{"id":"https://openalex.org/W4318392954","doi":"https://doi.org/10.1093/bioinformatics/btad059","title":"Potent antibiotic design via guided search from antibacterial activity evaluations","display_name":"Potent antibiotic design via guided search from antibacterial activity evaluations","publication_year":2023,"publication_date":"2023-01-27","ids":{"openalex":"https://openalex.org/W4318392954","doi":"https://doi.org/10.1093/bioinformatics/btad059","pmid":"https://pubmed.ncbi.nlm.nih.gov/36707990"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad059","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad059","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad059/49086929/btad059.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/article-pdf/39/2/btad059/49086929/btad059.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100432093","display_name":"Lu Chen","orcid":"https://orcid.org/0000-0002-5685-7017"},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lu Chen","raw_affiliation_strings":["School of Computer Science and Technology, Xidian University , Xi\u2019an 710071, Shaanxi, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xidian University , Xi\u2019an 710071, Shaanxi, China","institution_ids":["https://openalex.org/I149594827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054977113","display_name":"Liang Yu","orcid":"https://orcid.org/0000-0002-8351-3332"},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Liang Yu","raw_affiliation_strings":["School of Computer Science and Technology, Xidian University , Xi\u2019an 710071, Shaanxi, China"],"raw_orcid":"https://orcid.org/0000-0002-8351-3332","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xidian University , Xi\u2019an 710071, Shaanxi, China","institution_ids":["https://openalex.org/I149594827"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060109811","display_name":"Lin Gao","orcid":"https://orcid.org/0000-0001-6396-0787"},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lin Gao","raw_affiliation_strings":["School of Computer Science and Technology, Xidian University , Xi\u2019an 710071, Shaanxi, China"],"raw_orcid":"https://orcid.org/0000-0001-6396-0787","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xidian University , Xi\u2019an 710071, Shaanxi, China","institution_ids":["https://openalex.org/I149594827"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5054977113"],"corresponding_institution_ids":["https://openalex.org/I149594827"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":13.2996,"has_fulltext":true,"cited_by_count":77,"citation_normalized_percentile":{"value":0.99141782,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"39","issue":"2","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":0.4108000099658966,"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":0.4108000099658966,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.1607999950647354,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11440","display_name":"Click Chemistry and Applications","score":0.04019999876618385,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/antibiotics","display_name":"Antibiotics","score":0.6971914768218994},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4729311764240265},{"id":"https://openalex.org/keywords/antibacterial-activity","display_name":"Antibacterial activity","score":0.44921281933784485},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.31591343879699707},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2029704749584198},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.1690049171447754},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.12204542756080627},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09547469019889832}],"concepts":[{"id":"https://openalex.org/C501593827","wikidata":"https://www.wikidata.org/wiki/Q12187","display_name":"Antibiotics","level":2,"score":0.6971914768218994},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4729311764240265},{"id":"https://openalex.org/C2780104969","wikidata":"https://www.wikidata.org/wiki/Q4774530","display_name":"Antibacterial activity","level":3,"score":0.44921281933784485},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.31591343879699707},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2029704749584198},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.1690049171447754},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.12204542756080627},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09547469019889832}],"mesh":[{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad059","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad059","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad059/49086929/btad059.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:36707990","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36707990","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:9897189","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9897189","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9897189/pdf/btad059.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/btad059","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad059","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad059/49086929/btad059.