{"id":"https://openalex.org/W4412805071","doi":"https://doi.org/10.1093/bioinformatics/btaf420","title":"MDGraphEmb: A Toolkit for Graph Embedding and Classification of Protein Conformational Ensembles","display_name":"MDGraphEmb: A Toolkit for Graph Embedding and Classification of Protein Conformational Ensembles","publication_year":2025,"publication_date":"2025-07-31","ids":{"openalex":"https://openalex.org/W4412805071","doi":"https://doi.org/10.1093/bioinformatics/btaf420","pmid":"https://pubmed.ncbi.nlm.nih.gov/40742756"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf420","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf420","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf420/63902659/btaf420.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","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/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf420/63902659/btaf420.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007636109","display_name":"Ferdoos Hossein Nezhad","orcid":"https://orcid.org/0009-0007-9892-7662"},"institutions":[{"id":"https://openalex.org/I124357947","display_name":"University of London","ror":"https://ror.org/04cw6st05","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947"]},{"id":"https://openalex.org/I59433898","display_name":"Brunel University of London","ror":"https://ror.org/00dn4t376","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I59433898"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Ferdoos Hossein Nezhad","raw_affiliation_strings":["Brunel University of London Department of Computer Science, , Uxbridge, UB8 3PH,","Department of Computer Science, Brunel University of London, Uxbridge UB8 3PH, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Brunel University of London Department of Computer Science, , Uxbridge, UB8 3PH,","institution_ids":["https://openalex.org/I59433898","https://openalex.org/I124357947"]},{"raw_affiliation_string":"Department of Computer Science, Brunel University of London, Uxbridge UB8 3PH, United Kingdom","institution_ids":["https://openalex.org/I59433898"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079500959","display_name":"Namir Oues","orcid":"https://orcid.org/0009-0003-2001-1065"},"institutions":[{"id":"https://openalex.org/I124357947","display_name":"University of London","ror":"https://ror.org/04cw6st05","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947"]},{"id":"https://openalex.org/I59433898","display_name":"Brunel University of London","ror":"https://ror.org/00dn4t376","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I59433898"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Namir Oues","raw_affiliation_strings":["Brunel University of London Department of Computer Science, , Uxbridge, UB8 3PH,","Department of Computer Science, Brunel University of London, Uxbridge UB8 3PH, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Brunel University of London Department of Computer Science, , Uxbridge, UB8 3PH,","institution_ids":["https://openalex.org/I59433898","https://openalex.org/I124357947"]},{"raw_affiliation_string":"Department of Computer Science, Brunel University of London, Uxbridge UB8 3PH, United Kingdom","institution_ids":["https://openalex.org/I59433898"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033176492","display_name":"Massimiliano Meli","orcid":"https://orcid.org/0000-0003-3304-6104"},"institutions":[{"id":"https://openalex.org/I4210136872","display_name":"Tecnologie Avanzate (Italy)","ror":"https://ror.org/04kevy945","country_code":"IT","type":"company","lineage":["https://openalex.org/I4210136872"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Massimiliano Meli","raw_affiliation_strings":["Consiglio Nazionale delle Ricerche Istituto di Scienze e Tecnologie Chimiche \u201cGiulio Natta\u201d \u2013 SCITEC, , Milano 20131,","Istituto di Scienze e Tecnologie Chimiche \u201cGiulio Natta\u201d\u2014SCITEC, Consiglio Nazionale delle Ricerche , Milano 20131,"],"affiliations":[{"raw_affiliation_string":"Consiglio Nazionale delle Ricerche Istituto di Scienze e Tecnologie Chimiche \u201cGiulio Natta\u201d \u2013 SCITEC, , Milano 20131,","institution_ids":["https://openalex.org/I4210136872"]},{"raw_affiliation_string":"Istituto di Scienze e Tecnologie Chimiche \u201cGiulio Natta\u201d\u2014SCITEC, Consiglio Nazionale delle Ricerche , Milano 20131,","institution_ids":["https://openalex.org/I4210136872"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079015407","display_name":"Alessandro Pandini","orcid":"https://orcid.org/0000-0002-4158-233X"},"institutions":[{"id":"https://openalex.org/I124357947","display_name":"University of London","ror":"https://ror.org/04cw6st05","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947"]},{"id":"https://openalex.org/I330495657","display_name":"Thomas Young Centre","ror":"https://ror.org/03hdrgy42","country_code":"GB","type":"other","lineage":["https://openalex.org/I330495657"]},{"id":"https://openalex.org/I59433898","display_name":"Brunel University of London","ror":"https://ror.org/00dn4t376","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I59433898"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Alessandro Pandini","raw_affiliation_strings":["Brunel University of London Department of Computer Science, , Uxbridge, UB8 3PH,","The Thomas Young Centre for Theory and Simulation of Materials , London, SW7 2AZ,","The Thomas Young Centre for Theory and Simulation of Materials, London SW7 2AZ, United Kingdom","Department of Computer Science, Brunel University of London, Uxbridge UB8 3PH, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Brunel University of London Department of