{"id":"https://openalex.org/W3082498841","doi":"https://doi.org/10.1371/journal.pcbi.1009284","title":"Deep geometric representations for modeling effects of mutations on protein-protein binding affinity","display_name":"Deep geometric representations for modeling effects of mutations on protein-protein binding affinity","publication_year":2021,"publication_date":"2021-08-04","ids":{"openalex":"https://openalex.org/W3082498841","doi":"https://doi.org/10.1371/journal.pcbi.1009284","mag":"3082498841","pmid":"https://pubmed.ncbi.nlm.nih.gov/34347784"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1009284","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009284","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009284&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009284&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037847115","display_name":"Xianggen Liu","orcid":"https://orcid.org/0000-0001-6368-2043"},"institutions":[{"id":"https://openalex.org/I4800084","display_name":"Southwest Jiaotong University","ror":"https://ror.org/00hn7w693","country_code":"CN","type":"education","lineage":["https://openalex.org/I4800084"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xianggen Liu","raw_affiliation_strings":["Beijing Innovation Center for Future Chip, Tsinghua University, Beijing, China","Laboratory for Brain and Intelligence and Department of Biomedical Engineering, Tsinghua University, Beijing, China","School of Computing and Artificial Intelligence, Southwest Jiaotong University, Chengdu, China"],"raw_orcid":"https://orcid.org/0000-0001-6368-2043","affiliations":[{"raw_affiliation_string":"Beijing Innovation Center for Future Chip, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Laboratory for Brain and Intelligence and Department of Biomedical Engineering, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"School of Computing and Artificial Intelligence, Southwest Jiaotong University, Chengdu, China","institution_ids":["https://openalex.org/I4800084"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040139742","display_name":"Yunan Luo","orcid":"https://orcid.org/0000-0001-7728-6412"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yunan Luo","raw_affiliation_strings":["Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-7728-6412","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036428356","display_name":"Pengyong Li","orcid":"https://orcid.org/0000-0001-5971-046X"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Pengyong Li","raw_affiliation_strings":["Beijing Innovation Center for Future Chip, Tsinghua University, Beijing, China","Laboratory for Brain and Intelligence and Department of Biomedical Engineering, Tsinghua University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0001-5971-046X","affiliations":[{"raw_affiliation_string":"Beijing Innovation Center for Future Chip, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Laboratory for Brain and Intelligence and Department of Biomedical Engineering, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013759262","display_name":"Sen Song","orcid":"https://orcid.org/0000-0001-5587-0730"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Sen Song","raw_affiliation_strings":["Beijing Innovation Center for Future Chip, Tsinghua University, Beijing, China","Laboratory for Brain and Intelligence and Department of Biomedical Engineering, Tsinghua University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Innovation Center for Future Chip, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Laboratory for Brain and Intelligence and Department of Biomedical Engineering, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061177999","display_name":"Jian Peng","orcid":"https://orcid.org/0000-0002-1736-2978"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jian Peng","raw_affiliation_strings":["Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-1736-2978","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5013759262","https://openalex.org/A5036428356","https://openalex.org/A5037847115","https://openalex.org/A5040139742","https://openalex.org/A5061177999"],"corresponding_institution_ids":["https://openalex.org/I157725225","https://openalex.org/I4800084","https://openalex.org/I99065089"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":6.6619,"has_fulltext":true,"cited_by_count":139,"citation_normalized_percentile":{"value":0.98064293,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"17","issue":"8","first_page":"e1009284","last_page":"e1009284"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9951000213623047,"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":0.9951000213623047,"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":0.9919000267982483,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9901000261306763,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5204677581787109},{"id":"https://openalex.org/keywords/plasma-protein-binding","display_name":"Plasma protein binding","score":0.4692627787590027},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.35141149163246155},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3457469940185547},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.34119418263435364},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2942328155040741}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5204677581787109},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.4692627787590027},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.35141149163246155},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3457469940185547},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.34119418263435364},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2942328155040741}],"mesh":[{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017354","descriptor_name":"Point Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017354","descriptor_name":"Point Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017354","descriptor_name":"Point Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1009284","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009284","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009284&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:34347784","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34347784","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:arXiv.org:2008.12473","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2008.12473","pdf_url":"https://arxiv.org/pdf/2008.12473","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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:doaj.org/article:e6b3c1e20d5048b595ed2fb8313558fb","is_oa":true,"landing_page_url":"https://doaj.org/article/e6b3c1e20d5048b595ed2fb8313558fb","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":"PLoS Computational Biology, Vol 17, Iss 8, p e1009284 