{"id":"https://openalex.org/W2097931415","doi":"https://doi.org/10.1186/s12859-015-0672-3","title":"Simulated unbound structures for benchmarking of protein docking in the Dockground resource","display_name":"Simulated unbound structures for benchmarking of protein docking in the Dockground resource","publication_year":2015,"publication_date":"2015-07-30","ids":{"openalex":"https://openalex.org/W2097931415","doi":"https://doi.org/10.1186/s12859-015-0672-3","mag":"2097931415","pmid":"https://pubmed.ncbi.nlm.nih.gov/26227548"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-015-0672-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0672-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-015-0672-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-015-0672-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063140366","display_name":"Tatsiana Kirys","orcid":null},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]},{"id":"https://openalex.org/I4210105192","display_name":"United Institute of Informatics Problems","ror":"https://ror.org/01ccbsb07","country_code":"BY","type":"facility","lineage":["https://openalex.org/I151823869","https://openalex.org/I4210105192","https://openalex.org/I4210116091"]}],"countries":["BY","US"],"is_corresponding":false,"raw_author_name":"Tatsiana Kirys","raw_affiliation_strings":["Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA. tatsiana.bylund@gmail.com","United Institute of Informatics Problems, National Academy of Sciences, 220012, Minsk, Belarus. tatsiana.bylund@gmail.com","United Institute of Informatics Problems, National Academy of Sciences, Minsk, Belarus","Center for Computational Biology, The University of Kansas, Lawrence, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA. tatsiana.bylund@gmail.com","institution_ids":[]},{"raw_affiliation_string":"United Institute of Informatics Problems, National Academy of Sciences, 220012, Minsk, Belarus. tatsiana.bylund@gmail.com","institution_ids":[]},{"raw_affiliation_string":"United Institute of Informatics Problems, National Academy of Sciences, Minsk, Belarus","institution_ids":["https://openalex.org/I4210105192"]},{"raw_affiliation_string":"Center for Computational Biology, The University of Kansas, Lawrence, USA","institution_ids":["https://openalex.org/I146416000"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088584178","display_name":"Anatoly M. Ruvinsky","orcid":"https://orcid.org/0000-0002-8979-7559"},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]},{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anatoly M. Ruvinsky","raw_affiliation_strings":["Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA. aruvinsky@yahoo.com","Schr\u00f6dinger, Inc., Cambridge, MA, 02142, USA. aruvinsky@yahoo.com","Schr\u00f6dinger, Inc., Cambridge, USA","Center for Computational Biology, The University of Kansas, Lawrence, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA. aruvinsky@yahoo.com","institution_ids":[]},{"raw_affiliation_string":"Schr\u00f6dinger, Inc., Cambridge, MA, 02142, USA. aruvinsky@yahoo.com","institution_ids":[]},{"raw_affiliation_string":"Schr\u00f6dinger, Inc., Cambridge, USA","institution_ids":["https://openalex.org/I203455613"]},{"raw_affiliation_string":"Center for Computational Biology, The University of Kansas, Lawrence, USA","institution_ids":["https://openalex.org/I146416000"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013534821","display_name":"Deepak Singla","orcid":"https://orcid.org/0000-0003-0131-7950"},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Deepak Singla","raw_affiliation_strings":["Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA. deepkumar1983@gmail.com","Center for Computational Biology, The University of Kansas, Lawrence, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA. deepkumar1983@gmail.com","institution_ids":[]},{"raw_affiliation_string":"Center for Computational Biology, The University of Kansas, Lawrence, USA","institution_ids":["https://openalex.org/I146416000"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004434095","display_name":"Alexander V. Tuzikov","orcid":"https://orcid.org/0000-0001-5970-4852"},"institutions":[{"id":"https://openalex.org/I4210105192","display_name":"United Institute of Informatics Problems","ror":"https://ror.org/01ccbsb07","country_code":"BY","type":"facility","lineage":["https://openalex.org/I151823869","https://openalex.org/I4210105192","https://openalex.org/I4210116091"]}],"countries":["BY"],"is_corresponding":false,"raw_author_name":"Alexander V. Tuzikov","raw_affiliation_strings":["United Institute of Informatics Problems, National Academy of Sciences, 220012, Minsk, Belarus. tuzikov@newman.bas-net.by","United Institute of Informatics Problems, National Academy of Sciences, Minsk, Belarus"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"United Institute of Informatics Problems, National Academy