alzheimer\u2019s and Parkinson\u2019s disease. Front Biosci. 2008;13:492\u2013504.","journal-title":"Front Biosci"},{"key":"2153_CR26","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1007\/s00018-009-0125-0","volume":"67","author":"RB Jacob","year":"2010","unstructured":"Jacob RB, McDougal OM. The M-superfamily of conotoxins: a review. Cell Mol Life Sci. 2010;67:17\u201327.","journal-title":"Cell Mol Life Sci"},{"key":"2153_CR27","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1002\/cbic.201300577","volume":"15","author":"VS Sambasivarao","year":"2014","unstructured":"Sambasivarao VS, Roberts J, Bharadwaj VS, Slingsby JG, Rohleder C, Mallory C, Groome JR, McDougal OM, Maupin CM. Acetycholine promotes binding of alpha-Conotoxin MII for \u03b1 3 \u03b2 2 nicotinic acetylcholine receptors. Chembiochem. 2014;15:413\u201324.","journal-title":"Chembiochem"},{"key":"2153_CR28","doi-asserted-by":"publisher","first-page":"944","DOI":"10.1124\/mol.65.4.944","volume":"65","author":"SC Harvey","year":"2004","unstructured":"Harvey SC, McIntosh JM, Cartier GE, Maddox FN, Luetje CW. Analogs of alpha-conotoxin MII are selective for alpha6-containing nicotinic acetylcholine receptors. Mol Pharmacol. 2004;65:944\u201352.","journal-title":"Mol Pharmacol"},{"key":"2153_CR29","doi-asserted-by":"publisher","first-page":"7522","DOI":"10.1074\/jbc.271.13.7522","volume":"271","author":"GE Cartier","year":"1996","unstructured":"Cartier GE, Yoshikami D, Gray WR, Luo S, Olivera BM, McIntosh JM. A new \u03b1-conotoxin which targets \u03b1 3 \u03b2 2 nicotinic acetylcholine receptors. J Biol Chem. 1996;271:7522\u20138.","journal-title":"J Biol Chem"},{"key":"2153_CR30","doi-asserted-by":"publisher","first-page":"4226","DOI":"10.2174\/138161211798999384","volume":"17","author":"M Muttenthaler","year":"2011","unstructured":"Muttenthaler M, Akondi KB, Alewood PF. Structure-activity studies on alpha-conotoxins. Curr Pharm Des. 2011;17:4226\u201341.","journal-title":"Curr Pharm Des"},{"key":"2153_CR31","doi-asserted-by":"publisher","first-page":"944","DOI":"10.1124\/mol.65.4.944","volume":"65","author":"JM McIntosh","year":"2004","unstructured":"McIntosh JM, Azam L, Staheli S, Dowell C, Lindstrom JM, Kuryatov A, Garrett JE, Marks MJ, Whiteaker P. Analogs of \u03b1-conotoxin MII are selective for \u03b16-containing nicotinic acetylcholine receptors. Mol Pharmacol. 2004;65:944\u201352.","journal-title":"Mol Pharmacol"},{"key":"2153_CR32","doi-asserted-by":"publisher","first-page":"1563","DOI":"10.1124\/mol.106.031492","volume":"71","author":"O Salminen","year":"2007","unstructured":"Salminen O, Drapeau JA, McIntosh JM, Collins AC, Marks MJ, Grady SR. Pharmacology of \u03b1-conotoxin MII-sensitive subtypes of nicotinic acetylcholine receptors isolated by breeding of null mutant mice. Mol Pharmacol. 2007;71:1563\u201371.","journal-title":"Mol Pharmacol"},{"key":"2153_CR33","doi-asserted-by":"crossref","first-page":"913","DOI":"10.1016\/S0026-895X(24)26500-7","volume":"57","author":"P Whiteaker","year":"2000","unstructured":"Whiteaker P, McIntosh JM, Luo S, Collins AC, Marks MJ. 125I-\u03b1-conotoxin MII identifies a novel nicotinic acetylcholine receptor population in mouse brain. Mol Pharmacol. 2000;57:913\u201325.","journal-title":"Mol Pharmacol"},{"key":"2153_CR34","doi-asserted-by":"publisher","first-page":"1304","DOI":"10.1002\/jcc.23928","volume":"36","author":"T Long","year":"2015","unstructured":"Long T, McDougal OM, Andersen T. GAMPMS: genetic algorithm managed peptide mutant screening. J Comput Chem. 2015;36:1304\u201310.","journal-title":"J Comput Chem"},{"key":"2153_CR35","doi-asserted-by":"publisher","unstructured":"King MD, Long T, Andersen T, McDougal OM. Genetic algorithm managed peptide mutant screening: optimizing peptide ligands for targeted receptor binding. J Chem Inf Model. 