{"id":"https://openalex.org/W2799876761","doi":"https://doi.org/10.1093/nar/gky357","title":"HPEPDOCK: a web server for blind peptide\u2013protein docking based on a hierarchical algorithm","display_name":"HPEPDOCK: a web server for blind peptide\u2013protein docking based on a hierarchical algorithm","publication_year":2018,"publication_date":"2018-04-30","ids":{"openalex":"https://openalex.org/W2799876761","doi":"https://doi.org/10.1093/nar/gky357","mag":"2799876761","pmid":"https://pubmed.ncbi.nlm.nih.gov/29746661"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gky357","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gky357","pdf_url":"https://academic.oup.com/nar/article-pdf/46/W1/W443/25110602/gky357.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/46/W1/W443/25110602/gky357.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029050819","display_name":"Pei Zhou","orcid":"https://orcid.org/0000-0002-0320-8363"},"institutions":[{"id":"https://openalex.org/I4210112540","display_name":"Institute of Biophysics","ror":"https://ror.org/01tyv8576","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112540"]},{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pei Zhou","raw_affiliation_strings":["Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China","institution_ids":["https://openalex.org/I4210112540","https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034739562","display_name":"Bowen Jin","orcid":"https://orcid.org/0000-0003-1442-6259"},"institutions":[{"id":"https://openalex.org/I4210112540","display_name":"Institute of Biophysics","ror":"https://ror.org/01tyv8576","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112540"]},{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bowen Jin","raw_affiliation_strings":["Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China","institution_ids":["https://openalex.org/I4210112540","https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100348508","display_name":"Hao Li","orcid":"https://orcid.org/0000-0001-8495-8467"},"institutions":[{"id":"https://openalex.org/I4210112540","display_name":"Institute of Biophysics","ror":"https://ror.org/01tyv8576","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112540"]},{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Li","raw_affiliation_strings":["Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China","institution_ids":["https://openalex.org/I4210112540","https://openalex.org/I47720641"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111803493","display_name":"Sheng-You Huang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210112540","display_name":"Institute of Biophysics","ror":"https://ror.org/01tyv8576","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112540"]},{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Sheng-You Huang","raw_affiliation_strings":["Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China","institution_ids":["https://openalex.org/I4210112540","https://openalex.org/I47720641"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5111803493"],"corresponding_institution_ids":["https://openalex.org/I4210112540","https://openalex.org/I47720641"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":10.6299,"has_fulltext":true,"cited_by_count":615,"citation_normalized_percentile":{"value":0.99078475,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"46","issue":"W1","first_page":"W443","last_page":"W450"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9980999827384949,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9980999827384949,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9977999925613403,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9976000189781189,"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/peptide","display_name":"Peptide","score":0.8131448030471802},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.7984346151351929},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.733386754989624},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5313554406166077},{"id":"https://openalex.org/keywords/macromolecular-docking","display_name":"Macromolecular docking","score":0.48809918761253357},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.4811519384384155},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.4573710262775421},{"id":"https://openalex.org/keywords/threading","display_name":"Threading (protein sequence)","score":0.44779348373413086},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.44421863555908203},{"id":"https://openalex.org/keywords/web-site","display_name":"Web site","score":0.4362662136554718},{"id":"https://openalex.org/keywords/searching-the-conformational-space-for-docking","display_name":"Searching the conformational space for docking","score":0.4361928105354309},{"id":"https://openalex.org/keywords/snapshot","display_name":"Snapshot (computer storage)","score":0.41919419169425964},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.41088899970054626},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4002916216850281},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.39376288652420044},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.3219011723995209},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2407817542552948},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.19970351457595825},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.17791882157325745},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.15408951044082642},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.14147254824638367},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.10084652900695801},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.10083207488059998}],"concepts":[{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.8131448030471802},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7984346151351929},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.733386754989624},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5313554406166077},{"id":"https://openalex.org/C116887118","wikidata":"https://www.wikidata.org/wiki/Q836685","display_name":"Macromolecular docking","level":3,"score":0.48809918761253357},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.4811519384384155},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.4573710262775421},{"id":"https://openalex.org/C200307862","wikidata":"https://www.wikidata.org/wiki/Q7797175","display_name":"Threading (protein sequence)","level":3,"score":0.44779348373413086},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.44421863555908203},{"id":"https://openalex.org/C2984519610","wikidata":"https://www.wikidata.org/wiki/Q35127","display_name":"Web site","level":3,"score":0.4362662136554718},{"id":"https://openalex.org/C44695244","wikidata":"https://www.wikidata.org/wiki/Q7441727","display_name":"Searching the conformational space for