Computer Science, , Uxbridge, UB8 3PH,","institution_ids":["https://openalex.org/I59433898","https://openalex.org/I124357947"]},{"raw_affiliation_string":"The Thomas Young Centre for Theory and Simulation of Materials , London, SW7 2AZ,","institution_ids":["https://openalex.org/I330495657"]},{"raw_affiliation_string":"The Thomas Young Centre for Theory and Simulation of Materials, London SW7 2AZ, United Kingdom","institution_ids":["https://openalex.org/I330495657"]},{"raw_affiliation_string":"Department of Computer Science, Brunel University of London, Uxbridge UB8 3PH, United Kingdom","institution_ids":["https://openalex.org/I59433898"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5007636109"],"corresponding_institution_ids":["https://openalex.org/I124357947","https://openalex.org/I59433898"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.16600483,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"9","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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":0.9987000226974487,"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":0.9984999895095825,"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/computer-science","display_name":"Computer science","score":0.7547545433044434},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6568814516067505},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5679326057434082},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5530564785003662},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5351579785346985},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.48953303694725037},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4615822434425354},{"id":"https://openalex.org/keywords/graph-embedding","display_name":"Graph embedding","score":0.4509522318840027},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.43748319149017334},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09835374355316162},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.09372597932815552}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7547545433044434},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6568814516067505},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5679326057434082},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5530564785003662},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5351579785346985},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.48953303694725037},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4615822434425354},{"id":"https://openalex.org/C75564084","wikidata":"https://www.wikidata.org/wiki/Q5597085","display_name":"Graph embedding","level":3,"score":0.4509522318840027},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.43748319149017334},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09835374355316162},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.09372597932815552}],"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":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016333","descriptor_name":"HIV Protease","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btaf420","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf420","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf420/63902659/btaf420.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40742756","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40742756","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:bura.brunel.ac.uk:2438/31752","is_oa":true,"landing_page_url":"https://orcid.org/0009-0007-9892-7662","pdf_url":null,"source":{"id":"https://openalex.org/S4306401473","display_name":"Brunel University Research Archive (BURA) (Brunel University London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I59433898","host_organization_name":"Brunel University of London","host_organization_lineage":["https://openalex.org/I59433898"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:europepmc.org:11262693","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12453676","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12453676","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12453676/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf420","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf420","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf420/63902659/btaf420.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2620866968","display_name":null,"funder_award_id":"EP/X035603","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G5337665435","display_name":null,"funder_award_id":"HECBioSim","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G7262751522","display_name":"DTP 2020-2021 Brunel University London","funder_award_id":"EP/T518116/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G943500646","display_name":"HECBioSim: The UK High End Computing Consortium for Biomolecular Simulation.","funder_award_id":"EP/X035603/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412805071.pdf","grobid_xml":"https://content.openalex.org/works/W4412805071.grobid-xml"},"referenced_works_count":1,"referenced_works":["https://openalex.org/W2970119293"],"related_works":["https://openalex.org/W3206528106","https://openalex.org/W3036264823","https://openalex.org/W2912814903","https://openalex.org/W2123605750","https://openalex.org/W2088740331","https://openalex.org/W3038102983","https://openalex.org/W2950907416","https://openalex.org/W1559483280","https://openalex.org/W2082479932","https://openalex.org/W2932872266"],"abstract_inverted_index":{"MDGraphEMB":[0],"GitHub":[1],"Repository:":[2],"https://github.com/FerdoosHN/MDGraphEMB.":[3]},"counts_by_year":[],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
