{"id":"https://openalex.org/W4401404691","doi":"https://doi.org/10.1093/bioinformatics/btae492","title":"Locuaz: an <i>in silico</i> platform for protein binders optimization","display_name":"Locuaz: an <i>in silico</i> platform for protein binders optimization","publication_year":2024,"publication_date":"2024-08-01","ids":{"openalex":"https://openalex.org/W4401404691","doi":"https://doi.org/10.1093/bioinformatics/btae492"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae492","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae492","pdf_url":null,"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"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btae492","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041716603","display_name":"German P. Barletta","orcid":"https://orcid.org/0000-0002-0806-0812"},"institutions":[{"id":"https://openalex.org/I12323705","display_name":"The Abdus Salam International Centre for Theoretical Physics (ICTP)","ror":"https://ror.org/009gyvm78","country_code":"IT","type":"facility","lineage":["https://openalex.org/I12323705","https://openalex.org/I1286959531","https://openalex.org/I1293226324","https://openalex.org/I2801247003"]},{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"German P Barletta","raw_affiliation_strings":["CONCEPT, Istituto Italiano di Tecnologia , Via Enrico Melen, 83 Genova Liguria 16152, Italy","The Abdus Salam International Centre for Theoretical Physics (ICTP) , Str. Costiera, 11 , Trieste, Friuli-Venezia Giulia, 34151, Italy"],"affiliations":[{"raw_affiliation_string":"CONCEPT, Istituto Italiano di Tecnologia , Via Enrico Melen, 83 Genova Liguria 16152, Italy","institution_ids":["https://openalex.org/I30771326"]},{"raw_affiliation_string":"The Abdus Salam International Centre for Theoretical Physics (ICTP) , Str. Costiera, 11 , Trieste, Friuli-Venezia Giulia, 34151, Italy","institution_ids":["https://openalex.org/I12323705"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042180550","display_name":"Rika Tandiana","orcid":null},"institutions":[{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Rika Tandiana","raw_affiliation_strings":["CONCEPT, Istituto Italiano di Tecnologia , Via Enrico Melen, 83 Genova Liguria 16152, Italy"],"affiliations":[{"raw_affiliation_string":"CONCEPT, Istituto Italiano di Tecnologia , Via Enrico Melen, 83 Genova Liguria 16152, Italy","institution_ids":["https://openalex.org/I30771326"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010767528","display_name":"Miguel A. Soler","orcid":"https://orcid.org/0000-0002-5780-9949"},"institutions":[{"id":"https://openalex.org/I129043915","display_name":"University of Udine","ror":"https://ror.org/05ht0mh31","country_code":"IT","type":"education","lineage":["https://openalex.org/I129043915"]},{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Miguel Soler","raw_affiliation_strings":["CONCEPT, Istituto Italiano di Tecnologia , Via Enrico Melen, 83 Genova Liguria 16152, Italy","Dipartimento di Scienze Matematiche, Informatiche e Fisiche (DMIF), University of Udine , Via delle Scienze, 206 , Udine, Friuli-Venezia Giulia, 33100, Italy"],"affiliations":[{"raw_affiliation_string":"CONCEPT, Istituto Italiano di Tecnologia , Via Enrico Melen, 83 Genova Liguria 16152, Italy","institution_ids":["https://openalex.org/I30771326"]},{"raw_affiliation_string":"Dipartimento di Scienze Matematiche, Informatiche e Fisiche (DMIF), University of Udine , Via delle Scienze, 206 , Udine, Friuli-Venezia Giulia, 33100, Italy","institution_ids":["https://openalex.org/I129043915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047636020","display_name":"Sara Fortuna","orcid":"https://orcid.org/0000-0002-8059-6064"},"institutions":[{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]},{"id":"https://openalex.org/I4210122246","display_name":"Cresset (United Kingdom)","ror":"https://ror.org/02qfkfg14","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210122246"]}],"countries":["GB","IT"],"is_corresponding":false,"raw_author_name":"Sara Fortuna","raw_affiliation_strings":["CONCEPT, Istituto Italiano di Tecnologia , Via Enrico Melen, 83 Genova Liguria 16152, Italy","Cresset, New Cambridge House , Litlington, Royston, SG8-0SS, United Kingdom"],"affiliations":[{"raw_affiliation_string":"CONCEPT, Istituto Italiano di Tecnologia , Via Enrico Melen, 83 Genova Liguria 16152, Italy","institution_ids":["https://openalex.org/I30771326"]},{"raw_affiliation_string":"Cresset, New Cambridge House , Litlington, Royston, SG8-0SS, United Kingdom","institution_ids":["https://openalex.org/I4210122246"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089704088","display_name":"Walter Rocchia","orcid":"https://orcid.org/0000-0003-2480-7151"},"institutions":[{"id":"https://openalex.org/I30771326","display_name":"Italian Institute of Technology","ror":"https://ror.org/042t93s57","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Walter Rocchia","raw_affiliation_strings":["CONCEPT, Istituto Italiano di Tecnologia , Via Enrico