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One of the most challenging problems in drug discovery is the protein\u2013ligand binding pose prediction. To predict the most stable structure of the complex, the performance of conventional structure-based molecular docking methods heavily depends on the accuracy of scoring or energy functions (as an approximation of affinity) for each pose of the protein\u2013ligand docking complex to effectively guide the search in an exponentially large solution space. However, due to the heterogeneity of molecular structures, the existing scoring calculation methods are either tailored to a particular data set or fail to exhibit high accuracy. In this paper, we propose a convolutional neural network (CNN)-based model that learns to predict the stability factor of the protein\u2013ligand complex and exhibits the ability of CNNs to improve the existing docking software. Evaluated results on PDBbind data set indicate that our approach reduces the execution time of the traditional docking-based method while improving the accuracy. Our code, experiment scripts, and pretrained models are available at https:\/\/github.com\/j9650\/MedusaNet.<\/jats:p>","DOI":"10.1021\/acs.jcim.0c00542","type":"journal-article","created":{"date-parts":[[2020,10,14]],"date-time":"2020-10-14T14:15:17Z","timestamp":1602684917000},"page":"4594-4602","source":"Crossref","is-referenced-by-count":25,"title":["Guiding Conventional Protein\u2013Ligand Docking\nSoftware with Convolutional Neural Networks"],"prefix":"10.1021","volume":"60","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8160-1611","authenticated-orcid":true,"given":"Huaipan","family":"Jiang","sequence":"first","affiliation":[{"name":"Pennsylvania State University , , ,","place":["State\nCollege, United States, 16802"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5352-8568","authenticated-orcid":true,"given":"Mengran","family":"Fan","sequence":"additional","affiliation":[{"name":"Pennsylvania State University , , ,","place":["State\nCollege, United States, 16802"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7768-2802","authenticated-orcid":true,"given":"Jian","family":"Wang","sequence":"additional","affiliation":[{"name":"Pennsylvania State College of Medicine , , ,","place":["Hershey, United States, 17033"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0098-4498","authenticated-orcid":true,"given":"Anup","family":"Sarma","sequence":"additional","affiliation":[{"name":"Pennsylvania State University , , ,","place":["State\nCollege, United States, 16802"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9494-1861","authenticated-orcid":true,"given":"Shruti","family":"Mohanty","sequence":"additional","affiliation":[{"name":"Pennsylvania State University , , ,","place":["State\nCollege, United States, 16802"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8225-4025","authenticated-orcid":true,"given":"Nikolay V.","family":"Dokholyan","sequence":"additional","affiliation":[{"name":"Pennsylvania State College of Medicine , , ,","place":["Hershey, United States, 17033"]},{"name":"Pennsylvania State University , , ,","place":["State College, United States, 16802"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2679-6679","authenticated-orcid":true,"given":"Mehrdad","family":"Mahdavi","sequence":"additional","affiliation":[{"name":"Pennsylvania State University , , ,","place":["State\nCollege, United States, 16802"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9940-9951","authenticated-orcid":true,"given":"Mahmut T.","family":"Kandemir","sequence":"additional","affiliation":[{"name":"Pennsylvania State University , , ,","place":["State\nCollege, United States, 16802"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2020,10,14]]},"reference":[{"key":"2026081804380590800_cit1","unstructured":"Biopharmaceutical Research\n& Development: The Process Behind\nNew Medicines; PhRMA, 2015."},{"key":"2026081804380590800_cit2","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1016\/j.healthpol.2010.12.002","article-title":"The cost of drug development:\na systematic review","volume":"100","author":"Morgan","year":"2011","journal-title":"Health Policy"},{"key":"2026081804380590800_cit3","first-page":"172","article-title":"The cost of new\ndrug discovery and development","volume":"4","author":"Dickson","year":"2009","journal-title":"Discovery Med."},{"key":"2026081804380590800_cit4","doi-asserted-by":"publisher","DOI":"10.1021\/cen-v081n050.p008a","article-title":"Drug development\ncosts about $1.7 billion","volume":"81","author":"Mullin","year":"2003","journal-title":"Chem. 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