{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T11:45:02Z","timestamp":1785498302672,"version":"3.56.0"},"reference-count":59,"publisher":"Wiley","issue":"7","license":[{"start":{"date-parts":[[2026,4,24]],"date-time":"2026-04-24T00:00:00Z","timestamp":1776988800000},"content-version":"vor","delay-in-days":10,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T00:00:00Z","timestamp":1776124800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["chemistry-europe.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["ChemMedChem"],"published-print":{"date-parts":[[2026,4,14]]},"abstract":"<jats:p>Since 2012, with the publication of our foundational work \u201cSolvent structure improves docking prediction in lectin\u2013carbohydrate complexes,\u201d our group has been devoted to the study of protein\u2013ligand interactions using molecular simulation tools. Over the past decade, we have shown that protein\u2013solvent interactions, particularly when simulated in mixed solvents containing probes such as ethanol, phenol, and isopropanol, often mimic the interactions observed in experimental protein\u2013ligand complexes. This knowledge can be used to improve docking performance by guiding pose prediction and scoring. We termed this strategy\u2010biased docking. Over the years, we demonstrated its applicability to pose prediction, virtual screening (VS), protein\u2013protein docking, and metalloprotein docking. In this short review, we summarize our results and contextualize them within the broader literature, offering a concise description of how to implement the biased docking strategy using current docking software. We also explore the physicochemical rationale behind its effectiveness and discuss how this knowledge can inform emerging Machine Learning and AI\u2010based methodologies.<\/jats:p>","DOI":"10.1002\/cmdc.202501058","type":"journal-article","created":{"date-parts":[[2026,4,25]],"date-time":"2026-04-25T04:35:33Z","timestamp":1777091733000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["How and Why Does Knowledge\u2010Based Biased Docking Improve Molecular Docking Performance?"],"prefix":"10.1002","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-2838-0356","authenticated-orcid":false,"given":"Juan Manuel","family":"Prieto","sequence":"first","affiliation":[{"name":"Instituto de Qu\u00edmica Biol\u00f3gica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET  CABA Buenos Aires Argentina"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-7415-024X","authenticated-orcid":false,"given":"Jorge Octavio","family":"Lannot","sequence":"additional","affiliation":[{"name":"Instituto de Qu\u00edmica Biol\u00f3gica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET  CABA Buenos Aires Argentina"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6746-4449","authenticated-orcid":false,"given":"Camila Mara","family":"Clemente","sequence":"additional","affiliation":[{"name":"Instituto de Qu\u00edmica Biol\u00f3gica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET  CABA Buenos Aires Argentina"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5352-7234","authenticated-orcid":false,"given":"Carlos","family":"Modenutti","sequence":"additional","affiliation":[{"name":"Instituto de Qu\u00edmica Biol\u00f3gica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET  CABA Buenos Aires Argentina"},{"name":"Departamento de Qu\u00edmica Biol\u00f3gica Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires (FCEyN\u2010UBA)  CABA Buenos Aires Argentina"},{"name":"Consiglio Nazionale delle Ricerche (CNR) Istituto di Biologia e Biotecnologia Agraria (IBBA)  Milano Italia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2190-137X","authenticated-orcid":false,"given":"Adrian","family":"Turjanski","sequence":"additional","affiliation":[{"name":"Instituto de Qu\u00edmica Biol\u00f3gica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET  CABA Buenos Aires Argentina"},{"name":"Departamento de Qu\u00edmica Biol\u00f3gica Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires (FCEyN\u2010UBA)  CABA Buenos Aires Argentina"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7911-9340","authenticated-orcid":false,"given":"Marcelo A.","family":"Mart\u00ed","sequence":"additional","affiliation":[{"name":"Instituto de Qu\u00edmica Biol\u00f3gica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET  CABA Buenos Aires Argentina"},{"name":"Departamento de Qu\u00edmica Biol\u00f3gica Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires (FCEyN\u2010UBA)  CABA Buenos Aires Argentina"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,4,24]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2018.01382"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.23244"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1021\/jp9723574"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1021\/ja0771033"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.2174\/156802610790232288"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv411"},{"key":"e_1_2_8_8_1","first-page":"75","volume-title":"Methods in Molecular Biology","author":"Faller C. E.","year":"2015"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.1021\/ci4005628"},{"key":"e_1_2_8_10_1","doi-asserted-by":"publisher","DOI":"10.1039\/D1SC01781K"},{"key":"e_1_2_8_11_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.4c01189"},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.6b00678"},{"key":"e_1_2_8_13_1","first-page":"393","volume-title":"Methods