{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T20:13:53Z","timestamp":1767903233177,"version":"3.49.0"},"reference-count":54,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2020,6,1]],"date-time":"2020-06-01T00:00:00Z","timestamp":1590969600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2020,6,1]],"date-time":"2020-06-01T00:00:00Z","timestamp":1590969600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"European Open Science Cloud","award":["824087"],"award-info":[{"award-number":["824087"]}]},{"DOI":"10.13039\/501100003542","name":"Ministerium f\u00fcr Wissenschaft, Forschung und Kunst Baden-W\u00fcrttemberg","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100003542","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"crossref","award":["031 A538A de.NBI-RBC"],"award-info":[{"award-number":["031 A538A de.NBI-RBC"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"crossref"}]},{"name":"German Research Foundation for the Collaborative Research Center 992 Medical Epigenetics","award":["SFB 992\/1 2012"],"award-info":[{"award-number":["SFB 992\/1 2012"]}]},{"name":"German Research Foundation for the Collaborative Research Center 992 Medical Epigenetics","award":["SFB 992\/2 2016"],"award-info":[{"award-number":["SFB 992\/2 2016"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Cheminform"],"published-print":{"date-parts":[[2020,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Here, we introduce the ChemicalToolbox, a publicly available web server for performing cheminformatics analysis. The ChemicalToolbox provides an intuitive, graphical interface for common tools for downloading, filtering, visualizing and simulating small molecules and proteins. The ChemicalToolbox is based on Galaxy, an open-source web-based platform which enables accessible and reproducible data analysis. There is already an active Galaxy cheminformatics community using and developing tools. Based on their work, we provide four example workflows which illustrate the capabilities of the ChemicalToolbox, covering assembly of a compound library, hole filling, protein-ligand docking, and construction of a quantitative structure-activity relationship (QSAR) model. These workflows may be modified and combined flexibly, together with the many other tools available, to fit the needs of a particular project. The ChemicalToolbox is hosted on the European Galaxy server and may be accessed via<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/cheminformatics.usegalaxy.eu\">https:\/\/cheminformatics.usegalaxy.eu<\/jats:ext-link>.<\/jats:p>","DOI":"10.1186\/s13321-020-00442-7","type":"journal-article","created":{"date-parts":[[2020,6,2]],"date-time":"2020-06-02T18:04:51Z","timestamp":1591121091000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":35,"title":["The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform"],"prefix":"10.1186","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0621-6705","authenticated-orcid":false,"given":"Simon A.","family":"Bray","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0887-3976","authenticated-orcid":false,"given":"Xavier","family":"Lucas","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2068-4695","authenticated-orcid":false,"given":"Anup","family":"Kumar","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3079-6586","authenticated-orcid":false,"given":"Bj\u00f6rn A.","family":"Gr\u00fcning","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,6,1]]},"reference":[{"issue":"D1","key":"442_CR1","doi-asserted-by":"publisher","first-page":"945","DOI":"10.1093\/nar\/gkw1074","volume":"45","author":"A Gaulton","year":"2016","unstructured":"Gaulton A, Hersey A, Nowotka M, Bento AP, Chambers J, Mendez D, Mutowo P, Atkinson F, Bellis LJ, Cibri\u00e1n-Uhalte E et al (2016) The ChEMBL database in 2017. Nucleic Acids Res 45(D1):945\u2013954","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"442_CR2","doi-asserted-by":"publisher","first-page":"1202","DOI":"10.1093\/nar\/gkv951","volume":"44","author":"S Kim","year":"2015","unstructured":"Kim S, Thiessen PA, Bolton EE, Chen J, Fu G, Gindulyte A, Han L, He J, He S, Shoemaker BA et al (2015) PubChem substance and compound databases. Nucleic Acids Res 44(D1):1202\u20131213","journal-title":"Nucleic Acids Res"},{"key":"442_CR3","unstructured":"Landrum G (2019) RDKit: Open-Source Cheminformatics Software. https:\/\/www.rdkit.org. Accessed 23 Jan 20."