{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,21]],"date-time":"2026-02-21T15:46:25Z","timestamp":1771688785080,"version":"3.50.1"},"publisher-location":"Cham","reference-count":12,"publisher":"Springer Nature Switzerland","isbn-type":[{"value":"9783031902512","type":"print"},{"value":"9783031902529","type":"electronic"}],"license":[{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025]]},"DOI":"10.1007\/978-3-031-90252-9_17","type":"book-chapter","created":{"date-parts":[[2025,4,24]],"date-time":"2025-04-24T20:03:52Z","timestamp":1745525032000},"page":"260-263","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Learning a\u00a0CoNCISE Language for\u00a0Small-Molecule Binding"],"prefix":"10.1007","author":[{"given":"Mert","family":"Erden","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6093-6260","authenticated-orcid":false,"given":"Kapil","family":"Devkota","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0009-0009-8740-8490","authenticated-orcid":false,"given":"Lia","family":"Varghese","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6698-6413","authenticated-orcid":false,"given":"Lenore","family":"Cowen","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4084-7340","authenticated-orcid":false,"given":"Rohit","family":"Singh","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,4,25]]},"reference":[{"key":"17_CR1","unstructured":"Bepler, T.,\u00a0Berger, B.: Learning protein sequence embeddings using information from structure. In: ICLR 2019 (2019)"},{"key":"17_CR2","unstructured":"Corso, G., et\u00a0al.: Diffdock: diffusion steps, twists, and turns for molecular docking. arXiv preprint arXiv:2210.01776 (2022)"},{"key":"17_CR3","doi-asserted-by":"crossref","unstructured":"Devkota K., et\u00a0al.: Miniaturizing, modifying, and augmenting nature\u2019s proteins with Raygun. In: bioRxiv, p. 2024\u201308 (2024)","DOI":"10.1101\/2024.08.13.607858"},{"issue":"18","key":"17_CR4","doi-asserted-by":"publisher","first-page":"6938","DOI":"10.1021\/acs.jcim.4c00422","volume":"64","author":"G Guichaoua","year":"2024","unstructured":"Guichaoua, G., et al.: Drug\u2013target interactions prediction at scale: the komet algorithm with the lcidb dataset. J. Chem. Inf. Model. 64(18), 6938\u20136956 (2024)","journal-title":"J. Chem. Inf. Model."},{"issue":"7873","key":"17_CR5","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","volume":"596","author":"J Jumper","year":"2021","unstructured":"Jumper, J., et al.: Highly accurate protein structure prediction with AlphaFold. Nature 596(7873), 583\u2013589 (2021)","journal-title":"Nature"},{"issue":"12","key":"17_CR6","doi-asserted-by":"publisher","first-page":"2075","DOI":"10.3390\/molecules22122075","volume":"22","author":"P Minkiewicz","year":"2017","unstructured":"Minkiewicz, P., et al.: Annotation of peptide structures using SMILES and other chemical codes-practical solutions. Molecules 22(12), 2075 (2017)","journal-title":"Molecules"},{"issue":"2","key":"17_CR7","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1021\/c160017a018","volume":"5","author":"HL Morgan","year":"1965","unstructured":"Morgan, H.L.: The generation of a unique machine description for chemical structures-a technique developed at chemical abstracts service. J. Chem. Doc. 5(2), 107\u2013113 (1965)","journal-title":"J. Chem. Doc."},{"issue":"15","key":"17_CR8","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2016239118","volume":"118","author":"A Rives","year":"2021","unstructured":"Rives, A., et al.: Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences. Proc. Natl. Acad. Sci. 118(15), e2016239118 (2021)","journal-title":"Proc. Natl. Acad. Sci."},{"issue":"24","key":"17_CR9","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2220778120","volume":"120","author":"R Singh","year":"2023","unstructured":"Singh, R., et al.: Contrastive learning in protein language space predicts interactions between drugs and protein targets. Proc. Natl. Acad. Sci. 120(24), e2220778120 (2023)","journal-title":"Proc. Natl. Acad. Sci."},{"key":"17_CR10","doi-asserted-by":"crossref","unstructured":"Sledzieski, S., et\u00a0al.: TT3D: leveraging precomputed protein 3d sequence models to predict protein\u2013protein interactions. Bioinformatics 39(11), btad663 (2023)","DOI":"10.1093\/bioinformatics\/btad663"},{"key":"17_CR11","unstructured":"Tamkin, A., et\u00a0al.: Codebook features: sparse and discrete interpretability for neural networks. arXiv:2310.17230 (2023)"},{"key":"17_CR12","unstructured":"Van Den\u00a0Oord, A., et\u00a0al.: Neural discrete representation learning. Adv. Neural Inf. Process. Syst. 30 (2017)"}],"container-title":["Lecture Notes in Computer Science","Research in Computational Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-031-90252-9_17","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,24]],"date-time":"2025-04-24T20:03:56Z","timestamp":1745525036000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-031-90252-9_17"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"ISBN":["9783031902512","9783031902529"],"references-count":12,"URL":"https:\/\/doi.org\/10.1007\/978-3-031-90252-9_17","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"value":"0302-9743","type":"print"},{"value":"1611-3349","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025]]},"assertion":[{"value":"25 April 2025","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"M.E., K.D., L.C., and R.S. have filed patents related to this work with provisional patent (#63\/735,991).","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Disclosure of Interests"}},{"value":"RECOMB","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Conference on Research in Computational Molecular Biology","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Seoul","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Korea (Republic of)","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2025","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"26 April 2025","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"29 April 2025","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"29","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"recomb2025","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/recomb.org\/recomb2025\/index.html","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}}]}}