{"id":"https://openalex.org/W2768579122","doi":"https://doi.org/10.1021/acs.jcim.7b00310","title":"Descriptor Data Bank (DDB): A Cloud Platform for Multiperspective Modeling of Protein\u2013Ligand Interactions","display_name":"Descriptor Data Bank (DDB): A Cloud Platform for Multiperspective Modeling of Protein\u2013Ligand Interactions","publication_year":2017,"publication_date":"2017-11-30","ids":{"openalex":"https://openalex.org/W2768579122","doi":"https://doi.org/10.1021/acs.jcim.7b00310","mag":"2768579122","pmid":"https://pubmed.ncbi.nlm.nih.gov/29186950"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.7b00310","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.7b00310","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038216756","display_name":"Hossam M. Ashtawy","orcid":"https://orcid.org/0000-0002-5589-9274"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hossam M. Ashtawy","raw_affiliation_strings":["Department of Electrical\rand Computer Engineering, Michigan State University, East Lansing, Michigan 48824-1226, United States"],"raw_orcid":"https://orcid.org/0000-0002-5589-9274","affiliations":[{"raw_affiliation_string":"Department of Electrical\rand Computer Engineering, Michigan State University, East Lansing, Michigan 48824-1226, United States","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108624212","display_name":"Nihar R. Mahapatra","orcid":"https://orcid.org/0000-0002-3821-3330"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nihar R. Mahapatra","raw_affiliation_strings":["Department of Electrical\rand Computer Engineering, Michigan State University, East Lansing, Michigan 48824-1226, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical\rand Computer Engineering, Michigan State University, East Lansing, Michigan 48824-1226, United States","institution_ids":["https://openalex.org/I87216513"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5038216756","https://openalex.org/A5108624212"],"corresponding_institution_ids":["https://openalex.org/I87216513"],"apc_list":null,"apc_paid":null,"fwci":1.3749,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.83540682,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"58","issue":"1","first_page":"134","last_page":"147"},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9932000041007996,"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"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9855999946594238,"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/cloud-computing","display_name":"Cloud computing","score":0.5403192043304443},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5212529301643372},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5140773057937622},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.4988541603088379},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.47786492109298706},{"id":"https://openalex.org/keywords/data-bank","display_name":"Data bank","score":0.42335301637649536},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3891527056694031},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26763564348220825},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.2555443048477173},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.2334120273590088},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2191474735736847},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.102975994348526}],"concepts":[{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.5403192043304443},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5212529301643372},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5140773057937622},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.4988541603088379},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47786492109298706},{"id":"https://openalex.org/C2779786304","wikidata":"https://www.wikidata.org/wiki/Q5227243","display_name":"Data bank","level":2,"score":0.42335301637649536},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3891527056694031},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26763564348220825},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.2555443048477173},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2334120273590088},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2191474735736847},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.102975994348526},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000067917","descriptor_name":"Cloud Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057927","descriptor_name":"Hydrophobic and Hydrophilic Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.7b00310","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.7b00310","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:29186950","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29186950","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/12","score":0.5199999809265137,"display_name":"Responsible consumption and production"}],"awards":[{"id":"https://openalex.org/G4967229250","display_name":null,"funder_award_id":"1117900","funder_id":"https://openalex.org/F4320335353","funder_display_name":"National Science Foundation of Sri Lanka"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320335353","display_name":"National Science Foundation of Sri