},{"issue":"1","key":"442_CR4","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/1758-2946-3-33","volume":"3","author":"NM O\u2019Boyle","year":"2011","unstructured":"O\u2019Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011) OpenBabel: an open chemical toolbox. J Cheminform 3(1):33","journal-title":"J Cheminform"},{"issue":"1","key":"442_CR5","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/s13321-017-0220-4","volume":"9","author":"EL Willighagen","year":"2017","unstructured":"Willighagen EL, Mayfield JW, Alvarsson J, Berg A, Carlsson L, Jeliazkova N, Kuhn S, Pluskal T, Rojas-Chert\u00f3 M, Spjuth O et al (2017) The Chemistry Development Kit (CDK) v2. 0: atom typing, depiction, molecular formulas, and substructure searching. J Cheminform 9(1):33","journal-title":"J Cheminform"},{"issue":"2","key":"442_CR6","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","volume":"31","author":"O Trott","year":"2009","unstructured":"Trott O, Olson AJ (2009) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31(2):455\u2013461","journal-title":"J Comput Chem"},{"issue":"4","key":"442_CR7","doi-asserted-by":"publisher","first-page":"1003571","DOI":"10.1371\/journal.pcbi.1003571","volume":"10","author":"S Ruiz-Carmona","year":"2014","unstructured":"Ruiz-Carmona S, Alvarez-Garcia D, Foloppe N, Garmendia-Doval AB, Juhos S, Schmidtke P, Barril X, Hubbard RE, Morley SD (2014) rDock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids. PLoS Comput Biol 10(4):1003571","journal-title":"PLoS Comput Biol"},{"issue":"4","key":"442_CR8","doi-asserted-by":"publisher","first-page":"556","DOI":"10.1002\/wcms.93","volume":"2","author":"JM Turney","year":"2012","unstructured":"Turney JM, Simmonett AC, Parrish RM, Hohenstein EG, Evangelista FA, Fermann JT, Mintz BJ, Burns LA, Wilke JJ, Abrams ML et al (2012) Psi4: an open-source ab initio electronic structure program. Wiley Interdiscip Rev Comput Mol Sci 2(4):556\u2013565","journal-title":"Wiley Interdiscip Rev Comput Mol Sci"},{"key":"442_CR9","doi-asserted-by":"crossref","unstructured":"Taschuk M, Wilson G (2017) Ten simple rules for making research software more robust. PLoS Comput Biol 13(4)","DOI":"10.1371\/journal.pcbi.1005412"},{"issue":"7","key":"442_CR10","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1038\/s41592-018-0046-7","volume":"15","author":"B Gr\u00fcning","year":"2018","unstructured":"Gr\u00fcning B, Dale R, Sj\u00f6din A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, K\u00f6ster J (2018) Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods 15(7):475","journal-title":"Nat Methods"},{"issue":"239","key":"442_CR11","first-page":"2","volume":"2014","author":"D Merkel","year":"2014","unstructured":"Merkel D (2014) Docker: lightweight Linux containers for consistent development and deployment. Linux J 2014(239):2","journal-title":"Linux J"},{"issue":"1","key":"442_CR12","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1145\/2723872.2723882","volume":"49","author":"C Boettiger","year":"2015","unstructured":"Boettiger C (2015) An introduction to Docker for reproducible research. ACM SIGOPS Oper Syst Rev 49(1):71\u201379","journal-title":"ACM SIGOPS Oper Syst Rev"},{"issue":"5","key":"442_CR13","doi-asserted-by":"publisher","first-page":"0177459","DOI":"10.1371\/journal.pone.0177459","volume":"12","author":"GM