in Molecular Biology","author":"Li Z.","year":"2012"},{"key":"e_1_2_8_14_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.2c00264"},{"key":"e_1_2_8_15_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21256"},{"key":"e_1_2_8_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz152"},{"key":"e_1_2_8_17_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.0c01006"},{"key":"e_1_2_8_18_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.1c00203"},{"key":"e_1_2_8_19_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.3c01853"},{"key":"e_1_2_8_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr651"},{"key":"e_1_2_8_21_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102105\u201010\u2010168"},{"key":"e_1_2_8_22_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac381"},{"key":"e_1_2_8_23_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp240"},{"key":"e_1_2_8_24_1","doi-asserted-by":"publisher","DOI":"10.1093\/glycob\/cws147"},{"key":"e_1_2_8_25_1","doi-asserted-by":"publisher","DOI":"10.1093\/glycob\/cwu102"},{"key":"e_1_2_8_26_1","doi-asserted-by":"publisher","DOI":"10.1093\/glycob\/cwag005"},{"key":"e_1_2_8_27_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.5b00834"},{"key":"e_1_2_8_28_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.0c00373"},{"key":"e_1_2_8_29_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.febslet.2010.02.027"},{"key":"e_1_2_8_30_1","doi-asserted-by":"publisher","DOI":"10.1021\/jm300687e"},{"key":"e_1_2_8_31_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1072"},{"key":"e_1_2_8_32_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.20512"},{"key":"e_1_2_8_33_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad1004"},{"key":"e_1_2_8_34_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrd1343"},{"key":"e_1_2_8_35_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1603929113"},{"key":"e_1_2_8_36_1","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1998.1843"},{"key":"e_1_2_8_37_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu097"},{"key":"e_1_2_8_38_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh354"},{"key":"e_1_2_8_39_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btg371"},{"key":"e_1_2_8_40_1","doi-asserted-by":"publisher","DOI":"10.1021\/ja026939x"},{"key":"e_1_2_8_41_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn216"},{"key":"e_1_2_8_42_1","doi-asserted-by":"publisher","DOI":"10.1101\/2021.10.04.463034"},{"key":"e_1_2_8_43_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abj8754"},{"key":"e_1_2_8_44_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature08300"},{"key":"e_1_2_8_45_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.copbio.2011.11.005"},{"key":"e_1_2_8_46_1","doi-asserted-by":"publisher","DOI":"10.1021\/ci500209e"},{"key":"e_1_2_8_47_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbac620"},{"key":"e_1_2_8_48_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11721\u2010007\u20100006\u20109"},{"key":"e_1_2_8_49_1","doi-asserted-by":"publisher","DOI":"10.1039\/D2SC06576B"},{"key":"e_1_2_8_50_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.8b01310"},{"key":"e_1_2_8_51_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.6b00623"},{"key":"e_1_2_8_52_1","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.0c01002"},{"key":"e_1_2_8_53_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010024\u201007487\u2010w"},{"key":"e_1_2_8_54_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.adl2528"},{"key":"e_1_2_8_55_1","doi-asserted-by":"publisher","DOI":"10.1101\/2025.06.14.659707"},{"key":"e_1_2_8_56_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42256\u2010021\u201000409\u20109"},{"key":"e_1_2_8_57_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13321\u2010021\u201000522\u20102"},{"key":"e_1_2_8_58_1","volume-title":"Proc. 11th International Conference on Learning Representations (ICLR 2023)","author":"Corso G.","year":"2022"},{"key":"e_1_2_8_59_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467\u2010024\u201051321\u2010w"},{"key":"e_1_2_8_60_1","doi-asserted-by":"publisher","DOI":"10.48550\/ARXIV.1510.02855"}],"container-title":["ChemMedChem"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/chemistry-europe.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/cmdc.202501058","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/chemistry-europe.onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/cmdc.202501058","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/chemistry-europe.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/cmdc.202501058","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T06:19:30Z","timestamp":1777357170000},"score":1,"resource":{"primary":{"URL":"https:\/\/chemistry-europe.onlinelibrary.wiley.com\/doi\/10.1002\/cmdc.202501058"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,14]]},"references-count":59,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2026,4,14]]}},"alternative-id":["10.1002\/cmdc.202501058"],"URL":"https:\/\/doi.org\/10.1002\/cmdc.202501058","archive":["Portico"],"relation":{},"ISSN":["1860-7179","1860-7187"],"issn-type":[{"value":"1860-7179","type":"print"},{"value":"1860-7187","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,14]]},"assertion":[{"value":"2025-11-21","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-01-20","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-04-24","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e202501058"}}