{"id":"https://openalex.org/W4394488299","doi":"https://doi.org/10.6084/m9.figshare.24201603","title":"MD package of wtXPD-damaged-ssDNA","display_name":"MD package of wtXPD-damaged-ssDNA","publication_year":2023,"publication_date":"2023-01-01","ids":{"openalex":"https://openalex.org/W4394488299","doi":"https://doi.org/10.6084/m9.figshare.24201603"},"language":"en","primary_location":{"id":"pmh:oai:figshare.com:article/24201603","doi":null,"is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_b_MD_package_of_wtXPD-damaged-ssDNA_b_/24201603","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},"volume":null,"type":"dataset","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://figshare.com/articles/dataset/_b_MD_package_of_wtXPD-damaged-ssDNA_b_/24201603","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021545726","display_name":"Iwen Fu","orcid":"https://orcid.org/0000-0003-2502-2882","observed_orcids":["https://orcid.org/0000-0003-2502-2882"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fu, Iwen","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018460703","display_name":"Nicholas E. Geacintov","orcid":"https://orcid.org/0000-0002-7961-2231","observed_orcids":["https://orcid.org/0000-0002-7961-2231"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"E Geacintov, Nicholas","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5045073997","display_name":"Suse B. Broyde","orcid":"https://orcid.org/0000-0002-3802-7511","observed_orcids":["https://orcid.org/0000-0002-3802-7511"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Broyde, Suse","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"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":{"id":"https://openalex.org/T10123","display_name":"DNA Repair Mechanisms","score":0.9726999998092651,"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"}},"topics":[{"id":"https://openalex.org/T10123","display_name":"DNA Repair Mechanisms","score":0.9726999998092651,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.01850000023841858,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.002099999925121665,"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/xpd-helicase","display_name":"XPD helicase","score":0.984000027179718},{"id":"https://openalex.org/keywords/dna-damage","display_name":"DNA damage","score":0.5289999842643738},{"id":"https://openalex.org/keywords/single-stranded-dna","display_name":"single-stranded DNA","score":0.8379999995231628},{"id":"https://openalex.org/keywords/cyclobutane-pyrimidine-dimers","display_name":"cyclobutane pyrimidine dimers","score":0.9409999847412109},{"id":"https://openalex.org/keywords/dna-translocation","display_name":"DNA translocation","score":0.7369999885559082},{"id":"https://openalex.org/keywords/tfiih","display_name":"TFIIH","score":0.8370000123977661},{"id":"https://openalex.org/keywords/dna-repair","display_name":"DNA repair","score":0.6669999957084656},{"id":"https://openalex.org/keywords/molecular-dynamics-simulation","display_name":"molecular dynamics simulation","score":0.5329999923706055}],"concepts":[{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.3817571699619293},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2936878800392151},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12470430135726929}],"mesh":[],"locations_count":4,"locations":[{"id":"pmh:oai:figshare.com:article/24201603","doi":null,"is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_b_MD_package_of_wtXPD-damaged-ssDNA_b_/24201603","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},{"id":"doi:10.6084/m9.figshare.24201603","doi":"https://doi.org/10.6084/m9.figshare.24201603","is_oa":true,"landing_page_url":"https://doi.org/10.6084/m9.figshare.24201603","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