2016; https:\/\/doi.org\/10.1021\/acs.jcim.6b00095 .","DOI":"10.1021\/acs.jcim.6b00095"},{"key":"2153_CR36","doi-asserted-by":"publisher","first-page":"D668","DOI":"10.1093\/nar\/gkj067","volume":"34","author":"DS Wishart","year":"2006","unstructured":"Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 2006;34:D668\u201372.","journal-title":"Nucleic Acids Res"},{"key":"2153_CR37","doi-asserted-by":"publisher","first-page":"D198","DOI":"10.1093\/nar\/gkl999","volume":"35","author":"T Liu","year":"2007","unstructured":"Liu T, Lin Y, Wen X, Jorissen RN, Gilson MK. BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res. 2007;35:D198\u2013201.","journal-title":"Nucleic Acids Res"},{"key":"2153_CR38","doi-asserted-by":"publisher","first-page":"1123","DOI":"10.1021\/ed100697w","volume":"87","author":"HE Pence","year":"2010","unstructured":"Pence HE, Williams A. ChemSpider: an online chemical information resource. J Chem Educ. 2010;87:1123\u20134.","journal-title":"J Chem Educ"},{"key":"2153_CR39","doi-asserted-by":"publisher","first-page":"D1100","DOI":"10.1093\/nar\/gkr777","volume":"40","author":"A Gaulton","year":"2012","unstructured":"Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, Overington JP. ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res. 2012;40:D1100\u20137.","journal-title":"Nucleic Acids Res"},{"key":"2153_CR40","unstructured":"National Center for Biotechnology Information. PubChem Compound Database; CID=1, http:\/\/pubchem.ncbi.nlm.nih.gov\/compound\/25131416 ."},{"key":"2153_CR41","unstructured":"National Center for Biotechnology Information. PubChem Compound Database; CID=25131416, http:\/\/pubchem.ncbi.nlm.nih.gov\/compound\/25131416 ."},{"key":"2153_CR42","unstructured":"National Center for Biotechnology Information. PubChem Compound Database; CID=58420086, http:\/\/pubchem.ncbi.nlm.nih.gov\/compound\/58420086 ."},{"key":"2153_CR43","unstructured":"National Center for Biotechnology Information. PubChem Compound Database; CID=46883273, http:\/\/pubchem.ncbi.nlm.nih.gov\/compound\/46883273 ."},{"key":"2153_CR44","unstructured":"National Center for Biotechnology Information. PubChem Compound Database; CID=11017883, http:\/\/pubchem.ncbi.nlm.nih.gov\/compound\/11017883 ."},{"key":"2153_CR45","unstructured":"National Center for Biotechnology Information. PubChem Compound Database; CID=46702076, http:\/\/pubchem.ncbi.nlm.nih.gov\/compound\/46702076 ."},{"key":"2153_CR46","unstructured":"National Center for Biotechnology Information. PubChem Compound Database; CID=19311642, http:\/\/pubchem.ncbi.nlm.nih.gov\/compound\/19311642 ."},{"key":"2153_CR47","unstructured":"National Center for Biotechnology Information. PubChem Compound Database; CID=19311407, http:\/\/pubchem.ncbi.nlm.nih.gov\/compound\/19311407 ."},{"key":"2153_CR48","unstructured":"National Center for Biotechnology Information. PubChem Compound Database; CID=19303632, http:\/\/pubchem.ncbi.nlm.nih.gov\/compound\/19303632 ."},{"key":"2153_CR49","unstructured":"National Center for Biotechnology Information. PubChem Compound Database; CID=69091626, http:\/\/pubchem.ncbi.nlm.nih.gov\/compound\/69091626 ."},{"key":"2153_CR50","unstructured":"National Center for Biotechnology Information. PubChem Compound Database; CID=19311613, http:\/\/pubchem.ncbi.nlm.nih.gov\/compound\/19311613 ."