Lanka","ror":"https://ror.org/010xaa060"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W1497260480","https://openalex.org/W1531524766","https://openalex.org/W1592950931","https://openalex.org/W1605578858","https://openalex.org/W1605923270","https://openalex.org/W1656114533","https://openalex.org/W1757990252","https://openalex.org/W1964357740","https://openalex.org/W1969017960","https://openalex.org/W1977467384","https://openalex.org/W1984021058","https://openalex.org/W1985588649","https://openalex.org/W1988037271","https://openalex.org/W1988111902","https://openalex.org/W1988437166","https://openalex.org/W1992441011","https://openalex.org/W1993046136","https://openalex.org/W1993403967","https://openalex.org/W1995808589","https://openalex.org/W1998031351","https://openalex.org/W1998568556","https://openalex.org/W2003356525","https://openalex.org/W2013085020","https://openalex.org/W2023637112","https://openalex.org/W2028609644","https://openalex.org/W2028629022","https://openalex.org/W2030286884","https://openalex.org/W2047099264","https://openalex.org/W2050456292","https://openalex.org/W2052030759","https://openalex.org/W2061583504","https://openalex.org/W2062884696","https://openalex.org/W2067831935","https://openalex.org/W2070493638","https://openalex.org/W2076779488","https://openalex.org/W2092285329","https://openalex.org/W2096541451","https://openalex.org/W2096560421","https://openalex.org/W2096864392","https://openalex.org/W2102245393","https://openalex.org/W2108243628","https://openalex.org/W2128332459","https://openalex.org/W2130479394","https://openalex.org/W2134967712","https://openalex.org/W2135472700","https://openalex.org/W2137052779","https://openalex.org/W2137841449","https://openalex.org/W2148512505","https://openalex.org/W2159887157","https://openalex.org/W2171656814","https://openalex.org/W2295598076","https://openalex.org/W2911964244","https://openalex.org/W3102476541","https://openalex.org/W3146467503"],"related_works":["https://openalex.org/W91965561","https://openalex.org/W2996612103","https://openalex.org/W4385715780","https://openalex.org/W1488329660","https://openalex.org/W180201063","https://openalex.org/W1978763597","https://openalex.org/W1966041739","https://openalex.org/W2755266720","https://openalex.org/W1516459493","https://openalex.org/W2611158379"],"abstract_inverted_index":{"Protein-ligand":[0],"(PL)":[1],"interactions":[2,286],"play":[3],"a":[4,41,92,122,133,166,276],"key":[5],"role":[6],"in":[7,287,294],"many":[8],"life":[9],"processes":[10],"such":[11],"as":[12],"molecular":[13,15],"recognition,":[14],"binding,":[16],"signal":[17],"transmission,":[18],"and":[19,35,46,58,66,114,119,141,143,148,163,184,202,219,228,232,244],"cell":[20],"metabolism.":[21],"Examples":[22],"of":[23,44,76,80,102,125,222,279,302,317],"interaction":[24,51,126],"forces":[25,52],"include":[26],"hydrogen":[27],"bonding,":[28],"hydrophobic":[29],"effects,":[30],"steric":[31],"clashes,":[32],"electrostatic":[33],"contacts,":[34],"van":[36],"der":[37],"Waals":[38],"attractions.":[39],"Currently,":[40],"large":[42,123,277],"number":[43,124,278],"hypotheses":[45],"perspectives":[47],"to":[48,156,164,237,240,261],"model":[49],"these":[50],"are":[53,211,214],"scattered":[54],"throughout":[55],"the":[56,74,96,187,241,248,315],"literature":[57],"largely":[59],"forgotten.":[60],"Instead,":[61],"had":[62],"they":[63,69],"been":[64],"assembled":[65],"utilized":[67],"collectively,":[68],"would":[70],"have":[71],"substantially":[72],"improved":[73],"accuracy":[75,316],"predicting":[77],"binding":[78],"affinity":[79],"protein-ligand":[81,204],"complexes.":[82,205],"In":[83],"this":[84],"work,":[85],"we":[86,209],"present":[87],"Descriptor":[88],"Data":[89],"Bank":[90],"(DDB),":[91],"data-driven":[93],"platform":[94,130],"on":[95,216,254],"cloud":[97],"for":[98,110,121,137],"facilitating":[99],"multiperspective":[100,270],"modeling":[101,127],"PL":[103,285],"interactions.":[104],"DDB":[105,175,281],"is":[106,154],"an":[107,299],"open-access":[108],"hub":[109],"depositing,":[111],"hosting,":[112],"executing,":[113],"sharing":[115],"descriptor":[116,139,151,179],"extraction":[117,180],"tools":[118,181,190],"data":[120,256],"hypotheses.":[128],"The":[129,150,189,206],"also":[131,307],"implements":[132],"machine-learning":[134],"(ML)":[135],"toolbox":[136],"automatic":[138],"filtering":[140,152],"analysis":[142],"scoring":[144],"function":[145],"(SF)":[146],"fitting":[147],"prediction.":[149],"module":[153],"used":[155,233],"filter":[157],"out":[158],"irrelevant":[159],"and/or":[160],"noisy":[161],"descriptors":[162,195,208,243,282,313],"produce":[165],"compact":[167],"subset":[168],"from":[169,186,247],"all":[170,295],"available":[171],"features.":[172],"We":[173,230,250,267,306],"seed":[174],"with":[176,298],"16":[177],"diverse":[178,280],"developed":[182],"in-house":[183,207,242],"collected":[185,246],"literature.":[188,249],"altogether":[191],"generate":[192],"over":[193],"2700":[194],"that":[196,258,269,272,309],"characterize":[197],"(i)":[198],"proteins,":[199],"(ii)":[200],"ligands,":[201],"(iii)":[203],"extract":[210],"protein-specific":[212,312],"which":[213],"based":[215],"pairwise":[217],"primary":[218],"tertiary":[220],"alignment":[221],"protein":[223],"structures":[224],"followed":[225],"by":[226],"clustering":[227],"trilateration.":[229],"built":[231],"DDB's":[234],"ML":[235],"library":[236],"fit":[238],"SFs":[239,271],"those":[245],"then":[251],"evaluated":[252],"them":[253],"several":[255],"sets":[257],"were":[259,273],"constructed":[260,274],"reflect":[262],"real-world":[263],"drug":[264],"screening":[265],"scenarios.":[266],"found":[268,308],"using":[275],"capturing":[283],"various":[284],"different":[288],"ways":[289],"outperformed":[290],"their":[291],"single-perspective":[292],"counterparts":[293],"evaluation":[296],"scenarios,":[297],"average":[300],"improvement":[301],"more":[303],"than":[304],"15%.":[305],"our":[310],"proposed":[311],"improve":[314],"SFs.":[318]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}