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":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.5600000023841858}],"awards":[{"id":"https://openalex.org/G2734538976","display_name":null,"funder_award_id":"62132015","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G375568310","display_name":"\u57fa\u4e8e\u591a\u7ec4\u5b66\u6570\u636e\u878d\u5408\u7684\u675c\u6c0f\u808c\u8425\u517b\u4e0d\u826f\u6f5c\u5728\u836f\u7269\u9884\u6d4b\u65b9\u6cd5\u7814\u7a76","funder_award_id":"62072353","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"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4318392954.pdf"},"referenced_works_count":67,"referenced_works":["https://openalex.org/W1965555277","https://openalex.org/W2176516200","https://openalex.org/W2192203593","https://openalex.org/W2300011769","https://openalex.org/W2523971282","https://openalex.org/W2529996553","https://openalex.org/W2578240541","https://openalex.org/W2610148085","https://openalex.org/W2613666205","https://openalex.org/W2747592475","https://openalex.org/W2769860552","https://openalex.org/W2773987374","https://openalex.org/W2805002767","https://openalex.org/W2805310212","https://openalex.org/W2883583109","https://openalex.org/W2887447356","https://openalex.org/W2900090807","https://openalex.org/W2900694120","https://openalex.org/W2911535432","https://openalex.org/W2913351693","https://openalex.org/W2914635984","https://openalex.org/W2919115771","https://openalex.org/W2953128081","https://openalex.org/W2955727640","https://openalex.org/W2963028280","https://openalex.org/W2966357564","https://openalex.org/W2972741532","https://openalex.org/W2980863799","https://openalex.org/W2985931096","https://openalex.org/W2989693255","https://openalex.org/W2990537780","https://openalex.org/W2991330881","https://openalex.org/W3006176441","https://openalex.org/W3007309629","https://openalex.org/W3025593963","https://openalex.org/W3027325047","https://openalex.org/W3035409428","https://openalex.org/W3038319509","https://openalex.org/W3041089282","https://openalex.org/W3047589804","https://openalex.org/W3089428833","https://openalex.org/W3096418018","https://openalex.org/W3098269892","https://openalex.org/W3100751385","https://openalex.org/W3112172360","https://openalex.org/W3113228261","https://openalex.org/W3116865743","https://openalex.org/W3125566655","https://openalex.org/W3133523400","https://openalex.org/W3135156311","https://openalex.org/W3181844989","https://openalex.org/W3184087886","https://openalex.org/W3192334993","https://openalex.org/W3194188670","https://openalex.org/W3207373390","https://openalex.org/W3209056694","https://openalex.org/W4206677002","https://openalex.org/W4207028073","https://openalex.org/W4210683988","https://openalex.org/W4211049957","https://openalex.org/W4213451219","https://openalex.org/W4220696791","https://openalex.org/W4220742882","https://openalex.org/W4226184982","https://openalex.org/W4226250938","https://openalex.org/W4286901673","https://openalex.org/W6786960682"],"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":{"MOTIVATION:":[0],"The":[1],"emergence":[2],"of":[3,9,62,131,149,157],"drug-resistant":[4],"bacteria":[5],"makes":[6],"the":[7,20,53,60,69,81,125,135,147,158],"discovery":[8],"new":[10,17],"antibiotics":[11,130],"an":[12,25],"urgent":[13],"issue,":[14],"but":[15],"finding":[16],"molecules":[18],"with":[19,76,90],"desired":[21],"antibacterial":[22,54,78,94,103,121],"activity":[23,55,79,104],"is":[24],"extremely":[26],"difficult":[27],"task.":[28],"To":[29],"address":[30],"this":[31,67],"challenge,":[32],"we":[33],"established":[34],"a":[35,143],"framework,":[36],"MDAGS":[37,71,98],"(Molecular":[38],"Design":[39],"via":[40],"Attribute-Guided":[41],"Search),":[42],"to":[43,116,129,146],"optimize":[44],"and":[45,58,86,105,160],"generate":[46,73],"potent":[47],"antibiotic":[48],"molecules.":[49],"RESULTS:":[50],"By":[51],"designing":[52],"latent":[56],"space":[57],"guiding":[59],"optimization":[61],"functional":[63],"compounds":[64,75,95,122],"based":[65],"on":[66,114],"space,":[68],"model":[70,159],"can":[72,162],"novel":[74],"desirable":[77],"without":[80,111],"need":[82],"for":[83],"extensive":[84],"expensive":[85],"time-consuming":[87],"evaluations.":[88],"Compared":[89],"existing":[91],"antibiotics,":[92,118],"candidate":[93,120],"generated":[96],"by":[97],"always":[99],"possessed":[100],"significantly":[101],"better":[102],"ensured":[106],"high":[107],"similarity.":[108],"Furthermore,":[109],"although":[110],"explicit":[112],"constraints":[113],"similarity":[115,128],"known":[117],"these":[119],"all":[123],"exhibited":[124],"highest":[126],"structural":[127],"expected":[132],"function":[133],"in":[134],"DrugBank":[136],"database":[137],"query.":[138],"Overall,":[139],"our":[140],"approach":[141],"provides":[142],"viable":[144],"solution":[145],"problem":[148],"bacterial":[150],"drug":[151],"resistance.":[152],"AVAILABILITY":[153],"AND":[154],"IMPLEMENTATION:":[155],"Code":[156],"datasets":[161],"be":[163],"downloaded":[164],"from":[165],"GitHub":[166],"(https://github.com/LiangYu-Xidian/MDAGS).":[167],"SUPPLEMENTARY":[168],"INFORMATION:":[169],"Supplementary":[170],"data":[171],"are":[172],"available":[173],"at":[174],"Bioinformatics":[175],"online.":[176]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":50},{"year":2023,"cited_by_count":16}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