},{"key":"2153_CR51","unstructured":"National Center for Biotechnology Information. PubChem Compound Database; CID=58320126, http:\/\/pubchem.ncbi.nlm.nih.gov\/compound\/58320126 ."},{"key":"2153_CR52","unstructured":"National Center for Biotechnology Information. PubChem Compound Database; CID=67754078, http:\/\/pubchem.ncbi.nlm.nih.gov\/compound\/67754078 ."},{"key":"2153_CR53","doi-asserted-by":"publisher","first-page":"26457","DOI":"10.1074\/jbc.M414476200","volume":"280","author":"PHN Celie","year":"2005","unstructured":"Celie PHN, Klaassen RV, van Rossum-Fikkert SE, van Elk R, van Nierop P, Smit AB, Sixma TK. Crystal structure of acetylcholine-binding protein form Bulinus trucatus reveals the conserved structural scaffold and sites of variation in nicotinic acetylcholine receptors. J Biol Chem. 2005;280:26457\u201366.","journal-title":"J Biol Chem"},{"key":"2153_CR54","doi-asserted-by":"publisher","first-page":"3635","DOI":"10.1038\/sj.emboj.7600828","volume":"24","author":"SB Hansen","year":"2005","unstructured":"Hansen SB, Sulzenbacher G, Huxford T, Marchot P, Taylor P, Bourne Y. Structures of Aplysia AChBP complexes with nicotinic agonists and antagonists reveal distinct binding interfaces and conformations. EMBO J. 2005;24:3635\u201346.","journal-title":"EMBO J"},{"key":"2153_CR55","doi-asserted-by":"publisher","first-page":"e134","DOI":"10.1371\/journal.pcbi.0020134","volume":"2","author":"X Cheng","year":"2006","unstructured":"Cheng X, Wang H, Grant B, Sine SM, McCammon JA. Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors. PLoS Comput Biol. 2006;2:e134.","journal-title":"PLoS Comput Biol"},{"key":"2153_CR56","doi-asserted-by":"publisher","first-page":"3099","DOI":"10.1021\/ci300367a","volume":"52","author":"F Cheng","year":"2012","unstructured":"Cheng F, Li W, Zhou Y, Shen J, Wu Z, Liu G, Lee PW, Tang Y. admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties. J Chem Inf Model. 2012;52:3099\u2013105.","journal-title":"J Chem Inf Model"},{"key":"2153_CR57","doi-asserted-by":"publisher","DOI":"10.1038\/srep42717","volume":"7","author":"A Daina","year":"2017","unstructured":"Daina A, Michielin O, Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep. 2017;7:42717.","journal-title":"Sci Rep"},{"key":"2153_CR58","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1007\/s10822-011-9440-2","volume":"25","author":"I Sushko","year":"2011","unstructured":"Sushko I, Novotarskyi S, Korner R, Pandey AK, Rupp M, Teetz W, Brandmaier S, Abdelaziz A, Prokopenko VV, Tanchuk VY, Todeschini R, Varnek A, Marcou G, Ertl P, Potemkin V, Grishina M, Gasteiger J, Schwab C, Baskin II, Palyulin VA, Radchenko EV, Welsh WJ, Kholodovych V, Chekmarev D, Cherkasov A, Aires-de-Sousa J, Zhang QY, Bender A, Nigsch F, Patiny L, Williams A, Tkachenko V, Tetko IV. Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information. J Comput Aided Mol Des. 2011;25:533\u201354.","journal-title":"J Comput Aided Mol Des"},{"key":"2153_CR59","doi-asserted-by":"publisher","first-page":"2310","DOI":"10.1021\/ci300245q","volume":"52","author":"I Sushko","year":"2012","unstructured":"Sushko I, Salmina E, Potemkin VA, Poda G, Tetko IV. ToxAlerts: a web server of structural alerts for toxic chemicals and compounds with potential adverse reactions. J Chem Inf Model. 