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8366979","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8366979","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1009284","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009284","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009284&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4300000071525574,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G6671297155","display_name":null,"funder_award_id":"CAREER","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6721438513","display_name":"CAREER: Large-scale biological network integration with applications to automated function annotation","funder_award_id":"1652815","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G701568075","display_name":null,"funder_award_id":"No. 61836004","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7861851748","display_name":"\u901a\u7528\u7c7b\u8111\u8ba1\u7b97\u67b6\u6784\u6a21\u578b\u4e0e\u65b9\u6cd5\u7814\u7a76","funder_award_id":"61836004","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320318547","display_name":"Baidu","ror":"https://ror.org/03vs3wt56"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322392","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":88,"referenced_works":["https://openalex.org/W1498436455","https://openalex.org/W1522301498","https://openalex.org/W1534406401","https://openalex.org/W1677182931","https://openalex.org/W1678356000","https://openalex.org/W1965827393","https://openalex.org/W1984909504","https://openalex.org/W1991955074","https://openalex.org/W1994891218","https://openalex.org/W2008505479","https://openalex.org/W2011658408","https://openalex.org/W2023490488","https://openalex.org/W2035056536","https://openalex.org/W2036108598","https://openalex.org/W2046301150","https://openalex.org/W2050754173","https://openalex.org/W2069663555","https://openalex.org/W2093795463","https://openalex.org/W2101234009","https://openalex.org/W2102245393","https://openalex.org/W2105314995","https://openalex.org/W2106648157","https://openalex.org/W2111326065","https://openalex.org/W2117541321","https://openalex.org/W2125677968","https://openalex.org/W2128674962","https://openalex.org/W2132851824","https://openalex.org/W2135847964","https://openalex.org/W2138449457","https://openalex.org/W2138913459","https://openalex.org/W2144354855","https://openalex.org/W2153983456","https://openalex.org/W2157807259","https://openalex.org/W2165319219","https://openalex.org/W2165531467","https://openalex.org/W2169017143","https://openalex.org/W2170564629","https://openalex.org/W2187089797","https://openalex.org/W2201713963","https://openalex.org/W2283896596","https://openalex.org/W2340330302","https://openalex.org/W2400041270","https://openalex.org/W2519539312","https://openalex.org/W2554576124","https://openalex.org/W2557283755","https://openalex.org/W2583933435","https://openalex.org/W2798528327","https://openalex.org/W2804586639","https://openalex.org/W2806151064","https://openalex.org/W2896457183","https://openalex.org/W2899771611","https://openalex.org/W2902812092","https://openalex.org/W2942512732","https://openalex.org/W2945403072","https://openalex.org/W2949787032","https://openalex.org/W2951122824","https://openalex.org/W2952254971","https://openalex.org/W2953103783","https://openalex.org/W2962756421","https://openalex.org/W2963341956","https://openalex.org/W2963420272","https://openalex.org/W2963858333","https://openalex.org/W2964121744","https://openalex.org/W2969325782","https://openalex.org/W2980681402","https://openalex.org/W2996604169","https://openalex.org/W3005552578","https://openalex.org/W3005822506","https://openalex.org/W3007500173","https://openalex.org/W3016025838","https://openalex.org/W3021559842","https://openalex.org/W3024602798","https://openalex.org/W3034548712","https://openalex.org/W3035459690","https://openalex.org/W3036386821","https://openalex.org/W3036446966","https://openalex.org/W3048714202","https://openalex.org/W3080610776","https://openalex.org/W3085586916","https://openalex.org/W3092403777","https://openalex.org/W3099152386","https://openalex.org/W3108043937","https://openalex.org/W4297733535","https://openalex.org/W6631190155","https://openalex.org/W6675354045","https://openalex.org/W6736685754","https://openalex.org/W6756040250","https://openalex.org/W6772452955"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487"],"abstract_inverted_index":{"Modeling":[0],"the":[1,33,42,59,80,121,143,156,161,167],"impact":[2],"of":[3,35,45,58,82,145,160,169],"amino":[4],"acid":[5],"mutations":[6,130],"on":[7,41,131],"protein-protein":[8,83],"interaction":[9],"plays":[10],"a":[11,26,46,51,63,149,172],"crucial":[12],"role":[13],"in":[14,103,119,178],"protein":[15,60,104,179],"engineering":[16],"and":[17,128,155,174,181,185],"drug":[18],"design.":[19],"In":[20,106],"this":[21],"study,":[22],"we":[23,111,136],"develop":[24],"GeoPPI,":[25],"novel":[27],"structure-based":[28],"deep-learning":[29],"framework":[30],"to":[31,78,94],"predict":[32,79],"change":[34],"binding":[36,84,122,146],"affinity":[37,85,123],"upon":[38,86,125],"mutations.":[39,87],"Based":[40],"three-dimensional":[43],"structure":[44,61],"protein,":[47],"GeoPPI":[48,91,114,139,170],"first":[49],"learns":[50],"geometric":[52],"representation":[53],"that":[54,90,98,113,138],"encodes":[55],"topology":[56],"features":[57,73,97],"via":[62],"self-supervised":[64],"learning":[65],"scheme.":[66],"These":[67,164],"representations":[68],"are":[69,187],"then":[70],"used":[71],"as":[72,171],"for":[74],"training":[75],"gradient-boosting":[76],"trees":[77],"changes":[81,124],"We":[88],"find":[89],"is":[92],"able":[93],"learn":[95],"meaningful":[96],"characterize":[99],"interactions":[100],"between":[101,148],"atoms":[102],"structures.":[105],"addition,":[107],"through":[108],"extensive":[109],"experiments,":[110],"show":[112,137],"achieves":[115],"new":[116],"state-of-the-art":[117],"performance":[118],"predicting":[120],"both":[126],"single-":[127],"multi-point":[129],"six":[132],"benchmark":[133],"datasets.":[134],"Moreover,":[135],"can":[140],"accurately":[141],"estimate":[142],"difference":[144],"affinities":[147],"few":[150],"recently":[151],"identified":[152],"SARS-CoV-2":[153],"antibodies":[154],"receptor-binding":[157],"domain":[158],"(RBD)":[159],"S":[162],"protein.":[163],"results":[165],"demonstrate":[166],"potential":[168],"powerful":[173],"useful":[175],"computational":[176],"tool":[177],"design":[180],"engineering.":[182],"Our":[183],"code":[184],"datasets":[186],"available":[188],"at:":[189],"https://github.com/Liuxg16/GeoPPI.":[190]},"counts_by_year":[{"year":2026,"cited_by_count":13},{"year":2025,"cited_by_count":38},{"year":2024,"cited_by_count":45},{"year":2023,"cited_by_count":27},{"year":2022,"cited_by_count":16}],"updated_date":"2026-07-31T08:31:51.225901","created_date":"2025-10-10T00:00:00"}