{"id":"https://openalex.org/W4405231340","doi":"https://doi.org/10.1093/bioinformatics/btae730","title":"TargetSA: adaptive simulated annealing for target-specific drug design","display_name":"TargetSA: adaptive simulated annealing for target-specific drug design","publication_year":2024,"publication_date":"2024-12-04","ids":{"openalex":"https://openalex.org/W4405231340","doi":"https://doi.org/10.1093/bioinformatics/btae730","pmid":"https://pubmed.ncbi.nlm.nih.gov/39656791"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae730","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae730","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae730/60951329/btae730.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/btae730/60951329/btae730.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111205759","display_name":"Zhe Xue","orcid":null},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]},{"id":"https://openalex.org/I37574244","display_name":"Sichuan Agricultural University","ror":"https://ror.org/0388c3403","country_code":"CN","type":"education","lineage":["https://openalex.org/I37574244"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhe Xue","raw_affiliation_strings":["College of Computer Science, Sichuan University , Chengdu, Sichuan 610065,","College of Computer Science, Sichuan University, Chengdu, Sichuan 610065, China"],"raw_orcid":"https://orcid.org/0000-0002-3456-2832","affiliations":[{"raw_affiliation_string":"College of Computer Science, Sichuan University , Chengdu, Sichuan 610065,","institution_ids":["https://openalex.org/I24185976","https://openalex.org/I37574244"]},{"raw_affiliation_string":"College of Computer Science, Sichuan University, Chengdu, Sichuan 610065, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009791941","display_name":"Chenwei Sun","orcid":"https://orcid.org/0009-0005-1583-2891"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]},{"id":"https://openalex.org/I37574244","display_name":"Sichuan Agricultural University","ror":"https://ror.org/0388c3403","country_code":"CN","type":"education","lineage":["https://openalex.org/I37574244"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chenwei Sun","raw_affiliation_strings":["College of Computer Science, Sichuan University , Chengdu, Sichuan 610065,","College of Computer Science, Sichuan University, Chengdu, Sichuan 610065, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science, Sichuan University , Chengdu, Sichuan 610065,","institution_ids":["https://openalex.org/I24185976","https://openalex.org/I37574244"]},{"raw_affiliation_string":"College of Computer Science, Sichuan University, Chengdu, Sichuan 610065, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063105045","display_name":"Wenhao Zheng","orcid":"https://orcid.org/0000-0002-9618-2456"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]},{"id":"https://openalex.org/I37574244","display_name":"Sichuan Agricultural University","ror":"https://ror.org/0388c3403","country_code":"CN","type":"education","lineage":["https://openalex.org/I37574244"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenhao Zheng","raw_affiliation_strings":["College of Computer Science, Sichuan University , Chengdu, Sichuan 610065,","College of Computer Science, Sichuan University, Chengdu, Sichuan 610065, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science, Sichuan University , Chengdu, Sichuan 610065,","institution_ids":["https://openalex.org/I24185976","https://openalex.org/I37574244"]},{"raw_affiliation_string":"College of Computer Science, Sichuan University, Chengdu, Sichuan 610065, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110000303","display_name":"Jiancheng Lv","orcid":"https://orcid.org/0000-0003-3341-4034"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]},{"id":"https://openalex.org/I37574244","display_name":"Sichuan Agricultural University","ror":"https://ror.org/0388c3403","country_code":"CN","type":"education","lineage":["https://openalex.org/I37574244"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiancheng Lv","raw_affiliation_strings":["College of Computer Science, Sichuan University , Chengdu, Sichuan 610065,","College of Computer Science, Sichuan University, Chengdu, Sichuan 610065, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science, Sichuan University , Chengdu, Sichuan 610065,","institution_ids":["https://openalex.org/I24185976","https://openalex.org/I37574244"]},{"raw_affiliation_string":"College of Computer Science, Sichuan University, Chengdu, Sichuan 610065, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"last","author":{"id":null,"display_name":"Xianggen Liu","orcid":"https://orcid.org/0009-0000-7502-7572"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]},{"id":"https://openalex.org/I37574244","display_name":"Sichuan Agricultural University","ror":"https://ror.org/0388c3403","country_code":"CN","type":"education","lineage":["https://openalex.org/I37574244"]},{"id":"https://openalex.org/I4210089761","display_name":"West China Hospital of Sichuan University","ror":"https://ror.org/007mrxy13","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210089761"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xianggen Liu","raw_affiliation_strings":["College of Computer Science, Sichuan University , Chengdu, Sichuan 610065,","Laboratory