{"id":"https://openalex.org/W4393646592","doi":"https://doi.org/10.5281/zenodo.6873024","title":"Prop3D-20","display_name":"Prop3D-20","publication_year":2022,"publication_date":"2022-07-25","ids":{"openalex":"https://openalex.org/W4393646592","doi":"https://doi.org/10.5281/zenodo.6873024"},"language":"en","primary_location":{"id":"pmh:oai:zenodo.org:6873024","is_oa":true,"landing_page_url":"https://zenodo.org/record/6873024","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/other"},"type":"dataset","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://zenodo.org/record/6873024","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068604431","display_name":"Eli J. Draizen","orcid":"https://orcid.org/0000-0002-5645-5050"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Draizen, Eli J.","raw_affiliation_strings":["University of Virginia"],"raw_orcid":"https://orcid.org/0000-0002-5645-5050","affiliations":[{"raw_affiliation_string":"University of Virginia","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022761529","display_name":"Cameron Mura","orcid":"https://orcid.org/0000-0001-7985-2561"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mura, Cameron","raw_affiliation_strings":["University of Virginia"],"raw_orcid":"https://orcid.org/0000-0001-7985-2561","affiliations":[{"raw_affiliation_string":"University of Virginia","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075833022","display_name":"Philip E. Bourne","orcid":"https://orcid.org/0000-0002-7618-7292"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bourne, Philip E.","raw_affiliation_strings":["University of Virginia"],"raw_orcid":"https://orcid.org/0000-0002-7618-7292","affiliations":[{"raw_affiliation_string":"University of Virginia","institution_ids":["https://openalex.org/I51556381"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3082118034362793}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3082118034362793}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:zenodo.org:6873024","is_oa":true,"landing_page_url":"https://zenodo.org/record/6873024","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/other"},{"id":"doi:10.5281/zenodo.6873024","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.6873024","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"dataset"}],"best_oa_location":{"id":"pmh:oai:zenodo.org:6873024","is_oa":true,"landing_page_url":"https://zenodo.org/record/6873024","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/other"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W4391913857","https://openalex.org/W2350741829","https://openalex.org/W2530322880"],"abstract_inverted_index":{"Prop3D-20":[0],"is":[1],"a":[2,62],"protein":[3,272],"structure":[4,23],"dataset":[5,105,154,161],"that":[6],"combines":[7],"3D":[8],"atomic":[9,70],"coordinates":[10],"with":[11,38,43,53,275],"biophysical":[12],"and":[13,46,48,68,78,116,162],"evolutionary":[14],"properties":[15],"for":[16,89,100,133],"every":[17,20],"atom":[18],"in":[19,61,109,135],"\"cleaned\"":[21],"domain":[22],"from":[24,93],"&lt;b&gt;20":[25],"CATH":[26,59],"[1]":[27],"Homologous":[28],"Superfamilies.