{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,3,2]],"date-time":"2024-03-02T21:52:08Z","timestamp":1709416328720},"reference-count":61,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2023,10,16]],"date-time":"2023-10-16T00:00:00Z","timestamp":1697414400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2023,10,16]],"date-time":"2023-10-16T00:00:00Z","timestamp":1697414400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["441958208"],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"deutsche forschungsgemeinschaft","doi-asserted-by":"crossref","award":["239748522"],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100012957","name":"Friedrich-Schiller-Universit\u00e4t Jena","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100012957","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Cheminform"],"abstract":"Abstract<\/jats:title>In recent years, cheminformatics has experienced significant advancements through the development of new open-source software tools based on various cheminformatics programming toolkits. However, adopting these toolkits presents challenges, including proper installation, setup, deployment, and compatibility management. In this work, we present the Cheminformatics Microservice. This open-source solution provides a unified interface for accessing commonly used functionalities of multiple cheminformatics toolkits, namely RDKit, Chemistry Development Kit (CDK), and Open Babel. In addition, more advanced functionalities like structure generation and Optical Chemical Structure Recognition (OCSR) are made available through the Cheminformatics Microservice based on pre-existing tools. The software service also enables developers to extend the functionalities easily and to seamlessly integrate them with existing workflows and applications. It is built on FastAPI and containerized using Docker, making it highly scalable. An instance of the microservice is publicly available at https:\/\/api.naturalproducts.net<\/jats:ext-link>. The source code is publicly accessible on GitHub, accompanied by comprehensive documentation, version control, and continuous integration and deployment workflows. All resources can be found at the following link: https:\/\/github.com\/Steinbeck-Lab\/cheminformatics-microservice<\/jats:ext-link>.<\/jats:p>\n Graphical Abstract<\/jats:bold><\/jats:p>","DOI":"10.1186\/s13321-023-00762-4","type":"journal-article","created":{"date-parts":[[2023,10,16]],"date-time":"2023-10-16T05:01:42Z","timestamp":1697432502000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Cheminformatics Microservice: unifying access to open cheminformatics toolkits"],"prefix":"10.1186","volume":"15","author":[{"given":"Venkata","family":"Chandrasekhar","sequence":"first","affiliation":[]},{"given":"Nisha","family":"Sharma","sequence":"additional","affiliation":[]},{"given":"Jonas","family":"Schaub","sequence":"additional","affiliation":[]},{"given":"Christoph","family":"Steinbeck","sequence":"additional","affiliation":[]},{"given":"Kohulan","family":"Rajan","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,10,16]]},"reference":[{"key":"762_CR1","first-page":"257","volume-title":"Methods in pharmacology and toxicology","author":"P Ambure","year":"2014","unstructured":"Ambure P, Aher RB, Roy K (2014) Recent advances in the open access cheminformatics toolkits, software tools, workflow environments, and databases. In: Zhang Wei (ed) Methods in pharmacology and toxicology. New York, Springer, pp 257\u2013296"},{"key":"762_CR2","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1145\/2366316.2366334","volume":"55","author":"JK Wegner","year":"2012","unstructured":"Wegner JK, Sterling A, Guha R, Bender A, Faulon J-L, Hastings J, O\u2019Boyle N, Overington J, Van Vlijmen H, Willighagen E (2012) Cheminformatics. Commun ACM 55:65\u201375. https:\/\/doi.org\/10.1145\/2366316.2366334","journal-title":"Commun ACM"},{"key":"762_CR3","unstructured":"Landrum G, et al. RDKit: open-source cheminformatics software. 