},{"id":"doi:10.6084/m9.figshare.24201603.v1","doi":"https://doi.org/10.6084/m9.figshare.24201603.v1","is_oa":true,"landing_page_url":"https://doi.org/10.6084/m9.figshare.24201603.v1","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},{"id":"doi:10.6084/m9.figshare.24201603.v2","doi":"https://doi.org/10.6084/m9.figshare.24201603.v2","is_oa":true,"landing_page_url":"https://doi.org/10.6084/m9.figshare.24201603.v2","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"}],"best_oa_location":{"id":"pmh:oai:figshare.com:article/24201603","doi":null,"is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_b_MD_package_of_wtXPD-damaged-ssDNA_b_/24201603","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4283067856","https://openalex.org/W4416791447","https://openalex.org/W4388464046","https://openalex.org/W126808637","https://openalex.org/W2156324690","https://openalex.org/W6888909353","https://openalex.org/W4414495455","https://openalex.org/W2064853448","https://openalex.org/W7220757605","https://openalex.org/W7133564619"],"abstract_inverted_index":{"MD":[0,8],"simulation:":[1],"wtXPD-damaged-ssDNAXPD-64PP.tgz":[2],"and":[3,119,142,170,215],"XPD-CPD.tgz":[4],"The":[5,151],"8":[6],"\u00b5s":[7],"simulations":[9,38],"of":[10,31,36,41,73,122,158,161,177,190,227],"human":[11],"XPD":[12,172,186,216],"bound":[13,163],"to":[14,57,164,174],"damaged":[15],"ssDNA,":[16],"containing":[17],"a":[18,22,86,113],"6\u22124PP":[19,45],"(XPD-64PP)":[20],"or":[21],"CPD":[23,77],"(XPD-CPD)":[24],"lesion":[25],"right":[26],"outside":[27,48,80],"the":[28,49,55,65,69,81,89,103,120,123,159,165,175,178,182,188,191,195,203,223,233],"entry":[29,50,83],"pore":[30,51,84],"XPD,":[32],"are":[33,94,106,130,144],"provided.":[34],"Descriptions":[35],"each":[37,101],"1.":[39,139],"Simulation":[40,72],"XPD-64PP":[42],"reveals":[43,75],"that":[44,76],"initially":[46,78],"positioned":[47,79],"is":[52,200],"translocated":[53],"in":[54,108,126,147,222],"3'":[56],"5'":[58],"direction":[59],"as":[60],"its":[61,92],"bases":[62,93],"flip":[63],"into":[64,88],"unoccupied":[66],"space":[67],"within":[68,181,194],"pore.":[70],"2.":[71,150],"XPD-CPD":[74],"DNA":[82],"undergoes":[85],"backbone-translocation":[87],"pore,":[90],"but":[91],"blocked":[95],"from":[96,202],"entering.":[97],"Files":[98],"included":[99,146],"For":[100],"system,":[102],"trajectory":[104],"files":[105],"presented":[107],"binary":[109],"NETCDF":[110],"format,":[111],"*.nc,":[112],"corresponding":[114],"topology":[115],"PRMTOP":[116],"files,":[117,128],"*.top,":[118],"coordinates":[121],"initial":[124],"structure":[125,226,237],"PDB":[127,238],"*.pdb":[129],"also":[131],"provided,":[132],"where":[133],"*":[134],"=":[135],"XPD-64PP,":[136],"XPD-CPD.":[137],"Note":[138],"Water":[140],"molecules":[141],"ions":[143],"not":[145],"all":[148],"files.":[149],"trajectories":[152],"were":[153,218],"saved":[154],"every":[155],"1":[156],"ns.Coordinates":[157],"model":[160,199,205],"XPG-XPD-XPB":[162],"open":[166],"bubble":[167],"substrate":[168],"XPG-XPD-XPB-initial.pdb":[169],"XPG-XPD-XPB-final.pdbXPG-XPD-XPB-initial.pdb:":[171],"prior":[173],"shift":[176,189],"Arch":[179,192],"domain":[180,193],"XPG-XPD-XPB-DNA":[183,196],"complex.":[184],"XPG-XPD-XPB-final.pdb:":[185],"after":[187],"complex.Note":[197],"This":[198],"derived":[201],"structural":[204],"provided":[206],"by":[207],"Bralic":[208],"et":[209],"al.":[210],"In":[211],"this":[212],"model,":[213],"XPB":[214],"helicase":[217],"replaced":[219,231],"with":[220,232],"those":[221],"exiting":[224],"cryo-EM":[225],"TFIIH-XPA-DNA;":[228],"XPG":[229,235],"was":[230],"existing":[234],"crystal":[236],"3Q8K.":[239]},"counts_by_year":[],"updated_date":"2026-10-08T09:06:37.294493","created_date":"2024-04-08T00:00:00"}
