{"id":"https://openalex.org/W3091673587","doi":"https://doi.org/10.1186/s12859-020-3523-9","title":"Decoy selection for protein structure prediction via extreme gradient boosting and ranking","display_name":"Decoy selection for protein structure prediction via extreme gradient boosting and ranking","publication_year":2020,"publication_date":"2020-12-01","ids":{"openalex":"https://openalex.org/W3091673587","doi":"https://doi.org/10.1186/s12859-020-3523-9","mag":"3091673587","pmid":"https://pubmed.ncbi.nlm.nih.gov/33297949"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-3523-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3523-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-3523-9","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":"preprint","indexed_in":["arxiv","crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-3523-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101677914","display_name":"Nasrin Akhter","orcid":"https://orcid.org/0000-0001-8976-5875"},"institutions":[{"id":"https://openalex.org/I162714631","display_name":"George Mason University","ror":"https://ror.org/02jqj7156","country_code":"US","type":"education","lineage":["https://openalex.org/I162714631"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nasrin Akhter","raw_affiliation_strings":["Department of Computer Science, George Mason University, Fairfax, 22030, VA, USA","Department of Computer Science, George Mason University, Fairfax, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, George Mason University, Fairfax, 22030, VA, USA","institution_ids":["https://openalex.org/I162714631"]},{"raw_affiliation_string":"Department of Computer Science, George Mason University, Fairfax, USA#TAB#","institution_ids":["https://openalex.org/I162714631"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063725454","display_name":"Gopinath Chennupati","orcid":"https://orcid.org/0000-0002-6223-8570"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]},{"id":"https://openalex.org/I4210131040","display_name":"Los Alamos National Security (United States)","ror":"https://ror.org/037ddaj94","country_code":"US","type":"company","lineage":["https://openalex.org/I4210131040"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gopinath Chennupati","raw_affiliation_strings":["Information Sciences (CCS-3) Group, Los Alamos National Laboratory, Bikini At al Rd., Los Alamos, 87545, USA. gchennupati@lanl.gov","Information Sciences (CCS-3) Group, Los Alamos National Laboratory, Los Alamos, USA"],"raw_orcid":"https://orcid.org/0000-0002-6223-8570","affiliations":[{"raw_affiliation_string":"Information Sciences (CCS-3) Group, Los Alamos National Laboratory, Bikini At al Rd., Los Alamos, 87545, USA. gchennupati@lanl.gov","institution_ids":["https://openalex.org/I4210131040","https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Information Sciences (CCS-3) Group, Los Alamos National Laboratory, Los Alamos, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057625550","display_name":"Hristo Djidjev","orcid":"https://orcid.org/0000-0001-9286-8824"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hristo Djidjev","raw_affiliation_strings":["Information Sciences (CCS-3) Group, Los Alamos National Laboratory, Bikini At al Rd., Los Alamos, 87545, USA","Information Sciences (CCS-3) Group, Los Alamos National Laboratory, Los Alamos, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Information Sciences (CCS-3) Group, Los Alamos National Laboratory, Bikini At al Rd., Los Alamos, 87545, USA","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Information Sciences (CCS-3) Group, Los Alamos National Laboratory, Los Alamos, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044722808","display_name":"Amarda Shehu","orcid":"https://orcid.org/0000-0001-5230-4610"},"institutions":[{"id":"https://openalex.org/I162714631","display_name":"George Mason University","ror":"https://ror.org/02jqj7156","country_code":"US","type":"education","lineage":["https://openalex.org/I162714631"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amarda Shehu","raw_affiliation_strings":["Department of Bioengineering, George Mason University, Fairfax, 22030, VA, USA","Department of Computer Science, George Mason University, Fairfax, 22030, VA, USA","School of Systems Biology, George Mason University, Manassas, 20110, VA, USA","School of Systems Biology, George Mason University, Manassas, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, George Mason University, Fairfax, 22030, VA, USA","institution_ids":["https://openalex.org/I162714631"]},{"raw_affiliation_string":"Department of Computer Science, George Mason University, Fairfax, 22030, VA, USA","institution_ids":["https://openalex.org/I162714631"]},{"raw_affiliation_string":"School of Systems Biology, George Mason University, Manassas, 20110, VA, USA","institution_ids":["https://openalex.org/I162714631"]},{"raw_affiliation_string":"School of Systems Biology, George Mason University, Manassas, USA","institution_ids":["https://openalex.org/I162714631"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.09587199,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"21","issue":"S1","first_page":"189","last_page":"189"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.5716000199317932,"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":0.5716000199317932,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.32839998602867126,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.03929999843239784,"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/decoy","display_name":"Decoy","score":0.989683985710144},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6582846641540527},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6515408754348755},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5760035514831543},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5657994747161865},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.5491939187049866},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.515426754951477},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.42594707012176514},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.42145881056785583},{"id":"https://openalex.org/keywords/boosting","display_name":"Boosting (machine learning)","score":0.4105171859264374},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08988043665885925}],"concepts":[{"id":"https://openalex.org/C2779179475","wikidata":"https://www.wikidata.org/wiki/Q3545649","display_name":"Decoy","level":3,"score":0.989683985710144},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6582846641540527},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6515408754348755},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5760035514831543},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5657994747161865},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.5491939187049866},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.515426754951477},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.42594707012176514},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42145881056785583},{"id":"https://openalex.org/C46686674","wikidata":"https://www.wikidata.org/wiki/Q466303","display_name":"Boosting (machine learning)","level":2,"score":0.4105171859264374},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08988043665885925},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[{"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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","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}],"locations_count":8,"locations":[{"id":"doi:10.1186/s12859-020-3523-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3523-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-3523-9","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:33297949","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33297949","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:arXiv.org:2010.01441","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2010.01441","pdf_url":"https://arxiv.org/pdf/2010.01441","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":null,"raw_type":"text"},{"id":"pmh:oai:osti.gov:1768531","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1768531","pdf_url":"https://www.osti.gov/servlets/purl/1768531","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"mag:3091673587","is_oa":true,"landing_page_url":"http://export.arxiv.org/pdf/2010.01441","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":"pmh:oai:doaj.org/article:522b3a9cc96546df81ad0651428c5fb2","is_oa":true,"landing_page_url":"https://doaj.org/article/522b3a9cc96546df81ad0651428c5fb2","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 21, Iss S1, Pp 1-21 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7724862","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7724862","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"},{"id":"doi:10.48550/arxiv.2010.01441","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2010.01441","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":"Preprint"}],"best_oa_location":{"id":"doi:10.1186/s12859-020-3523-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-3523-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-3523-9","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":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.8600000143051147}],"awards":[{"id":"https://openalex.org/G1466238046","display_name":null,"funder_award_id":"1900061","funder_id":"https://openalex.org/F4320335353","funder_display_name":"National Science Foundation of Sri Lanka"},{"id":"https://openalex.org/G2356915424","display_name":null,"funder_award_id":"89233218CNA000001","funder_id":"https://openalex.org/F4320337547","funder_display_name":"Laboratory Directed Research and Development"},{"id":"https://openalex.org/G2613504715","display_name":null,"funder_award_id":"DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320332369","funder_display_name":"National Nuclear Security Administration"},{"id":"https://openalex.org/G2980544840","display_name":null,"funder_award_id":"Contract No. DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320338304","funder_display_name":"Los Alamos National Laboratory"},{"id":"https://openalex.org/G3237169770","display_name":"FET: Medium: Collaborative Research: Automated Analysis and Exploration of High-dimensional and Multimodal Molecular Energy Landscapes","funder_award_id":"1900061","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G359075050","display_name":null,"funder_award_id":"DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G3700687868","display_name":null,"funder_award_id":"AC52-06NA25396","funder_id":"https://openalex.org/F4320338304","funder_display_name":"Los Alamos National Laboratory"},{"id":"https://openalex.org/G4169061630","display_name":null,"funder_award_id":"Contract No. DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G4844714250","display_name":null,"funder_award_id":"No. DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320338304","funder_display_name":"Los Alamos National Laboratory"},{"id":"https://openalex.org/G5083158263","display_name":null,"funder_award_id":"DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5657628048","display_name":null,"funder_award_id":"AC52-06NA25396","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6932788750","display_name":null,"funder_award_id":"DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320337547","funder_display_name":"Laboratory Directed Research and Development"},{"id":"https://openalex.org/G6995210142","display_name":null,"funder_award_id":"89233218CNA000001","funder_id":"https://openalex.org/F4320332369","funder_display_name":"National Nuclear Security Administration"},{"id":"https://openalex.org/G70659677","display_name":null,"funder_award_id":"89233218CNA000001","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7500863821","display_name":null,"funder_award_id":"89233218CNA000001","funder_id":"https://openalex.org/F4320338304","funder_display_name":"Los Alamos National