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Here, we expand the capabilities of the BCL to include structure-based virtual screening. We introduce two new score functions, BCL-AffinityNet and BCL-DockANNScore, based on novel distance-dependent signed protein\u2013ligand atomic property correlations. Both metrics are conventional feed-forward dropout neural networks trained on the new descriptors. We demonstrate that BCL-AffinityNet is one of the top performing score functions on the comparative assessment of score functions 2016 affinity prediction and affinity ranking tasks. We also demonstrate that BCL-AffinityNet performs well on the CSAR-NRC HiQ I and II test sets. Furthermore, we demonstrate that BCL-DockANNScore is competitive with multiple state-of-the-art methods on the docking power and screening power tasks. Finally, we show how our models can be decomposed into human-interpretable pharmacophore maps to aid in hit\/lead optimization. Altogether, our results expand the utility of the BCL for structure-based scoring to aid small molecule discovery and design. BCL-AffinityNet, BCL-DockANNScore, and the pharmacophore mapping application, as well as the remainder of the BCL cheminformatics toolkit, are freely available with an academic license at the BCL Commons site hosted on http:\/\/meilerlab.org\/.<\/jats:p>","DOI":"10.1021\/acs.jcim.0c01001","type":"journal-article","created":{"date-parts":[[2021,1,26]],"date-time":"2021-01-26T10:12:04Z","timestamp":1611655924000},"page":"603-620","source":"Crossref","is-referenced-by-count":38,"title":["General Purpose Structure-Based Drug Discovery Neural\nNetwork Score Functions with Human-Interpretable Pharmacophore Maps"],"prefix":"10.1021","volume":"61","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5296-087X","authenticated-orcid":true,"given":"Benjamin P.","family":"Brown","sequence":"first","affiliation":[{"name":"Vanderbilt University , , , ,","place":["Nashville, Tennessee, United States, 37232"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey","family":"Mendenhall","sequence":"additional","affiliation":[{"name":"Vanderbilt University , , , ,","place":["Nashville, Tennessee, United States, 37232"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander R.","family":"Geanes","sequence":"additional","affiliation":[{"name":"Vanderbilt University , , , ,","place":["Nashville, Tennessee, United States, 37232"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jens","family":"Meiler","sequence":"additional","affiliation":[{"name":"Vanderbilt University , , , ,","place":["Nashville, Tennessee, United States, 37232"]},{"name":"Vanderbilt University , , , ,","place":["Nashville, Tennessee, United States, 37212"]},{"name":"Leipzig University Medical School , , ,","place":["Leipzig, Germany, SAC 04103"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2021,1,26]]},"reference":[{"key":"2026092806084198300_cit1","doi-asserted-by":"publisher","first-page":"2694","DOI":"10.3762\/bjoc.12.267","article-title":"Computational Methods in Drug Discovery","volume":"12","author":"Leelananda","year":"2016","journal-title":"Beilstein J. 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