2016. http:\/\/www.rdkit.org\/. https:\/\/github.com\/rdkit\/rdkit. Accessed 10 July 2023"},{"key":"762_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) Open babel: an open chemical toolbox. J Cheminform 3:33. https:\/\/doi.org\/10.1186\/1758-2946-3-33","journal-title":"J Cheminform"},{"key":"762_CR5","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-017-0220-4","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 Cheminf. https:\/\/doi.org\/10.1186\/s13321-017-0220-4","journal-title":"J Cheminf"},{"key":"762_CR6","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1021\/ci025584y","volume":"43","author":"C Steinbeck","year":"2003","unstructured":"Steinbeck C, Han Y, Kuhn S, Horlacher O, Luttmann E, Willighagen E (2003) The chemistry development kit (CDK): an open-source java library for chemo- and bioinformatics. J Chem Inf Comput Sci 43:493\u2013500. https:\/\/doi.org\/10.1021\/ci025584y","journal-title":"J Chem Inf Comput Sci"},{"key":"762_CR7","unstructured":"Indigo Toolkit. https:\/\/lifescience.opensource.epam.com\/indigo\/. Accessed 25 June 2020."},{"key":"762_CR8","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1186\/s13321-022-00616-5","volume":"14","author":"BR Terlouw","year":"2022","unstructured":"Terlouw BR, Vromans SPJM, Medema MH (2022) PIKAChU: a python-based informatics kit for analysing chemical units. J Cheminform 14:34. https:\/\/doi.org\/10.1186\/s13321-022-00616-5","journal-title":"J Cheminform"},{"key":"762_CR9","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1186\/s13321-022-00609-4","volume":"14","author":"HO Brinkhaus","year":"2022","unstructured":"Brinkhaus HO, Rajan K, Zielesny A, Steinbeck C (2022) RanDepict: random chemical structure depiction generator. J Cheminform 14:31. https:\/\/doi.org\/10.1186\/s13321-022-00609-4","journal-title":"J Cheminform"},{"key":"762_CR10","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1186\/s13321-023-00695-y","volume":"15","author":"M Zulfiqar","year":"2023","unstructured":"Zulfiqar M, Gadelha L, Steinbeck C, Sorokina M, Peters K (2023) MAW: the reproducible metabolome annotation workflow for untargeted tandem mass spectrometry. J Cheminform 15:32. https:\/\/doi.org\/10.1186\/s13321-023-00695-y","journal-title":"J Cheminform"},{"key":"762_CR11","doi-asserted-by":"publisher","first-page":"649","DOI":"10.1108\/gkmc-07-2020-0103","volume":"71","author":"M Ashiq","year":"2022","unstructured":"Ashiq M, Usmani MH, Naeem M (2022) A systematic literature review on research data management practices and services. Glob Knowl Mem Commun 71:649\u2013671. https:\/\/doi.org\/10.1108\/gkmc-07-2020-0103","journal-title":"Glob Knowl Mem Commun"},{"key":"762_CR12","unstructured":"Van Gurp J, Prehofer C. Version management tools as a basis for integrating product derivation and software product families. In: Proceedings of the proceedings of the workshop on variability management-working with variability mechanisms at SPLC; 2006; pp. 48\u201358."},{"key":"762_CR13","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1145\/3277539.3277541","volume":"16","author":"S Esparrachiari","year":"2018","unstructured":"Esparrachiari S, Reilly T, Rentz A (2018) Tracking and controlling microservice dependencies. ACM Queue 16:44\u201365. https:\/\/doi.org\/10.1145\/3277539.3277541","journal-title":"ACM Queue"},{"key":"762_CR14","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1142\/9789812389718_0005","volume-title":"Handbook of software engineering and knowledge engineering","author":"G Canfora","year":"2001","unstructured":"Canfora G, Cimitile A (2001) Software maintenance. In: Chang SK (ed) Handbook of software engineering and knowledge engineering. World Scientific Publishing Company, Singapore, pp 91\u2013120"},{"key":"762_CR15","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/s13321-020-00481-0","volume":"13","author":"Y-C Huang","year":"2021","unstructured":"Huang Y-C, Tremouilhac P, Nguyen A, Jung N, Br\u00e4se S (2021) ChemSpectra: a web-based spectra editor for analytical data. J Cheminform 13:8. https:\/\/doi.org\/10.1186\/s13321-020-00481-0","journal-title":"J Cheminform"},{"key":"762_CR16","doi-asserted-by":"publisher","first-page":"3587","DOI":"10.1039\/d0sc05337f","volume":"12","author":"KM Jablonka","year":"2020","unstructured":"Jablonka KM, Moosavi SM, Asgari M, Ireland C, Patiny L, Smit B (2020) A data-driven perspective on the colours of metal-organic frameworks. Chem Sci 12:3587\u20133598. https:\/\/doi.org\/10.1039\/d0sc05337f","journal-title":"Chem