&lt;/b&gt;":[29],"Domain":[30],"structures":[31],"are":[32],"'cleaned'":[33],"by":[34],"adding":[35],"missing":[36,41],"residues":[37],"MODELLER":[39],"[2],":[40],"atoms":[42],"SCWRL4":[44],"[3],":[45],"protonating":[47],"energy":[49],"minimizing":[50],"(simple":[51],"de-bump)":[52],"PDB2PQR":[54],"[4].":[55],"We":[56,126],"follow":[57],"the":[58,110,138,149,337],"hierarchy":[60],"hierarchical":[63],"data":[64,130],"format":[65],"(HDF)":[66],"file":[67,123,140],"include":[69],"level":[71,74],"features,":[72,75],"residue":[73],"residue-residue":[76],"contact,":[77],"pre-calculated":[79],"train":[80],"(~80%)":[81],"/":[82,85],"test":[83],"(~10%)":[84,87],"validation":[86],"splits":[88],"each":[90],"superfamily":[91],"derived":[92],"CATH's":[94],"sequence":[95],"identity":[96],"clusters":[97],"(e.g.":[98],"S35":[99],"35%":[101],"seq":[102],"ID).":[103],"This":[104],"was":[106,117],"originally":[107],"stored":[108],"Highly":[111],"Scalable":[112],"Data":[113],"Service":[114],"([HSDS](http://www.github.com/HDFGroup/hsds)),":[115],"exported":[118],"into":[119,131],"this":[120,129,153,160,175],"raw":[121],".h5":[122,139],"as":[124,145],"backup.":[125],"recommend":[127],"loading":[128],"HSDS":[132,172],"use":[134,159],"[h5pyd](http://www.github.com/HDFGroup/h5pyd),":[136],"but":[137],"can":[141],"opened":[142],"using":[143],"[h5py](http://www.github.com/h5py/h5py)":[144],"well.":[146],"Please":[147],"see":[148,178],"REAME":[150],"attached":[151],"to":[152,155,158,336],"learn":[156],"how":[157,163],"it":[164],"organized.":[165],"For":[166],"more":[167],"information":[168],"on":[169],"setting":[170],"up":[171],"and/or":[173],"recreate":[174],"dataset,":[176],"please":[177],"[http://www.github.com/bouralab/Prop3D/README.md](http://www.github.com/bouralab/Prop3D/README.md)":[179],"References":[180],"1.":[181],"Sillitoe":[182],"I,":[183],"Bordin":[184],"N,":[185,187,201],"Dawson":[186],"Waman":[188],"VP,":[189],"Ashford":[190],"P,":[191,310],"Scholes":[192],"HM,":[193],"Pang":[194],"CSM,":[195],"Woodridge":[196],"L,":[197,302],"Rauer":[198],"C,":[199],"Sen":[200],"Abbasian":[202],"M,":[203,308],"Le":[204],"Cornu":[205],"S,":[206],"Lam":[207],"SD,":[208],"Berka":[209],"K,":[210,292,294,306],"Varekova":[211],"IH,":[212],"Svobodova":[213],"R,":[214,316,326],"Lees":[215],"J,":[216,296,304],"Orengo":[217],"CA.":[218],"CATH:":[219],"increased":[220],"structural":[221],"coverage":[222],"of":[223,271],"functional":[224],"space.":[225],"Nucleic":[226],"Acids":[227],"Res.":[228],"2021":[229],"Jan":[230],"8;49(D1):D266-D273.":[231],"doi:":[232,255,280,347],"10.1093/nar/gkaa1079.":[233],"PMID:":[234,257,282,353],"33237325;":[235],"PMCID:":[236,259,284,355],"PMC7778904.":[237],"2.":[238],"Webb":[239],"B,":[240],"Sali":[241],"A.":[242],"Comparative":[243],"Protein":[244,343],"Structure":[245],"Modeling":[246],"Using":[247],"MODELLER.":[248],"Curr":[249],"Protoc":[250],"Bioinformatics.":[251],"2016":[252],"Jun":[253],"20;54:5.6.1-5.6.37.":[254],"10.1002/cpbi.3.":[256],"27322406;":[258],"PMC5031415.":[260],"3.":[261],"Krivov":[262],"GG,":[263],"Shapovalov":[264],"MV,":[265],"Dunbrack":[266],"RL":[267],"Jr.":[268],"Improved":[269],"prediction":[270],"side-chain":[273],"conformations":[274],"SCWRL4.":[276],"Proteins.":[277],"2009":[278],"Dec;77(4):778-95.":[279],"10.1002/prot.22488.":[281],"19603484;":[283],"PMC2885146.":[285],"4.":[286],"Jurrus":[287],"E,":[288],"Engel":[289],"D,":[290],"Star":[291],"Monson":[293],"Brandi":[295],"Felberg":[297],"LE,":[298],"Brookes":[299],"DH,":[300],"Wilson":[301],"Chen":[303],"Liles":[305],"Chun":[307],"Li":[309],"Gohara":[311],"DW,":[312],"Dolinsky":[313],"T,":[314,322],"Konecny":[315],"Koes":[317],"DR,":[318],"Nielsen":[319],"JE,":[320],"Head-Gordon":[321],"Geng":[323],"W,":[324],"Krasny":[325],"Wei":[327],"GW,":[328],"Holst":[329],"MJ,":[330],"McCammon":[331],"JA,":[332],"Baker":[333],"NA.":[334],"Improvements":[335],"APBS":[338],"biomolecular":[339],"solvation":[340],"software":[341],"suite.":[342],"Sci.":[344],"2018":[345],"Jan;27(1):112-128.":[346],"10.1002/pro.3280.":[348],"Epub":[349],"2017":[350],"Oct":[351],"24.":[352],"28836357;":[354],"PMC5734301.":[356],"<br>":[357]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2024-04-03T00:00:00"}