Kurtzer","year":"2017","unstructured":"Kurtzer GM, Sochat V, Bauer MW (2017) Singularity: scientific containers for mobility of compute. PloS ONE 12(5):0177459","journal-title":"PloS ONE"},{"issue":"2","key":"442_CR14","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1186\/gb4161","volume":"15","author":"D Blankenberg","year":"2014","unstructured":"Blankenberg D, Kuster GV, Bouvier E, Baker D, Afgan E, Stoler N, Taylor J, Nekrutenko A (2014) Dissemination of scientific software with Galaxy ToolShed. Genome Biol 15(2):403","journal-title":"Genome Biol"},{"issue":"W1","key":"442_CR15","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1093\/nar\/gkw343","volume":"44","author":"E Afgan","year":"2016","unstructured":"Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, \u010cech M, Chilton J, Clements D, Coraor N, Eberhard C, Gr\u00fcning B, Guerler A, Hillman-Jackson J, Von Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks J (2016) The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res 44(W1):3\u201310","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"442_CR16","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/s13321-018-0258-y","volume":"10","author":"H Moriwaki","year":"2018","unstructured":"Moriwaki H, Tian Y-S, Kawashita N, Takagi T (2018) Mordred: a molecular descriptor calculator. J Cheminform 10(1):4","journal-title":"J Cheminform"},{"issue":"7","key":"442_CR17","doi-asserted-by":"publisher","first-page":"1466","DOI":"10.1002\/jcc.21707","volume":"32","author":"CW Yap","year":"2011","unstructured":"Yap CW (2011) PaDEL-descriptor: an open source software to calculate molecular descriptors and fingerprints. J Comput Chem 32(7):1466\u20131474","journal-title":"J Comput Chem"},{"issue":"18","key":"442_CR18","doi-asserted-by":"publisher","first-page":"3508","DOI":"10.1093\/bioinformatics\/btz107","volume":"35","author":"T Senapathi","year":"2019","unstructured":"Senapathi T, Bray S, Barnett CB, Gr\u00fcning B, Naidoo KJ (2019) Biomolecular Reaction & Interaction Dynamics Global Environment (BRIDGE). Bioinformatics 35(18):3508\u20133509","journal-title":"Bioinformatics"},{"key":"442_CR19","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","volume":"1\u20132","author":"MJ Abraham","year":"2015","unstructured":"Abraham MJ, Murtola T, Schulz R, P\u00e1ll S, Smith JC, Hess B, Lindahl E (2015) GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1\u20132:19\u201325","journal-title":"SoftwareX"},{"key":"442_CR20","unstructured":"Case D, et al. (2018) AmberTools Manual 2018. University of California, San Francisco. University of California. http:\/\/ambermd.org\/doc12\/Amber18.pdf. Accessed 23 Jan 20."},{"key":"442_CR21","unstructured":"Swails J, Hernandez C, Mobley D, Nguyen H, Wang L, Janowski P (2016) ParmEd: Cross-program parameter and topology file editor and molecular mechanical simulator engine. https:\/\/parmed.github.io\/ParmEd\/html\/index.html. Accessed 23 Jan 20."},{"issue":"10","key":"442_CR22","doi-asserted-by":"publisher","first-page":"2319","DOI":"10.1002\/jcc.21787","volume":"32","author":"N Michaud-Agrawal","year":"2011","unstructured":"Michaud-Agrawal N, Denning EJ, Woolf TB, Beckstein O (2011) MDAnalysis: a toolkit for the analysis of molecular dynamics simulations. J Comput Chem 32(10):2319\u20132327","journal-title":"J Comput Chem"},{"issue":"21","key":"442_CR23","doi-asserted-by":"publisher","first-page":"3755","DOI":"10.1093\/bioinformatics\/bty419","volume":"34","author":"AS Rose","year":"2018","unstructured":"Rose AS, Bradley AR, Valasatava Y, Duarte JM, Prli\u0107 A, Rose PW (2018) NGL viewer: web-based molecular graphics for large complexes. Bioinformatics 34(21):3755\u20133758","journal-title":"Bioinformatics"},{"key":"442_CR24","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1016\/j.biocel.2017.07.002","volume":"93","author":"Y