Sci"},{"key":"762_CR17","doi-asserted-by":"publisher","first-page":"1223","DOI":"10.1021\/ci300563h","volume":"53","author":"L Patiny","year":"2013","unstructured":"Patiny L, Borel A (2013) ChemCalc: a building block for tomorrow\u2019s chemical infrastructure. J Chem Inf Model 53:1223\u20131228. https:\/\/doi.org\/10.1021\/ci300563h","journal-title":"J Chem Inf Model"},{"key":"762_CR18","doi-asserted-by":"publisher","first-page":"520","DOI":"10.1002\/mrc.4669","volume":"56","author":"L Patiny","year":"2018","unstructured":"Patiny L, Zasso M, Kostro D, Bernal A, Castillo AM, Bola\u00f1os A, Asencio MA, Pellet N, Todd M, Schloerer N et al (2018) The C6H6 NMR repository: an integral solution to control the flow of your data from the magnet to the public. Magn Reson Chem 56:520\u2013528. https:\/\/doi.org\/10.1002\/mrc.4669","journal-title":"Magn Reson Chem"},{"key":"762_CR19","doi-asserted-by":"publisher","first-page":"76","DOI":"10.4018\/ijeis.2019070105","volume":"15","author":"J Ofoeda","year":"2019","unstructured":"Ofoeda J, Boateng R, Effah J (2019) Application programming interface (API) research. Int J Enterp Inf Syst 15:76\u201395. https:\/\/doi.org\/10.4018\/ijeis.2019070105","journal-title":"Int J Enterp Inf Syst"},{"key":"762_CR20","volume-title":"Building microservices","author":"S Newman","year":"2015","unstructured":"Newman S (2015) Building microservices. O\u2019Reilly Media, Sebastopol"},{"key":"762_CR21","volume-title":"Microservices: flexible software architecture","author":"E Wolff","year":"2017","unstructured":"Wolff E (2017) Microservices: flexible software architecture. Addison-Wesley, Boston"},{"key":"762_CR22","doi-asserted-by":"crossref","unstructured":"Chen L. Microservices: architecting for continuous delivery and DevOps. In: Proceedings of the 2018 IEEE international conference on software architecture (ICSA); 2018; pp. 39\u2013397.","DOI":"10.1109\/ICSA.2018.00013"},{"key":"762_CR23","unstructured":"Containerization explained. https:\/\/www.ibm.com\/topics\/containerization. Accessed 22 June 2023."},{"key":"762_CR24","unstructured":"Turnbull J. The docker book: containerization is the new virtualization. James Turnbull. 2014"},{"key":"762_CR25","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1007\/978-1-4842-3012-1_6","volume-title":"Docker for data science: building scalable and extensible data infrastructure around the Jupyter notebook server","author":"J Cook","year":"2017","unstructured":"Cook J (2017) Docker hub. In: Cook J (ed) Docker for data science: building scalable and extensible data infrastructure around the Jupyter notebook server. Apress, Berkeley, pp 103\u2013118"},{"key":"762_CR26","doi-asserted-by":"crossref","unstructured":"Sohan SM, Maurer F, Anslow C, Robillard MP. A study of the effectiveness of usage examples in REST API documentation. In: Proceedings of the 2017 IEEE symposium on visual languages and human-centric computing (VL\/HCC). 2017; pp. 53\u201361.","DOI":"10.1109\/VLHCC.2017.8103450"},{"key":"762_CR27","doi-asserted-by":"crossref","unstructured":"Gokhale S, Poosarla R, Tikar S, Gunjawate S, Hajare A, Deshpande S, Gupta S, Karve K. Creating helm charts to ease deployment of enterprise application and its related services in kubernetes. In: Proceedings of the 2021 international conference on computing, communication and green engineering (CCGE); 2021; pp. 1\u20135.","DOI":"10.1109\/CCGE50943.2021.9776450"},{"key":"762_CR28","unstructured":"Nelson KE, Scherer MK, et al. JPype; Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States), 2020."},{"key":"762_CR29","unstructured":"The OpenAPI Specification (3.1.0). https:\/\/www.openapis.org. Accessed on 25 September 2023"},{"key":"762_CR30","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1016\/S0003-2670(01)83100-7","volume":"103","author":"W Bremser","year":"1978","unstructured":"Bremser W (1978) Hose\u2014a novel substructure code. Anal Chim Acta 103:355\u2013365. https:\/\/doi.org\/10.1016\/S0003-2670(01)83100-7","journal-title":"Anal Chim Acta"},{"key":"762_CR31","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1021\/ci700286x","volume":"48","author":"P Ertl","year":"2008","unstructured":"Ertl P, Roggo S, Schuffenhauer A (2008) Natural product-likeness score and its application for prioritization of compound libraries. J Chem Inf Model 