{"id":"https://openalex.org/W4415748649","doi":"https://doi.org/10.1007/978-1-0716-4828-5_14","title":"Protein\u2013Protein Interaction Site Prediction via EquiPPIS and Its Application in Studying Viral Replication","display_name":"Protein\u2013Protein Interaction Site Prediction via EquiPPIS and Its Application in Studying Viral Replication","publication_year":2025,"publication_date":"2025-10-31","ids":{"openalex":"https://openalex.org/W4415748649","doi":"https://doi.org/10.1007/978-1-0716-4828-5_14","pmid":"https://pubmed.ncbi.nlm.nih.gov/41174316"},"language":"en","primary_location":{"id":"doi:10.1007/978-1-0716-4828-5_14","doi":"https://doi.org/10.1007/978-1-0716-4828-5_14","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-1-0716-4828-5_14","pdf_url":null,"source":{"id":"https://openalex.org/S4210172139","display_name":"Methods in molecular biology","issn_l":"1064-3745","issn":["1064-3745","1940-6029"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-3","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Methods in Molecular Biology","raw_type":"book-chapter"},"volume":{"id":"https://openalex.org/W4415748683","display_name":"Protein Evolution"},"type":"book-chapter","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041995175","display_name":"Rahmatullah Roche","orcid":"https://orcid.org/0009-0005-8593-8210","observed_orcids":["https://orcid.org/0009-0005-8593-8210"]},"institutions":[{"id":"https://openalex.org/I199172307","display_name":"Columbus State University","ror":"https://ror.org/002nf6z37","country_code":"US","type":"education","lineage":["https://openalex.org/I199172307"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rahmatullah Roche","raw_affiliation_strings":["TSYS School of Computer Science, Columbus State University, Columbus, GA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TSYS School of Computer Science, Columbus State University, Columbus, GA, USA","institution_ids":["https://openalex.org/I199172307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029120254","display_name":"Sumit Tarafder","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sumit Tarafder","raw_affiliation_strings":["Department of Computer Science, Virginia Tech, Blacksburg, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech, Blacksburg, VA, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5095829467","display_name":"Parkesh Suseendran","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Parkesh Suseendran","raw_affiliation_strings":["School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100684337","display_name":"Xiaofeng Wang","orcid":"https://orcid.org/0000-0002-3850-3274","observed_orcids":["https://orcid.org/0000-0002-3850-3274"]},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaofeng Wang","raw_affiliation_strings":["School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018409409","display_name":"Debswapna Bhattacharya","orcid":"https://orcid.org/0000-0002-9630-0141","observed_orcids":["https://orcid.org/0000-0002-9630-0141"]},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Debswapna Bhattacharya","raw_affiliation_strings":["Department of Computer Science, Virginia Tech, Blacksburg, VA, USA. dbhattacharya@vt.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech, Blacksburg, VA, USA. dbhattacharya@vt.edu","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5018409409"],"corresponding_institution_ids":["https://openalex.org/I859038795"],"apc_list":null,"apc_paid":null,"fwci":1.7736,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.87486279,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"2979","issue":null,"first_page":"225","last_page":"235"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9589999914169312,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9589999914169312,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.029899999499320984,"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":0.003599999938160181,"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/protein-protein-interaction-site-prediction","display_name":"protein-protein interaction site prediction","score":0.9779999852180481},{"id":"https://openalex.org/keywords/virus-host-interactions","display_name":"host-virus interaction","score":0.7649999856948853},{"id":"https://openalex.org/keywords/viral-replication","display_name":"viral replication","score":0.9959999918937683},{"id":"https://openalex.org/keywords/rna-viruses","display_name":"RNA viruses","score":0.8840000033378601},{"id":"https://openalex.org/keywords/antiviral-strategies","display_name":"antiviral strategies","score":0.8999999761581421},{"id":"https://openalex.org/keywords/binding-site-prediction","display_name":"binding site