Guitton","year":"2017","unstructured":"Guitton Y, Tremblay-Franco M, Corguill\u00e9 GL, Martin J-F, P\u00e9t\u00e9ra M, Roger-Mele P, Delabri\u00e8re A, Goulitquer S, Monsoor M, Duperier C, Canlet C, Servien R, Tardivel P, Caron C, Giacomoni F, Th\u00e9venot EA (2017) Create, run, share, publish, and reference your LC\u2013MS, FIA\u2013MS, GC\u2013MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 galaxy online infrastructure for metabolomics. Int J Biochem Cell Biol 93:89\u2013101","journal-title":"Int J Biochem Cell Biol"},{"key":"442_CR25","doi-asserted-by":"publisher","first-page":"1649","DOI":"10.12688\/f1000research.12342.1","volume":"6","author":"M van Rijswijk","year":"2017","unstructured":"van Rijswijk M, Beirnaert C, Caron C, Cascante M, Dominguez V, Dunn WB, Ebbels TMD, Giacomoni F, Gonzalez-Beltran A, Hankemeier T, Haug K, Izquierdo-Garcia JL, Jimenez RC, Jourdan F, Kale N, Klapa MI, Kohlbacher O, Koort K, Kultima K, Corguill\u00e9 GL, Moschonas NK, Neumann S, O\u2019Donovan C, Reczko M, Rocca-Serra P, Rosato A, Salek RM, Sansone S-A, Satagopam V, Schober D, Shimmo R, Spicer RA, Spjuth O, Th\u00e9venot EA, Viant MR, Weber RJM, Willighagen EL, Zanetti G, Steinbeck C (2017) The future of metabolomics in ELIXIR. F1000Research 6:1649","journal-title":"F1000Research"},{"key":"442_CR26","doi-asserted-by":"crossref","unstructured":"Stewart PA, Kuenzi BM, Mehta S, Kumar P, Johnson JE, Jagtap P, Griffin TJ, Haura EB (2019) The Galaxy platform for reproducible affinity proteomic mass spectrometry data analysis. In: Methods in molecular biology. Springer, New York, p. 249\u201361","DOI":"10.1007\/978-1-4939-9232-4_16"},{"key":"442_CR27","unstructured":"Accelrys: BIOVIA Pipeline Pilot. 2019. https:\/\/www.3dsbiovia.com\/products\/collaborative-science\/biovia-pipeline-pilot. Accessed 23 Jan 20."},{"issue":"1","key":"442_CR28","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1145\/1656274.1656280","volume":"11","author":"MR Berthold","year":"2009","unstructured":"Berthold MR, Cebron N, Dill F, Gabriel TR, K\u00f6tter T, Meinl T, Ohl P, Thiel K, Wiswedel B (2009) KNIME\u2014the Konstanz Information Miner: version 2.0 and beyond. ACM SIGKDD Explor Newsl 11(1):26\u201331","journal-title":"ACM SIGKDD Explor Newsl"},{"key":"442_CR29","unstructured":"KNIME: Konstanz Information Miner. 2020. https:\/\/www.knime.com\/. Accessed 31 Mar 20."},{"issue":"7","key":"442_CR30","doi-asserted-by":"publisher","first-page":"801","DOI":"10.1007\/s10822-012-9577-7","volume":"26","author":"WA Warr","year":"2012","unstructured":"Warr WA (2012) Scientific workflow systems: Pipeline Pilot and KNIME. J Comput Aided Mole Des 26(7):801\u2013804","journal-title":"J Comput Aided Mole Des"},{"issue":"1","key":"442_CR31","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/1471-2105-14-257","volume":"14","author":"S Beisken","year":"2013","unstructured":"Beisken S, Meinl T, Wiswedel B, de Figueiredo LF, Berthold M, Steinbeck C (2013) KNIME-CDK: workflow-driven cheminformatics. BMC Bioinform 14(1):257","journal-title":"BMC Bioinform"},{"issue":"6","key":"442_CR32","doi-asserted-by":"publisher","first-page":"752","DOI":"10.1016\/j.cels.2018.05.012","volume":"6","author":"B Batut","year":"2018","unstructured":"Batut B, Hiltemann S, Bagnacani A, Baker D, Bhardwaj V, Blank C, Bretaudeau A, Brillet-Gu\u00e9guen L, \u010cech M, Chilton J et al (2018) Community-driven data analysis training for biology. Cell Syst 6(6):752\u2013758","journal-title":"Cell Syst"},{"key":"442_CR33","unstructured":"German Network for Bioinformatics Infrastructure: de.NBI cloud. 2020. https:\/\/www.denbi.de\/cloud. Accessed 31 Mar 20."},{"key":"442_CR34","unstructured":"ELIXIR network: ELIXIR. 2020. https:\/\/elixir-europe.org\/. Accessed 31 Mar 20."},{"key":"442_CR35","unstructured":"Kubernetes: Production-Grade Container Orchestration. 