48:68\u201374. https:\/\/doi.org\/10.1021\/ci700286x","journal-title":"J Chem Inf Model"},{"key":"762_CR32","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1186\/s13321-016-0174-y","volume":"8","author":"Y DjoumbouFeunang","year":"2016","unstructured":"DjoumbouFeunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E et al (2016) ClassyFire: automated chemical classification with a comprehensive, computable taxonomy. J Cheminform 8:61. https:\/\/doi.org\/10.1186\/s13321-016-0174-y","journal-title":"J Cheminform"},{"key":"762_CR33","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1186\/s13321-020-00456-1","volume":"12","author":"AP Bento","year":"2020","unstructured":"Bento AP, Hersey A, F\u00e9lix E, Landrum G, Gaulton A, Atkinson F, Bellis LJ, De Veij M, Leach AR (2020) An open source chemical structure curation pipeline using RDKit. J Cheminform 12:51. https:\/\/doi.org\/10.1186\/s13321-020-00456-1","journal-title":"J Cheminform"},{"key":"762_CR34","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1021\/ci00057a005","volume":"28","author":"D Weininger","year":"1988","unstructured":"Weininger D (1988) SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J Chem Inf Comput Sci 28:31\u201336. https:\/\/doi.org\/10.1021\/ci00057a005","journal-title":"J Chem Inf Comput Sci"},{"key":"762_CR35","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1186\/s13321-015-0068-4","volume":"7","author":"SR Heller","year":"2015","unstructured":"Heller SR, McNaught A, Pletnev I, Stein S, Tchekhovskoi D (2015) InChI, the IUPAC international chemical identifier. J Cheminform 7:23. https:\/\/doi.org\/10.1186\/s13321-015-0068-4","journal-title":"J Cheminform"},{"key":"762_CR36","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1515\/ci.2009.31.1.7","volume":"31","author":"SR Heller","year":"2009","unstructured":"Heller SR, McNaught AD (2009) The IUPAC international chemical identifier (InChI). Chem Int Newsmag IUPAC 31:7\u20139. https:\/\/doi.org\/10.1515\/ci.2009.31.1.7","journal-title":"Chem Int Newsmag IUPAC"},{"key":"762_CR37","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1021\/ci00062a008","volume":"29","author":"D Weininger","year":"1989","unstructured":"Weininger D, Weininger A, Weininger JL (1989) SMILES. 2. Algorithm for generation of unique SMILES notation. J Chem Inf Comput Sci 29:97\u2013101. https:\/\/doi.org\/10.1021\/ci00062a008","journal-title":"J Chem Inf Comput Sci"},{"key":"762_CR38","unstructured":"Chemaxon Extended SMILES and SMARTS\u2013CXSMILES and CXSMARTS. https:\/\/docs.chemaxon.com\/display\/docs\/chemaxon-extended-smiles-and-smarts-cxsmiles-and-cxsmarts.md. Accessed 22 June 2023."},{"key":"762_CR39","doi-asserted-by":"publisher","first-page":"045024","DOI":"10.1088\/2632-2153\/aba947","volume":"1","author":"M Krenn","year":"2020","unstructured":"Krenn M, H\u00e4se F, Nigam A, Friederich P, Aspuru-Guzik A (2020) Self-referencing embedded strings (SELFIES): a 100% robust molecular string representation. Mach Learn Sci Technol 1:045024. https:\/\/doi.org\/10.1088\/2632-2153\/aba947","journal-title":"Mach Learn Sci Technol"},{"key":"762_CR40","doi-asserted-by":"publisher","first-page":"100588","DOI":"10.1016\/j.patter.2022.100588","volume":"3","author":"M Krenn","year":"2022","unstructured":"Krenn M, Ai Q, Barthel S, Carson N, Frei A, Frey NC, Friederich P, Gaudin T, Gayle AA, Jablonka KM et al (2022) SELFIES and the future of molecular string representations. Patterns Prejud 3:100588. https:\/\/doi.org\/10.1016\/j.patter.2022.100588","journal-title":"Patterns Prejud"},{"key":"762_CR41","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1186\/s13321-021-00512-4","volume":"13","author":"K Rajan","year":"2021","unstructured":"Rajan K, Zielesny A, Steinbeck C (2021) STOUT: SMILES to IUPAC names using neural machine translation. J Cheminform 13:34. https:\/\/doi.org\/10.1186\/s13321-021-00512-4","journal-title":"J Cheminform"},{"key":"762_CR42","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1002\/anie.196603851","volume":"5","author":"RS Cahn","year":"1966","unstructured":"Cahn RS, Ingold C, Prelog V (1966) Specification of molecular chirality. Angew Chem Int Ed Engl 5:385\u2013415. https:\/\/doi.org\/10.1002\/anie.196603851","journal-title":"Angew Chem Int Ed