docking","level":3,"score":0.4361928105354309},{"id":"https://openalex.org/C55282118","wikidata":"https://www.wikidata.org/wiki/Q252683","display_name":"Snapshot (computer storage)","level":2,"score":0.41919419169425964},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.41088899970054626},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4002916216850281},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.39376288652420044},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3219011723995209},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2407817542552948},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.19970351457595825},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.17791882157325745},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.15408951044082642},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.14147254824638367},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.10084652900695801},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.10083207488059998},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","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":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","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":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","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":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gky357","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gky357","pdf_url":"https://academic.oup.com/nar/article-pdf/46/W1/W443/25110602/gky357.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:29746661","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29746661","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:europepmc.org:4991258","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6030929","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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"}],"best_oa_location":{"id":"doi:10.1093/nar/gky357","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gky357","pdf_url":"https://academic.oup.com/nar/article-pdf/46/W1/W443/25110602/gky357.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7476102074","display_name":null,"funder_award_id":"2016YFC1305805","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7582944686","display_name":null,"funder_award_id":"2016YFC1305800","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7618829171","display_name":"\u86cb\u767d\u8d28\u76f8\u4e92\u4f5c\u7528\u7684\u591a\u4f53\u5173\u8054\u6548\u5e94\u548c\u5206\u5b50\u67d4\u6027\u7814\u7a76","funder_award_id":"31670724","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321883","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2799876761.pdf","grobid_xml":"https://content.openalex.org/works/W2799876761.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1592950931","https://openalex.org/W1609599771","https://openalex.org/W1768303176","https://openalex.org/W1860382351","https://openalex.org/W1938743025","https://openalex.org/W1970431511","https://openalex.org/W1972043325","https://openalex.org/W1979201508","https://openalex.org/W1992450378","https://openalex.org/W1998624640","https://openalex.org/W2009015785","https://openalex.org/W2011703027","https://openalex.org/W2015292449","https://openalex.org/W2021310372","https://openalex.org/W2023272942","https://openalex.org/W2048739031","https://openalex.org/W2051210555","https://openalex.org/W2054394841","https://openalex.org/W2054954101","https://openalex.org/W2072180710","https://openalex.org/W2114520383","https://openalex.org/W2115133023","https://openalex.org/W2119636371","https://openalex.org/W2127322768","https://openalex.org/W2130479394","https://openalex.org/W2137015675","https://openalex.org/W2137167381","https://openalex.org/W2156876686","https://openalex.org/W2177731497","https://openalex.org/W2265106521","https://openalex.org/W2344689512","https://openalex.org/W2520917239","https://openalex.org/W2529000169","https://openalex.org/W2554109484","https://openalex.org/W2562674913","https://openalex.org/W2609643846","https://openalex.org/W2768968558","https://openalex.org/W2906926620","https://openalex.org/W6758076146","https://openalex.org/W6788151078"],"related_works":["https://openalex.org/W1489925612","https://openalex.org/W2533022751","https://openalex.org/W2152872596","https://openalex.org/W2585040066","https://openalex.org/W2018664033","https://openalex.org/W4246463539","https://openalex.org/W4213013656","https://openalex.org/W4235673852","https://openalex.org/W4248527317","https://openalex.org/W2477070048"],"abstract_inverted_index":{"Protein-peptide":[0],"interactions":[1],"are":[2],"crucial":[3],"in":[4,81,109],"many":[5],"cellular":[6],"functions.":[7],"Therefore,":[8],"determining":[9],"the":[10,19,55,93],"structure":[11],"of":[12,22,45,61,79,88,119,135,140,165],"protein-peptide":[13,38],"complexes":[14],"is":[15,31,158,187],"important":[16],"for":[17,36,102,151,168,177],"understanding":[18],"molecular":[20],"mechanism":[21],"related":[23],"biological":[24],"processes":[25],"and":[26,114,161,174],"developing":[27],"peptide":[28,51,56,62,72,127,153,171,180],"drugs.":[29],"HPEPDOCK":[30,53,74,105,129,156,184],"a":[32,41,76,86,116,131,138,169,178],"novel":[33],"web":[34,185],"server":[35,157,186],"blind":[37,70],"docking":[39,110,172,181],"through":[40,58],"hierarchical":[42],"algorithm.":[43],"Instead":[44],"running":[46],"lengthy":[47],"simulations":[48],"to":[49,100,149],"refine":[50],"conformations,":[52],"considers":[54],"flexibility":[57],"an":[59,163],"ensemble":[60],"conformations":[63],"generated":[64],"by":[65],"our":[66],"MODPEP":[67],"program.":[68],"For":[69,125],"global":[71,170],"docking,":[73,128],"obtained":[75,115],"success":[77,117,133],"rate":[78,118,134],"33.3%":[80],"binding":[82],"mode":[83],"prediction":[84],"on":[85,137],"benchmark":[87,139],"57":[89],"unbound":[90,142],"cases":[91,143],"when":[92],"top":[94,122,145],"10":[95,123,146],"models":[96,113],"were":[97],"considered,":[98],"compared":[99,148],"21.1%":[101],"pepATTRACT":[103],"server.":[104],"also":[106],"performed":[107],"well":[108],"against":[111],"homology":[112],"29.8%":[120],"within":[121,144],"predictions.":[124],"local":[126,179],"achieved":[130],"high":[132],"72.6%":[136],"62":[141],"predictions,":[147],"45.2%":[150],"HADDOCK":[152],"protocol.":[154],"Our":[155],"computationally":[159],"efficient":[160],"consumed":[162],"average":[164],"29.8":[166],"mins":[167,176],"job":[173],"14.2":[175],"job.":[182],"The":[183],"available":[188],"at":[189],"http://huanglab.phys.hust.edu.cn/hpepdock/.":[190]},"counts_by_year":[{"year":2026,"cited_by_count":66},{"year":2025,"cited_by_count":106},{"year":2024,"cited_by_count":126},{"year":2023,"cited_by_count":109},{"year":2022,"cited_by_count":79},{"year":2021,"cited_by_count":61},{"year":2020,"cited_by_count":50},{"year":2019,"cited_by_count":16},{"year":2018,"cited_by_count":2}],"updated_date":"2026-07-26T07:53:14.480251","created_date":"2025-10-10T00:00:00"}