of Anesthesia and Critical Care Medicine, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University , Chengdu, Sichuan 610041,","College of Computer Science, Sichuan University, Chengdu, Sichuan 610065, China","Laboratory of Anesthesia and Critical Care Medicine, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China"],"raw_orcid":"https://orcid.org/0009-0000-7502-7572","affiliations":[{"raw_affiliation_string":"College of Computer Science, Sichuan University , Chengdu, Sichuan 610065,","institution_ids":["https://openalex.org/I24185976","https://openalex.org/I37574244"]},{"raw_affiliation_string":"Laboratory of Anesthesia and Critical Care Medicine, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University , Chengdu, Sichuan 610041,","institution_ids":["https://openalex.org/I24185976","https://openalex.org/I4210089761"]},{"raw_affiliation_string":"College of Computer Science, Sichuan University, Chengdu, Sichuan 610065, China","institution_ids":["https://openalex.org/I24185976"]},{"raw_affiliation_string":"Laboratory of Anesthesia and Critical Care Medicine, Department of Anesthesiology, Translational Neuroscience Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China","institution_ids":["https://openalex.org/I24185976","https://openalex.org/I4210089761"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I24185976","https://openalex.org/I37574244","https://openalex.org/I4210089761"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.0212,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.88331393,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"41","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.8508999943733215,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.8508999943733215,"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"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.03680000081658363,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","score":0.01979999989271164,"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/simulated-annealing","display_name":"Simulated annealing","score":0.7788161039352417},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6639770865440369},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.5994693040847778},{"id":"https://openalex.org/keywords/adaptive-design","display_name":"Adaptive design","score":0.5029682517051697},{"id":"https://openalex.org/keywords/adaptive-simulated-annealing","display_name":"Adaptive simulated annealing","score":0.4609454572200775},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.32455122470855713},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32070207595825195},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1792115867137909},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1405453085899353},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.12076607346534729},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11469975113868713}],"concepts":[{"id":"https://openalex.org/C126980161","wikidata":"https://www.wikidata.org/wiki/Q863783","display_name":"Simulated annealing","level":2,"score":0.7788161039352417},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6639770865440369},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.5994693040847778},{"id":"https://openalex.org/C2982777018","wikidata":"https://www.wikidata.org/wiki/Q99268086","display_name":"Adaptive design","level":3,"score":0.5029682517051697},{"id":"https://openalex.org/C46714192","wikidata":"https://www.wikidata.org/wiki/Q4680763","display_name":"Adaptive simulated annealing","level":3,"score":0.4609454572200775},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.32455122470855713},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32070207595825195},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1792115867137909},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1405453085899353},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.12076607346534729},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11469975113868713},{"id":"https://openalex.org/C535046627","wikidata":"https://www.wikidata.org/wiki/Q30612","display_name":"Clinical trial","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae730","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae730","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae730/60951329/btae730.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:39656791","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39656791","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:pubmedcentral.nih.gov:12013812","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12013812","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12013812/pdf/btae730.pdf","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae730","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae730","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae730/60951329/btae730.