of Sciences, 220012, Minsk, Belarus. tuzikov@newman.bas-net.by","institution_ids":[]},{"raw_affiliation_string":"United Institute of Informatics Problems, National Academy of Sciences, Minsk, Belarus","institution_ids":["https://openalex.org/I4210105192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050411996","display_name":"Petras J. Kundrotas","orcid":"https://orcid.org/0000-0001-5080-1664"},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Petras J. Kundrotas","raw_affiliation_strings":["Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA. pkundro@ku.edu","Center for Computational Biology, The University of Kansas, Lawrence, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA. pkundro@ku.edu","institution_ids":[]},{"raw_affiliation_string":"Center for Computational Biology, The University of Kansas, Lawrence, USA","institution_ids":["https://openalex.org/I146416000"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013394507","display_name":"Ilya A. Vakser","orcid":"https://orcid.org/0000-0002-5743-2934"},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ilya A. Vakser","raw_affiliation_strings":["Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA. vakser@ku.edu","Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, 66045, USA. vakser@ku.edu","Center for Computational Biology, The University of Kansas, Lawrence, USA","Department of Molecular Biosciences, The University of Kansas, Lawrence, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA. vakser@ku.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, 66045, USA. vakser@ku.edu","institution_ids":[]},{"raw_affiliation_string":"Center for Computational Biology, The University of Kansas, Lawrence, USA","institution_ids":["https://openalex.org/I146416000"]},{"raw_affiliation_string":"Department of Molecular Biosciences, The University of Kansas, Lawrence, USA","institution_ids":["https://openalex.org/I146416000"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5013394507"],"corresponding_institution_ids":["https://openalex.org/I146416000"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.9035,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.74520094,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"16","issue":"1","first_page":"243","last_page":"243"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9143999814987183,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9143999814987183,"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/T10934","display_name":"Heat shock proteins research","score":0.011599999852478504,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.00570000009611249,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.8163368701934814},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.7440872192382812},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.5870641469955444},{"id":"https://openalex.org/keywords/macromolecular-docking","display_name":"Macromolecular docking","score":0.56513911485672},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5641894340515137},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.5011227130889893},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4728850722312927},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.41018328070640564},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3817652463912964},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3441547155380249},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.24484020471572876},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18997812271118164},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1380920112133026}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.8163368701934814},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7440872192382812},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.5870641469955444},{"id":"https://openalex.org/C116887118","wikidata":"https://www.wikidata.org/wiki/Q836685","display_name":"Macromolecular docking","level":3,"score":0.56513911485672},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5641894340515137},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.5011227130889893},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4728850722312927},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.41018328070640564},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3817652463912964},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3441547155380249},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.24484020471572876},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18997812271118164},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1380920112133026},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0}],"mesh":[{"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054730","descriptor_name":"Protein Interaction Domains and Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-015-0672-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0672-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-015-0672-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26227548","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26227548","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:kuscholarworks.ku.edu:1808/20064","is_oa":true,"landing_page_url":"http://hdl.handle.net/1808/20064","pdf_url":null,"source":{"id":"https://openalex.org/S4306400421","display_name":"KU ScholarWorks (The University of Kansas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I146416000","host_organization_name":"University of Kansas","host_organization_lineage":["https://openalex.org/I146416000"],"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":"","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4521349","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4521349","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-015-0672-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0672-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-015-0672-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1195433239","display_name":null,"funder_award_id":"DBI1262621","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G9237260","display_name":null,"funder_award_id":"R01GM074255","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2097931415.pdf","grobid_xml":"https://content.openalex.org/works/W2097931415.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1970309312","https://openalex.org/W1979912479","https://openalex.org/W1988972583","https://openalex.org/W1996503966","https://openalex.org/W2000443388","https://openalex.org/W2000464453","https://openalex.org/W2009906055","https://openalex.org/W2013534423","https://openalex.org/W2015403140","https://openalex.org/W2021041804","https://openalex.org/W2021343666","https://openalex.org/W2023972651","https://openalex.org/W2052789270","https://openalex.org/W2078302553","https://openalex.org/W2081639575","https://openalex.org/W2090683446","https://openalex.org/W2093221728","https://openalex.org/W2100543317","https://openalex.org/W2144954642","https://openalex.org/W2155796229","https://openalex.org/W2158071704","https://openalex.org/W2158100564","https://openalex.org/W2165531467","https://openalex.org/W2594681819","https://openalex.org/W2915344963"],"related_works":["https://openalex.org/W585106548","https://openalex.org/W4353055924","https://openalex.org/W2732388178","https://openalex.org/W2806488847","https://openalex.org/W4361279638","https://openalex.org/W2121688928","https://openalex.org/W3126783617","https://openalex.org/W3093468851","https://openalex.org/W4387012733","https://openalex.org/W2015390241"],"abstract_inverted_index":{"BACKGROUND:":[0],"Proteins":[1],"play":[2],"an":[3],"important":[4,26],"role":[5],"in":[6,9,38,58,95],"biological":[7],"processes":[8],"living":[10],"organisms.":[11],"Many":[12],"protein":[13,35,105,120,175],"functions":[14],"are":[15,44,75],"based":[16,132],"on":[17,133,144],"interaction":[18],"with":[19],"other":[20],"proteins.":[21],"The":[22,79,128,139,154,186,205],"structural":[23,102],"information":[24],"is":[25,60,69,156,207],"for":[27,46,101,158],"adequate":[28],"description":[29],"of":[30,34,48,55,66,89,98,104,117,147,162,172,198],"these":[31],"interactions.":[32],"Sets":[33],"structures":[36,74,121,141,189],"determined":[37,149,200],"both":[39],"bound":[40,126,152,201],"and":[41,92,111,151,165,202],"unbound":[42,73,119,150,174,184,188,203],"states":[43],"essential":[45],"benchmarking":[47,161],"the":[49,53,72,96,125,145,173,183],"docking":[50,109,163,176],"procedures.":[51],"However,":[52],"number":[54],"such":[56,67,107],"proteins":[57],"PDB":[59],"relatively":[61],"small.":[62],"A":[63,114,169],"radical":[64,170],"expansion":[65,171],"sets":[68],"possible":[70],"if":[71],"computationally":[76],"simulated.":[77],"RESULTS:":[78],"DOCKGROUND":[80],"public":[81],"resource":[82],"provides":[83],"data":[84],"to":[85,93,193],"improve":[86],"our":[87],"understanding":[88],"protein-protein":[90],"interactions":[91],"assist":[94],"development":[97],"better":[99],"tools":[100],"modeling":[103,129],"complexes,":[106],"as":[108],"algorithms":[110,164],"scoring":[112,166],"functions.":[113,167],"large":[115,159],"set":[116,155,178,206],"simulated":[118,140,187],"was":[122,131,179],"generated":[123],"from":[124,195],"structures.":[127,153,185,204],"protocol":[130],"1":[134],"ns":[135],"Langevin":[136],"dynamics":[137],"simulation.":[138],"were":[142,190],"validated":[143],"ensemble":[146],"experimentally":[148,199],"intended":[157],"scale":[160],"CONCLUSIONS:":[168],"benchmark":[177],"achieved":[180],"by":[181],"simulating":[182],"selected":[191],"according":[192],"criteria":[194],"systematic":[196],"comparison":[197],"publicly":[208],"available":[209],"at":[210],"http://dockground.compbio.ku.edu.":[211]},"counts_by_year":[{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