prediction","score":0.5799999833106995}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7396000027656555},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6096000075340271},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.5877000093460083},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5138999819755554},{"id":"https://openalex.org/C140704245","wikidata":"https://www.wikidata.org/wiki/Q3933202","display_name":"Viral replication","level":3,"score":0.4961000084877014},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.4487000107765198},{"id":"https://openalex.org/C12590798","wikidata":"https://www.wikidata.org/wiki/Q3933199","display_name":"Replication (statistics)","level":2,"score":0.42640000581741333},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40610000491142273},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.3490999937057495},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.32690000534057617},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.31610000133514404},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.28839999437332153},{"id":"https://openalex.org/C2780806968","wikidata":"https://www.wikidata.org/wiki/Q6045196","display_name":"Interaction model","level":2,"score":0.2842999994754791},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.2800000011920929},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.26930001378059387},{"id":"https://openalex.org/C38764148","wikidata":"https://www.wikidata.org/wiki/Q17098245","display_name":"Interaction information","level":2,"score":0.26249998807907104},{"id":"https://openalex.org/C2909613950","wikidata":"https://www.wikidata.org/wiki/Q158695","display_name":"Protein Interaction Networks","level":3,"score":0.26080000400543213},{"id":"https://openalex.org/C70636015","wikidata":"https://www.wikidata.org/wiki/Q4300350","display_name":"Molecular biophysics","level":2,"score":0.2583000063896179},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.2558000087738037},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2549000084400177}],"mesh":[{"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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014779","descriptor_name":"Virus Replication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1007/978-1-0716-4828-5_14","doi":"https://doi.org/10.1007/978-1-0716-4828-5_14","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-1-0716-4828-5_14","pdf_url":null,"source":{"id":"https://openalex.org/S4210172139","display_name":"Methods in molecular biology","issn_l":"1064-3745","issn":["1064-3745","1940-6029"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-3","vabb-shw"],"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Methods in Molecular Biology","raw_type":"book-chapter"},{"id":"pmid:41174316","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41174316","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,"listed_in":[],"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":"Methods in molecular biology (Clifton, N.J.)","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G4233128848","display_name":"Data-driven Computational Modeling and Refinement of Protein Structures on Genomic Scales","funder_award_id":"R35GM138146","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1789760598","https://openalex.org/W1966323687","https://openalex.org/W1976754433","https://openalex.org/W1976937534","https://openalex.org/W2008708467","https://openalex.org/W2020559109","https://openalex.org/W2031772330","https://openalex.org/W2100070946","https://openalex.org/W2102461176","https://openalex.org/W2108134720","https://openalex.org/W2122467688","https://openalex.org/W2132105926","https://openalex.org/W2136316164","https://openalex.org/W2141627824","https://openalex.org/W2142182685","https://openalex.org/W2142912491","https://openalex.org/W2150158737","https://openalex.org/W2155194485","https://openalex.org/W2158714788","https://openalex.org/W2160973386","https://openalex.org/W2164492221","https://openalex.org/W2165108787","https://openalex.org/W2722005050","https://openalex.org/W2739876930","https://openalex.org/W2767401463","https://openalex.org/W2944679105","https://openalex.org/W2950954328","https://openalex.org/W2955690154","https://openalex.org/W2971405760","https://openalex.org/W2990458240","https://openalex.org/W2992752586","https://openalex.org/W3013976849","https://openalex.org/W3080498684","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3197696221","https://openalex.org/W4206247924","https://openalex.org/W4281790889","https://openalex.org/W4286669150","https://openalex.org/W4327550249","https://openalex.org/W4377225006","https://openalex.org/W4396721167"],"related_works":["https://openalex.org/W2885821429","https://openalex.org/W2023994926","https://openalex.org/W7101026322","https://openalex.org/W7098588074","https://openalex.org/W7152007883","https://openalex.org/W2802984372","https://openalex.org/W2183923653","https://openalex.org/W3133705589","https://openalex.org/W7151049797","https://openalex.org/W2468937966"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2025-10-31T00:00:00"}