{"id":"https://openalex.org/W2606038116","doi":"https://doi.org/10.1109/3dv50981.2020.00103","title":"3D Deep Learning for Biological Function Prediction from Physical Fields","display_name":"3D Deep Learning for Biological Function Prediction from Physical Fields","publication_year":2020,"publication_date":"2020-11-01","ids":{"openalex":"https://openalex.org/W2606038116","doi":"https://doi.org/10.1109/3dv50981.2020.00103","mag":"2606038116"},"language":"en","primary_location":{"id":"doi:10.1109/3dv50981.2020.00103","is_oa":false,"landing_page_url":"https://doi.org/10.1109/3dv50981.2020.00103","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2020 International Conference on 3D Vision (3DV)","raw_type":"proceedings-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1704.04039","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070342342","display_name":"Vladimir Golkov","orcid":"https://orcid.org/0000-0002-8665-1335"},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Vladimir Golkov","raw_affiliation_strings":["Technical University of Munich"],"affiliations":[{"raw_affiliation_string":"Technical University of Munich","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057759361","display_name":"Marcin J. Skwark","orcid":"https://orcid.org/0000-0002-2022-6766"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marcin J. Skwark","raw_affiliation_strings":["InstaDeep","Vanderbilt University","Vanderbilt University,#TAB#"],"affiliations":[{"raw_affiliation_string":"InstaDeep","institution_ids":[]},{"raw_affiliation_string":"Vanderbilt University","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Vanderbilt University,#TAB#","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088121175","display_name":"Atanas Mirchev","orcid":null},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Atanas Mirchev","raw_affiliation_strings":["Technical University of Munich"],"affiliations":[{"raw_affiliation_string":"Technical University of Munich","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026903485","display_name":"Georgi Dikov","orcid":null},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]},{"id":"https://openalex.org/I2905213637","display_name":"TomTom (Netherlands)","ror":"https://ror.org/04as6y835","country_code":"NL","type":"company","lineage":["https://openalex.org/I2905213637"]}],"countries":["DE","NL"],"is_corresponding":false,"raw_author_name":"Georgi Dikov","raw_affiliation_strings":["Technical University of Munich","TomTom"],"affiliations":[{"raw_affiliation_string":"Technical University of Munich","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"TomTom","institution_ids":["https://openalex.org/I2905213637"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070815246","display_name":"Alexander R. Geanes","orcid":null},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander R. Geanes","raw_affiliation_strings":["Vanderbilt University","Vanderbilt University,#TAB#"],"affiliations":[{"raw_affiliation_string":"Vanderbilt University","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Vanderbilt University,#TAB#","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063610360","display_name":"Jeffrey Mendenhall","orcid":null},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeffrey Mendenhall","raw_affiliation_strings":["Vanderbilt University","Vanderbilt University,#TAB#"],"affiliations":[{"raw_affiliation_string":"Vanderbilt University","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Vanderbilt University,#TAB#","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025842562","display_name":"Jens Meiler","orcid":"https://orcid.org/0000-0001-8945-193X"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]},{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Jens Meiler","raw_affiliation_strings":["Leipzig University","Vanderbilt University","Vanderbilt University,#TAB#"],"affiliations":[{"raw_affiliation_string":"Leipzig University","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"Vanderbilt University","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Vanderbilt University,#TAB#","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087710605","display_name":"Daniel Cremers","orcid":"https://orcid.org/0000-0002-3079-7984"},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Daniel Cremers","raw_affiliation_strings":["Technical University of Munich"],"affiliations":[{"raw_affiliation_string":"Technical University of Munich","institution_ids":["https://openalex.org/I62916508"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5070342342"],"corresponding_institution_ids":["https://openalex.org/I62916508"],"apc_list":null,"apc_paid":null,"fwci":0.2887,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.5944411,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"928","last_page":"937"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/complementarity","display_name":"Complementarity (molecular biology)","score":0.5625295042991638},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5227989554405212},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.5218685865402222},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49640995264053345},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4592786133289337},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.4485796093940735},{"id":"https://openalex.org/keywords/intermolecular-force","display_name":"Intermolecular force","score":0.44516417384147644},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4444449245929718},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4430617094039917},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.4188605546951294},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.4116073548793793},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3849979639053345},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.33497557044029236},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.25829875469207764},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1877915859222412},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.13063019514083862},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08822086453437805}],"concepts":[{"id":"https://openalex.org/C202269582","wikidata":"https://www.wikidata.org/wiki/Q2644277","display_name":"Complementarity (molecular biology)","level":2,"score":0.5625295042991638},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5227989554405212},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.5218685865402222},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49640995264053345},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4592786133289337},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.4485796093940735},{"id":"https://openalex.org/C166950319","wikidata":"https://www.wikidata.org/wiki/Q245031","display_name":"Intermolecular force","level":3,"score":0.44516417384147644},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4444449245929718},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4430617094039917},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.4188605546951294},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.4116073548793793},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3849979639053345},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.33497557044029236},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.25829875469207764},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1877915859222412},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.13063019514083862},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08822086453437805},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1109/3dv50981.2020.00103","is_oa":false,"landing_page_url":"https://doi.org/10.1109/3dv50981.2020.00103","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2020 International Conference on 3D Vision (3DV)","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:1704.04039","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1704.04039","pdf_url":"https://arxiv.org/pdf/1704.04039","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"mag:2606038116","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1704.04039.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"doi:10.48550/arxiv.1704.04039","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1704.04039","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1704.04039","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1704.04039","pdf_url":"https://arxiv.org/pdf/1704.04039","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321636","display_name":"Deutsche Telekom Stiftung","ror":"https://ror.org/0550zmx90"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2606038116.pdf"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1493004075","https://openalex.org/W1985748743","https://openalex.org/W1986688691","https://openalex.org/W1988441172","https://openalex.org/W1996975182","https://openalex.org/W2001983964","https://openalex.org/W2014692495","https://openalex.org/W2079391392","https://openalex.org/W2088423689","https://openalex.org/W2090439943","https://openalex.org/W2090617952","https://openalex.org/W2102814386","https://openalex.org/W2103325328","https://openalex.org/W2112411768","https://openalex.org/W2124614417","https://openalex.org/W2130009286","https://openalex.org/W2143482176","https://openalex.org/W2162166182","https://openalex.org/W2198264407","https://openalex.org/W2211722331","https://openalex.org/W2214665483","https://openalex.org/W2227395312","https://openalex.org/W2289619256","https://openalex.org/W2384495648","https://openalex.org/W2551247304","https://openalex.org/W2949867299","https://openalex.org/W2962835968","https://openalex.org/W2964121744","https://openalex.org/W2982377621","https://openalex.org/W6631190155","https://openalex.org/W6637373629","https://openalex.org/W6684191040","https://openalex.org/W6688357764","https://openalex.org/W6729533798"],"related_works":["https://openalex.org/W3127021490","https://openalex.org/W2158805099","https://openalex.org/W3020169092","https://openalex.org/W2006403034","https://openalex.org/W2085043181","https://openalex.org/W2170200424","https://openalex.org/W2074002527","https://openalex.org/W2103382374","https://openalex.org/W2028450600","https://openalex.org/W3129166671","https://openalex.org/W3104345353","https://openalex.org/W2120773925","https://openalex.org/W3159672290","https://openalex.org/W1550947615","https://openalex.org/W2189928911","https://openalex.org/W2422799170","https://openalex.org/W1993826174","https://openalex.org/W2980128132","https://openalex.org/W3118279013"],"abstract_inverted_index":{"Predicting":[0],"the":[1,34,82,90,111],"biological":[2,56],"function":[3,57,73],"of":[4,30,37,58,92,122,125],"molecules,":[5],"be":[6],"it":[7],"proteins":[8],"or":[9],"drug-like":[10],"compounds,":[11],"from":[12,61,81],"their":[13,62],"atomic":[14],"structure":[15],"is":[16,79,95],"an":[17],"important":[18],"and":[19,26,68,116,124],"long-standing":[20],"problem.":[21],"The":[22],"electron":[23,66,84],"density":[24,67,85],"field":[25,29],"electrostatic":[27,69],"potential":[28,70],"a":[31],"molecule":[32,40],"contain":[33],"\u201craw":[35],"fingerprint\u201d":[36],"how":[38],"this":[39,47],"can":[41,54],"fit":[42],"to":[43,100],"binding":[44],"partners.":[45],"In":[46,87],"paper,":[48],"we":[49],"show":[50],"that":[51],"deep":[52],"learning":[53],"predict":[55],"molecules":[59,94,123],"directly":[60],"raw":[63],"3D":[64],"approximated":[65,83],"fields.":[71],"Protein":[72],"based":[74],"on":[75],"Enzyme":[76],"Commission":[77],"numbers":[78],"predicted":[80,96],"field.":[86],"another":[88],"experiment,":[89],"activity":[91],"small":[93],"with":[97,113],"quality":[98],"comparable":[99],"state-of-the-art":[101],"descriptor-based":[102],"methods.":[103],"We":[104,127],"propose":[105,129],"several":[106],"alternative":[107],"computational":[108],"models":[109],"for":[110,119],"GPU":[112],"different":[114,120],"memory":[115],"runtime":[117],"requirements":[118],"sizes":[121],"databases.":[126],"also":[128],"application-specific":[130],"multi-channel":[131],"data":[132],"representations.":[133]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-03-11T14:59:36.786465","created_date":"2025-10-10T00:00:00"}