Engl"},{"key":"762_CR43","doi-asserted-by":"publisher","first-page":"1322","DOI":"10.1093\/bioinformatics\/btu829","volume":"31","author":"N Rego","year":"2015","unstructured":"Rego N, Koes D (2015) 3Dmol.js: molecular visualization with WebGL. Bioinformatics 31:1322\u20131324. https:\/\/doi.org\/10.1093\/bioinformatics\/btu829","journal-title":"Bioinformatics"},{"key":"762_CR44","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1186\/s13321-021-00496-1","volume":"13","author":"K Rajan","year":"2021","unstructured":"Rajan K, Brinkhaus HO, Sorokina M, Zielesny A, Steinbeck C (2021) DECIMER-segmentation: automated extraction of chemical structure depictions from scientific literature. J Cheminform 13:20. https:\/\/doi.org\/10.1186\/s13321-021-00496-1","journal-title":"J Cheminform"},{"key":"762_CR45","doi-asserted-by":"publisher","DOI":"10.26434\/chemrxiv-2023-xhcx9","author":"K Rajan","year":"2023","unstructured":"Rajan K, Brinkhaus HO, Isabel Agea M, Zielesny A, Steinbeck C (2023) DECIMER.ai\u2014an open platform for automated optical chemical structure identification, segmentation and recognition in scientific publications. ChemRxiv. https:\/\/doi.org\/10.26434\/chemrxiv-2023-xhcx9","journal-title":"ChemRxiv"},{"key":"762_CR46","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1186\/s13321-022-00604-9","volume":"14","author":"BD McKay","year":"2022","unstructured":"McKay BD, Yirik MA, Steinbeck C (2022) Surge: a fast open-source chemical graph generator. J Cheminform 14:24. https:\/\/doi.org\/10.1186\/s13321-022-00604-9","journal-title":"J Cheminform"},{"key":"762_CR47","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1186\/s13321-020-00467-y","volume":"12","author":"J Schaub","year":"2020","unstructured":"Schaub J, Zielesny A, Steinbeck C, Sorokina M (2020) Too sweet: cheminformatics for deglycosylation in natural products. J Cheminform 12:67. https:\/\/doi.org\/10.1186\/s13321-020-00467-y","journal-title":"J Cheminform"},{"key":"762_CR48","doi-asserted-by":"publisher","first-page":"160018","DOI":"10.1038\/sdata.2016.18","volume":"3","author":"MD Wilkinson","year":"2016","unstructured":"Wilkinson MD, Dumontier M, Aalbersberg IJJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten J-W, da Silva Santos LB, Bourne PE et al (2016) The FAIR guiding principles for scientific data management and stewardship. Sci Data 3:160018. https:\/\/doi.org\/10.1038\/sdata.2016.18","journal-title":"Sci Data"},{"key":"762_CR49","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1186\/s13321-023-00730-y","volume":"15","author":"CT Hoyt","year":"2023","unstructured":"Hoyt CT, Zdrazil B, Guha R, Jeliazkova N, Martinez-Mayorga K, Nittinger E (2023) Improving reproducibility and reusability in the journal of cheminformatics. J Cheminform 15:62. https:\/\/doi.org\/10.1186\/s13321-023-00730-y","journal-title":"J Cheminform"},{"key":"762_CR50","unstructured":"Prometheus Overview. https:\/\/prometheus.io\/docs\/introduction\/overview\/. Accessed 23 June 2023."},{"key":"762_CR51","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1007\/978-1-4842-6888-9_6","volume-title":"Monitoring cloud-native applications: lead agile operations confidently using open source software","author":"M Chakraborty","year":"2021","unstructured":"Chakraborty M, Kundan AP (2021) Grafana. In: Chakraborty M, Kundan AP (eds) Monitoring cloud-native applications: lead agile operations confidently using open source software. Apress, Berkeley, pp 187\u2013240"},{"key":"762_CR52","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-1-4842-6464-5","volume-title":"Hands-on GitHub actions: implement CI\/CD with GitHub action workflows for your applications","author":"C Chandrasekara","year":"2021","unstructured":"Chandrasekara C, Herath P (2021) Introduction to GitHub Actions. In: Chandrasekara C, Herath P (eds) Hands-on GitHub actions: implement CI\/CD with GitHub action workflows for your applications. Apress, Berkeley, pp 1\u20138"},{"key":"762_CR53","doi-asserted-by":"publisher","first-page":"D945","DOI":"10.1093\/nar\/gkw1074","volume":"45","author":"A Gaulton","year":"2017","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 (2017) The ChEMBL database in 2017. Nucleic Acids Res 45:D945\u2013D954. https:\/\/doi.org\/10.1093\/nar\/gkw1074","journal-title":"Nucleic Acids