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":[{"score":0.4300000071525574,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G5203455355","display_name":null,"funder_award_id":"2023NS-FSC1408","funder_id":"https://openalex.org/F4320329861","funder_display_name":"Natural Science Foundation of Sichuan Province"},{"id":"https://openalex.org/G6195801520","display_name":null,"funder_award_id":"1082204112364","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6362919342","display_name":null,"funder_award_id":"1082204112364","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G8877878290","display_name":null,"funder_award_id":"62206192","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/F4320329861","display_name":"Natural Science Foundation of Sichuan Province","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4405231340.pdf","grobid_xml":"https://content.openalex.org/works/W4405231340.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W2023818227","https://openalex.org/W2146465875","https://openalex.org/W2151363206","https://openalex.org/W2786722833","https://openalex.org/W2914542247","https://openalex.org/W2921262115","https://openalex.org/W2962711740","https://openalex.org/W2962764565","https://openalex.org/W2970175280","https://openalex.org/W2977044154","https://openalex.org/W3082411326","https://openalex.org/W3098521774","https://openalex.org/W3104956673","https://openalex.org/W3110616988","https://openalex.org/W3137385578","https://openalex.org/W3165171933","https://openalex.org/W3174976929","https://openalex.org/W3177828909","https://openalex.org/W3196732196","https://openalex.org/W3209764902","https://openalex.org/W4200289210","https://openalex.org/W4221138292","https://openalex.org/W4221155201","https://openalex.org/W4224311800","https://openalex.org/W4235112493","https://openalex.org/W4242372416","https://openalex.org/W4280535976","https://openalex.org/W4297001088","https://openalex.org/W4298052734","https://openalex.org/W4307416138","https://openalex.org/W4310556487","https://openalex.org/W4319986489","https://openalex.org/W4323650483","https://openalex.org/W4378508570","https://openalex.org/W4389257854","https://openalex.org/W4390875024","https://openalex.org/W4391485436","https://openalex.org/W4392120633","https://openalex.org/W4392822048","https://openalex.org/W4393111365","https://openalex.org/W4393153201","https://openalex.org/W4394971461","https://openalex.org/W6775330246","https://openalex.org/W6843880952","https://openalex.org/W6846752334"],"related_works":["https://openalex.org/W2077092686","https://openalex.org/W2261837478","https://openalex.org/W3007136692","https://openalex.org/W1967687468","https://openalex.org/W2002077985","https://openalex.org/W2089397391","https://openalex.org/W173512906","https://openalex.org/W2382432451","https://openalex.org/W2394090522","https://openalex.org/W2979021254"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,89],"burgeoning":[2],"field":[3],"of":[4,97,151],"target-specific":[5,26,83],"drug":[6,53],"design":[7],"has":[8],"attracted":[9],"considerable":[10],"attention,":[11],"focusing":[12],"on":[13,37,121],"identifying":[14],"compounds":[15],"with":[16,59],"high":[17],"binding":[18],"affinity":[19],"toward":[20,101],"specific":[21],"target":[22],"pockets.":[23],"Nevertheless,":[24],"existing":[25],"deep":[27],"generative":[28],"models":[29,34],"encounter":[30],"notable":[31],"challenges.":[32],"Some":[33],"heavily":[35],"rely":[36],"elaborate":[38],"datasets":[39],"and":[40,86,124,136],"complicated":[41],"training":[42],"methodologies,":[43],"while":[44,188],"others":[45],"neglect":[46],"the":[47,93,102,107,152,169],"multi-constraint":[48,87],"optimization":[49],"problem":[50],"inherent":[51],"in":[52,56,180],"design,":[54],"resulting":[55],"generated":[57],"molecules":[58,183],"irrational":[60],"structures":[61],"or":[62],"chemical":[63,191],"properties.":[64,192],"RESULTS:":[65],"To":[66,110],"address":[67],"these":[68,139],"issues,":[69],"we":[70,114,156],"propose":[71,111],"a":[72,143,148,158],"novel":[73,112],"framework":[74],"(TargetSA)":[75],"that":[76,105,175],"leverages":[77],"adaptive":[78],"simulated":[79],"annealing":[80],"(SA)":[81],"for":[82],"molecular":[84,128],"generation":[85,170],"optimization.":[88],"SA":[90],"process":[91],"explores":[92],"discrete":[94],"structural":[95],"space":[96],"molecules,":[98],"progressively":[99],"converging":[100],"optimal":[103],"solution":[104],"fulfills":[106],"predefined":[108],"objective.":[109],"compounds,":[113],"first":[115],"predict":[116],"promising":[117],"editing":[118],"positions":[119],"based":[120],"historical":[122],"experience,":[123],"then":[125],"iteratively":[126],"edit":[127],"graphs":[129],"through":[130],"four":[131],"operations":[132,140],"(insertion,":[133],"replacement,":[134],"deletion,":[135],"cyclization).":[137],"Together,":[138],"collectively":[141],"constitute":[142],"complete":[144],"operation":[145],"set,":[146],"facilitating":[147],"thorough":[149],"exploration":[150],"drug-like":[153],"space.":[154],"Furthermore,":[155],"introduce":[157],"reversible":[159],"sampling":[160],"strategy":[161],"to":[162],"re-accept":[163],"currently":[164],"suboptimal":[165],"solutions,":[166],"greatly":[167],"enhancing":[168],"quality.":[171],"Empirical":[172],"evaluations":[173],"demonstrate":[174],"TargetSA":[176],"achieves":[177],"state-of-the-art":[178],"performance":[179],"generating":[181],"high-affinity":[182],"(average":[184],"vina":[185],"dock":[186],"-9.09)":[187],"maintaining":[189],"desirable":[190],"AVAILABILITY":[193],"AND":[194],"IMPLEMENTATION:":[195],"https://github.com/XueZhe-Zachary/TargetSA.":[196]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":4}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