Laboratory"},{"id":"https://openalex.org/G75892134","display_name":null,"funder_award_id":"DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320338304","funder_display_name":"Los Alamos National Laboratory"},{"id":"https://openalex.org/G8659807574","display_name":null,"funder_award_id":"89233218CNA000001","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332369","display_name":"National Nuclear Security Administration","ror":"https://ror.org/03sk1we31"},{"id":"https://openalex.org/F4320335353","display_name":"National Science Foundation of Sri Lanka","ror":"https://ror.org/010xaa060"},{"id":"https://openalex.org/F4320337547","display_name":"Laboratory Directed Research and Development","ror":"https://ror.org/01e41cf67"},{"id":"https://openalex.org/F4320338304","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":62,"referenced_works":["https://openalex.org/W1565746575","https://openalex.org/W1596324102","https://openalex.org/W1678356000","https://openalex.org/W1974680823","https://openalex.org/W1982959183","https://openalex.org/W1994272924","https://openalex.org/W2006782375","https://openalex.org/W2008505479","https://openalex.org/W2021797754","https://openalex.org/W2023477917","https://openalex.org/W2026129540","https://openalex.org/W2029699793","https://openalex.org/W2035885031","https://openalex.org/W2040823078","https://openalex.org/W2045186555","https://openalex.org/W2048440841","https://openalex.org/W2050595677","https://openalex.org/W2062166748","https://openalex.org/W2099286799","https://openalex.org/W2107538253","https://openalex.org/W2109801072","https://openalex.org/W2119068667","https://openalex.org/W2122199548","https://openalex.org/W2125677968","https://openalex.org/W2126711803","https://openalex.org/W2137470116","https://openalex.org/W2140574901","https://openalex.org/W2161337380","https://openalex.org/W2162166182","https://openalex.org/W2165550831","https://openalex.org/W2166575328","https://openalex.org/W2169267213","https://openalex.org/W2169284845","https://openalex.org/W2171559274","https://openalex.org/W2171755502","https://openalex.org/W2201713963","https://openalex.org/W2290412022","https://openalex.org/W2295598076","https://openalex.org/W2343931134","https://openalex.org/W2389430365","https://openalex.org/W2491059477","https://openalex.org/W2514534732","https://openalex.org/W2517233028","https://openalex.org/W2517375182","https://openalex.org/W2571387738","https://openalex.org/W2606439133","https://openalex.org/W2766352633","https://openalex.org/W2794328361","https://openalex.org/W2796925135","https://openalex.org/W2886725294","https://openalex.org/W2894584887","https://openalex.org/W2915583118","https://openalex.org/W2949867299","https://openalex.org/W2950609999","https://openalex.org/W2951639995","https://openalex.org/W2952663747","https://openalex.org/W2963457143","https://openalex.org/W2971780522","https://openalex.org/W2980184967","https://openalex.org/W3004896252","https://openalex.org/W3005019273","https://openalex.org/W3102476541"],"related_works":["https://openalex.org/W3111849700","https://openalex.org/W2973130686","https://openalex.org/W3120861253","https://openalex.org/W2794328361","https://openalex.org/W2993297058","https://openalex.org/W2809162758","https://openalex.org/W3080230718","https://openalex.org/W3128724941","https://openalex.org/W2941002594","https://openalex.org/W88781131","https://openalex.org/W2888004262","https://openalex.org/W2067516565","https://openalex.org/W2916865274","https://openalex.org/W2088388996","https://openalex.org/W2990673201","https://openalex.org/W2035885031","https://openalex.org/W2003563221","https://openalex.org/W2315317366","https://openalex.org/W3022926855","https://openalex.org/W2126128676"],"abstract_inverted_index":{"BACKGROUND:":[0],"Identifying":[1],"one":[2,13],"or":[3],"more":[4,44,181],"biologically-active/native":[5],"decoys":[6,11],"from":[7],"millions":[8],"of":[9,14,25,55,89,161],"non-native":[10,34],"is":[12,167],"the":[15,41,53,116,121,141,157],"major":[16],"challenges":[17],"in":[18,27,36,51,179,189,196],"computational":[19],"structural":[20,75],"biology.":[21],"The":[22,130],"extreme":[23],"lack":[24,88],"balance":[26],"positive":[28],"and":[29,33,67,136],"negative":[30],"samples":[31],"(native":[32],"decoys)":[35],"a":[37,96,104,110,126,168],"decoy":[38,56,65,68,82,106,128,158,172,194],"set":[39],"makes":[40],"problem":[42],"even":[43,155],"complicated.":[45],"Consensus":[46],"methods":[47],"show":[48,73,85],"varied":[49,92,148],"success":[50],"handling":[52],"challenge":[54],"selection":[57,83,107,195],"despite":[58],"some":[59],"issues":[60],"associated":[61,119],"with":[62,120],"clustering":[63,135],"large":[64],"sets":[66,69,159],"that":[70,114],"do":[71],"not":[72],"much":[74],"similarity.":[76],"Recent":[77],"investigations":[78],"into":[79],"energy":[80,117,137],"landscape-based":[81],"approaches":[84],"promises.":[86],"However,":[87],"generalization":[90],"over":[91],"test":[93],"cases":[94],"remains":[95],"bottleneck":[97],"for":[98,156,171,193],"these":[99],"methods.":[100],"RESULTS:":[101],"We":[102],"propose":[103],"novel":[105],"method,":[108],"ML-Select,":[109],"machine":[111,186],"learning":[112,187],"framework":[113],"exploits":[115],"landscape":[118],"structure":[122,199],"space":[123],"probed":[124],"through":[125],"template-free":[127,197],"generation.":[129],"proposed":[131],"method":[132,170],"outperforms":[133],"both":[134],"ranking-based":[138],"methods,":[139],"all":[140],"while":[142],"consistently":[143],"offering":[144],"better":[145],"performance":[146,192],"on":[147],"test-cases.":[149],"Moreover,":[150],"ML-Select":[151,166],"shows":[152],"promising":[153],"results":[154],"consisting":[160],"mostly":[162],"low-quality":[163],"decoys.":[164],"CONCLUSIONS:":[165],"useful":[169],"selection.":[173],"This":[174],"work":[175],"suggests":[176],"further":[177],"research":[178],"finding":[180],"effective":[182],"ways":[183],"to":[184],"adopt":[185],"frameworks":[188],"achieving":[190],"robust":[191],"protein":[198],"prediction.":[200]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