2020. https:\/\/kubernetes.io\/. Accessed 31 Mar 20."},{"key":"442_CR36","unstructured":"Adaptive Computing: QUEue Manager (TORQUE). 2013. http:\/\/www.adaptivecomputing.com\/products\/torque. Accessed 23 Jan 20."},{"key":"442_CR37","doi-asserted-by":"crossref","unstructured":"Troger P, Rajic H, Haas A, Domagalski P (2007) Standardization of an API for distributed resource management systems. In: Seventh IEEE international symposium on cluster computing and the grid (CCGrid 2007). IEEE, Rio de Janeiro","DOI":"10.1109\/CCGRID.2007.109"},{"key":"442_CR38","volume-title":"Beowulf cluster computing with Linux","author":"T Tannenbaum","year":"2001","unstructured":"Tannenbaum T, Wright D, Miller K, Livny M (2001) Condor\u2014a distributed job scheduler. In: Sterling T (ed) Beowulf cluster computing with Linux. MIT Press, Cambridge"},{"key":"442_CR39","unstructured":"Chilton J. Pulsar. 2019. https:\/\/github.com\/galaxyproject\/pulsar. Accessed 23 Jan 20."},{"key":"442_CR40","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1016\/j.ymeth.2014.08.010","volume":"71","author":"V Kumar","year":"2015","unstructured":"Kumar V, Krishna S, Siddiqi MI (2015) Virtual screening strategies: recent advances in the identification and design of anti-cancer agents. Methods 71:64\u201370","journal-title":"Methods"},{"issue":"7743","key":"442_CR41","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1038\/s41586-019-0917-9","volume":"566","author":"J Lyu","year":"2019","unstructured":"Lyu J, Wang S, Balius TE, Singh I, Levit A, Moroz YS, O\u2019Meara MJ, Che T, Algaa E, Tolmachova K, Tolmachev AA, Shoichet BK, Roth BL, Irwin JJ (2019) Ultra-large library docking for discovering new chemotypes. Nature 566(7743):224\u2013229","journal-title":"Nature"},{"issue":"1","key":"442_CR42","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1002\/(SICI)1098-1128(199601)16:1<3::AID-MED1>3.0.CO;2-6","volume":"16","author":"RS Bohacek","year":"1996","unstructured":"Bohacek RS, McMartin C, Guida WC (1996) The art and practice of structure-based drug design: a molecular modeling perspective. Med Res Rev 16(1):3\u201350","journal-title":"Med Res Rev"},{"issue":"D1","key":"442_CR43","doi-asserted-by":"publisher","first-page":"1121","DOI":"10.1093\/nar\/gkx1076","volume":"46","author":"YH Li","year":"2017","unstructured":"Li YH, Yu CY, Li XX, Zhang P, Tang J, Yang Q, Fu T, Zhang X, Cui X, Tu G et al (2017) Therapeutic Target Database update 2018: enriched resource for facilitating bench-to-clinic research of targeted therapeutics. Nucleic Acids Res 46(D1):1121\u20131127","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"442_CR44","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1186\/1758-2946-5-S1-P36","volume":"5","author":"A Dalke","year":"2013","unstructured":"Dalke A (2013) The FPS fingerprint format and chemfp toolkit. J Cheminform 5(1):36","journal-title":"J Cheminform"},{"issue":"4","key":"442_CR45","doi-asserted-by":"publisher","first-page":"747","DOI":"10.1021\/ci9803381","volume":"39","author":"D Butina","year":"1999","unstructured":"Butina D (1999) Unsupervised data base clustering based on daylight\u2019s fingerprint and Tanimoto similarity: a fast and automated way to cluster small and large data sets. J Chem Inf Comput Sci 39(4):747\u2013750","journal-title":"J Chem Inf Comput Sci"},{"issue":"11","key":"442_CR46","doi-asserted-by":"publisher","first-page":"2324","DOI":"10.1021\/acs.jcim.5b00559","volume":"55","author":"T Sterling","year":"2015","unstructured":"Sterling T, Irwin JJ (2015) ZINC 15-ligand discovery for everyone. J Chem Inf Model 55(11):2324\u20132337","journal-title":"J Chem Inf Model"},{"issue":"2","key":"442_CR47","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1007\/s12551-016-0247-1","volume":"9","author":"NS Pagadala","year":"2017","unstructured":"Pagadala NS, Syed K, Tuszynski J (2017) Software for molecular