Res"},{"key":"762_CR54","first-page":"77","volume":"2","author":"S Taneja","year":"2014","unstructured":"Taneja S, Gupta PR (2014) Python as a tool for web server application development. JIMS8I Int J Inf 2:77\u201383","journal-title":"JIMS8I Int J Inf"},{"key":"762_CR55","doi-asserted-by":"publisher","first-page":"1755","DOI":"10.1021\/acs.jcim.8b00324","volume":"58","author":"RM Hanson","year":"2018","unstructured":"Hanson RM, Musacchio S, Mayfield JW, Vainio MJ, Yerin A, Redkin D (2018) Algorithmic analysis of Cahn\u2013Ingold\u2013Prelog rules of stereochemistry: proposals for revised rules and a guide for machine implementation. J Chem Inf Model 58:1755\u20131765. https:\/\/doi.org\/10.1021\/acs.jcim.8b00324","journal-title":"J Chem Inf Model"},{"key":"762_CR56","volume-title":"Centres: perception and labelling of stereogenic centres in chemical structures (Version 10) [Computer software]","author":"M John","year":"2018","unstructured":"John M (2018) Centres: perception and labelling of stereogenic centres in chemical structures (Version 10) [Computer software]. Github, San Francisco"},{"key":"762_CR57","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1002\/bmb.2006.494034042644","volume":"34","author":"A Herr\u00e1ez","year":"2006","unstructured":"Herr\u00e1ez A (2006) Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ 34:255\u2013261. https:\/\/doi.org\/10.1002\/bmb.2006.494034042644","journal-title":"Biochem Mol Biol Educ"},{"key":"762_CR58","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1002\/ijch.201300024","volume":"53","author":"RM Hanson","year":"2013","unstructured":"Hanson RM, Prilusky J, Renjian Z, Nakane T, Sussman JL (2013) JSmol and the next-generation web-based representation of 3D molecular structure as applied to Proteopedia. Isr J Chem 53:207\u2013216. https:\/\/doi.org\/10.1002\/ijch.201300024","journal-title":"Isr J Chem"},{"key":"762_CR59","unstructured":"PubChem Testosterone. https:\/\/pubchem.ncbi.nlm.nih.gov\/compound\/6013. Accessed 23 June 2023."},{"key":"762_CR60","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jnatprod.3c00215","author":"G Dai","year":"2023","unstructured":"Dai G, Sun J, Peng X, Shen Q, Wu C, Sun Z, Sui H, Ren X, Zhang Y, Bian X (2023) Astellolides R-W, drimane-type sesquiterpenoids from an Aspergillus Parasiticus strain associated with an isopod. J Nat Prod. https:\/\/doi.org\/10.1021\/acs.jnatprod.3c00215","journal-title":"J Nat Prod"},{"key":"762_CR61","unstructured":"Senart T. Vegeta: HTTP load testing tool and library: it\u2019s over 9000. Github."}],"container-title":["Journal of Cheminformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-023-00762-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13321-023-00762-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13321-023-00762-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,21]],"date-time":"2023-11-21T13:58:27Z","timestamp":1700575107000},"score":1,"resource":{"primary":{"URL":"https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/s13321-023-00762-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,10,16]]},"references-count":61,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2023,12]]}},"alternative-id":["762"],"URL":"https:\/\/doi.org\/10.1186\/s13321-023-00762-4","relation":{"has-preprint":[{"id-type":"doi","id":"10.26434\/chemrxiv-2023-hk8zn-v2","asserted-by":"object"}]},"ISSN":["1758-2946"],"issn-type":[{"value":"1758-2946","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,10,16]]},"assertion":[{"value":"7 July 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 September 2023","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 October 2023","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 November 2023","order":4,"name":"change_date","label":"Change Date","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Update","order":5,"name":"change_type","label":"Change Type","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"We have replaced a link encoding on page 6","order":6,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"The authors have given their consent for the work to be published.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors do not have any competing interests to declare.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"98"}}