2012;52:2310\u20136.","journal-title":"J Chem Inf Model"},{"key":"2153_CR60","doi-asserted-by":"publisher","first-page":"2088","DOI":"10.2174\/1568026616666160216153457","volume":"16","author":"A Martorana","year":"2016","unstructured":"Martorana A, Perricone U, Lauria A. The repurposing of old drugs or unsuccessful lead compounds by in silico approaches: new advances and perspectives. Curr Top Med Chem. 2016;16:2088\u2013106.","journal-title":"Curr Top Med Chem"},{"key":"2153_CR61","first-page":"333","volume":"18","author":"Z Wu","year":"2016","unstructured":"Wu Z, Cheng F, Li J, Li W, Liu G, Tang Y. SDTNBI: An integrated network and chemoinformatics tool for systematic prediction of drug-target interactions and drug repositioning. Brief Bioinform. 2016;18:333\u201347.","journal-title":"Brief Bioinform"},{"key":"2153_CR62","doi-asserted-by":"publisher","first-page":"e1002503","DOI":"10.1371\/journal.pcbi.1002503","volume":"8","author":"F Cheng","year":"2012","unstructured":"Cheng F, Liu C, Jiang J, Lu W, Li W, Liu G, Zhou W, Huang J, Tang Y. Prediction of drug-target interactions and drug repositioning via network-based inference. PLoS Comput Biol. 2012;8:e1002503.","journal-title":"PLoS Comput Biol"},{"key":"2153_CR63","doi-asserted-by":"crossref","unstructured":"The UniProt Consortium. UniProt: a hub for protein information. Nucleic Acids Res. 2014:D204\u201312.","DOI":"10.1093\/nar\/gku989"},{"key":"2153_CR64","doi-asserted-by":"publisher","first-page":"967","DOI":"10.1016\/j.jmb.2004.12.031","volume":"346","author":"N Unwin","year":"2005","unstructured":"Unwin N. Refined structure of the nicotinic acetylcholine receptor at 4\u00c5 resolution. J Mol Biol. 2005;346:967\u201389.","journal-title":"J Mol Biol"},{"key":"2153_CR65","doi-asserted-by":"publisher","first-page":"779","DOI":"10.1006\/jmbi.1993.1626","volume":"234","author":"A Sali","year":"1993","unstructured":"Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 1993;234:779\u2013815.","journal-title":"J Mol Biol"},{"key":"2153_CR66","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/1752-153X-1-12","volume":"1","author":"F Fontaine","year":"2007","unstructured":"Fontaine F, Bolton E, Borodina Y, Bryant SH. Fast 3D shape screening of large chemical databases through alignment-recycling. Chem Cent J. 2007;1:12.","journal-title":"Chem Cent J"},{"key":"2153_CR67","doi-asserted-by":"publisher","first-page":"807","DOI":"10.1145\/571647.571648","volume":"21","author":"R Osada","year":"2002","unstructured":"Osada R, Funkhouser T, Chazelle B, DobKin D. Shape distributions. ACM Trans Graph. 2002;21:807\u201332.","journal-title":"ACM Trans Graph"},{"key":"2153_CR68","first-page":"1","volume-title":"In evolutionary computation","author":"CM Fonseca","year":"1995","unstructured":"Fonseca, C.M.; Fleming, P.J. An overview of evolutionary algorithms in multiobjective optimization. In evolutionary computation; Ed. De Jong, K.; Massachusetts Institute of Technology: Cambridge, 1995; 3, 1, 1\u201316."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2153-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-018-2153-y\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2153-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,3]],"date-time":"2025-07-03T17:59:47Z","timestamp":1751565587000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-018-2153-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,4,16]]},"references-count":68,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["2153"],"URL":"https:\/\/doi.org\/10.1186\/s12859-018-2153-y","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2018,4,16]]},"assertion":[{"value":"1 October 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 April 2018","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 April 2018","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare that they have no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"138"}}