docking: a review. Biophys Rev 9(2):91\u2013102","journal-title":"Biophys Rev"},{"issue":"1","key":"442_CR48","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1002\/prot.21082","volume":"65","author":"SF Sousa","year":"2006","unstructured":"Sousa SF, Fernandes PA, Ramos MJ (2006) Protein-ligand docking: current status and future challenges. Proteins Struct Funct Bioinform 65(1):15\u201326","journal-title":"Proteins Struct Funct Bioinform"},{"issue":"1","key":"442_CR49","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1186\/1471-2105-10-168","volume":"10","author":"V Le Guilloux","year":"2009","unstructured":"Le Guilloux V, Schmidtke P, Tuffery P (2009) Fpocket: an open source platform for ligand pocket detection. BMC Bioinform 10(1):168","journal-title":"BMC Bioinform"},{"issue":"4","key":"442_CR50","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1016\/j.ddtec.2004.11.007","volume":"1","author":"CA Lipinski","year":"2004","unstructured":"Lipinski CA (2004) Lead- and drug-like compounds: the rule-of-five revolution. Drug Discov Today Technol 1(4):337\u2013341","journal-title":"Drug Discov Today Technol"},{"issue":"14","key":"442_CR51","doi-asserted-by":"publisher","first-page":"3338","DOI":"10.1016\/j.bmcl.2005.05.046","volume":"15","author":"K-MJ Cheung","year":"2005","unstructured":"Cheung K-MJ, Matthews TP, James K, Rowlands MG, Boxall KJ, Sharp SY, Maloney A, Roe SM, Prodromou C, Pearl LH, Aherne GW, McDonald E, Workman P (2005) The identification, synthesis, protein crystal structure and in vitro biochemical evaluation of a new 3,4-diarylpyrazole class of Hsp90 inhibitors. Bioorg Med Chem Lett 15(14):3338\u20133343","journal-title":"Bioorg Med Chem Lett"},{"issue":"7329","key":"442_CR52","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1038\/nature09665","volume":"469","author":"DM Rosenbaum","year":"2011","unstructured":"Rosenbaum DM, Zhang C, Lyons JA, Holl R, Aragao D, Arlow DH, Rasmussen SGF, Choi H-J, DeVree BT, Sunahara RK, Chae PS, Gellman SH, Dror RO, Shaw DE, Weis WI, Caffrey M, Gmeiner P, Kobilka BK (2011) Structure and function of an irreversible agonist-$$\\beta _2$$ adrenoceptor complex. Nature 469(7329):236\u2013240","journal-title":"Nature"},{"key":"442_CR53","unstructured":"National Center for Advancing Translational Sciences: Tox21 Data Challenge 2014. 2014. https:\/\/tripod.nih.gov\/tox21\/challenge. Accessed 23 Jan 20"},{"key":"442_CR54","first-page":"2825","volume":"12","author":"F Pedregosa","year":"2011","unstructured":"Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, Blondel M, Prettenhofer P, Weiss R, Dubourg V, Vanderplas J, Passos A, Cournapeau D, Brucher M, Perrot M, Duchesnay E (2011) Scikit-learn: machine learning in Python. J Mach Learn Res 12:2825\u20132830","journal-title":"J Mach Learn Res"}],"container-title":["Journal of Cheminformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-020-00442-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13321-020-00442-7\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-020-00442-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,6]],"date-time":"2024-08-06T21:00:36Z","timestamp":1722978036000},"score":1,"resource":{"primary":{"URL":"https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/s13321-020-00442-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,6,1]]},"references-count":54,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2020,12]]}},"alternative-id":["442"],"URL":"https:\/\/doi.org\/10.1186\/s13321-020-00442-7","relation":{},"ISSN":["1758-2946"],"issn-type":[{"value":"1758-2946","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,6,1]]},"assertion":[{"value":"4 February 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 May 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 June 2020","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"}}],"article-number":"40"}}