Melen, 83 Genova Liguria 16152, Italy"],"affiliations":[{"raw_affiliation_string":"CONCEPT, Istituto Italiano di Tecnologia , Via Enrico Melen, 83 Genova Liguria 16152, Italy","institution_ids":["https://openalex.org/I30771326"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5041716603"],"corresponding_institution_ids":["https://openalex.org/I12323705","https://openalex.org/I30771326"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.1787,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.79008338,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"40","issue":"8","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"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/T11124","display_name":"Protein purification and stability","score":0.9966999888420105,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9958999752998352,"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/in-silico","display_name":"In silico","score":0.8531440496444702},{"id":"https://openalex.org/keywords/pruning","display_name":"Pruning","score":0.7801294922828674},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6922961473464966},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.6204123497009277},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5478978157043457},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.5349598526954651},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47557011246681213},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.41381973028182983},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3606170117855072},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16623541712760925},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12513947486877441},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.11873689293861389},{"id":"https://openalex.org/keywords/systems-engineering","display_name":"Systems engineering","score":0.08579239249229431},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.07775330543518066}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.8531440496444702},{"id":"https://openalex.org/C108010975","wikidata":"https://www.wikidata.org/wiki/Q500094","display_name":"Pruning","level":2,"score":0.7801294922828674},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6922961473464966},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.6204123497009277},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5478978157043457},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.5349598526954651},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47557011246681213},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.41381973028182983},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3606170117855072},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16623541712760925},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12513947486877441},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.11873689293861389},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.08579239249229431},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.07775330543518066},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C6557445","wikidata":"https://www.wikidata.org/wiki/Q173113","display_name":"Agronomy","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae492","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae492","pdf_url":null,"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":"pmh:oai:pubmedcentral.nih.gov:11324344","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11324344","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11324344/pdf/btae492.pdf","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"},{"id":"pmh:oai:iris.unive.it:10278/5106676","is_oa":true,"landing_page_url":"https://hdl.handle.net/10278/5106676","pdf_url":null,"source":{"id":"https://openalex.org/S4306402336","display_name":"ARCA (Universit\u00e0 Ca' Foscari Venezia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149461666","host_organization_name":"Ca' Foscari University of Venice","host_organization_lineage":["https://openalex.org/I149461666"],"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":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae492","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae492","pdf_url":null,"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/9","score":0.41999998688697815,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G1009127416","display_name":null,"funder_award_id":"fellowship","funder_id":"https://openalex.org/F4320323054","funder_display_name":"Associazione Italiana per la Ricerca sul Cancro"},{"id":"https://openalex.org/G1364224112","display_name":null,"funder_award_id":"IG 2020","funder_id":"https://openalex.org/F4320323054","funder_display_name":"Associazione Italiana per la Ricerca sul Cancro"},{"id":"https://openalex.org/G489053898","display_name":null,"funder_award_id":"24589","funder_id":"https://openalex.org/F4320317988","funder_display_name":"Artificial Intelligence Research Center"},{"id":"https://openalex.org/G5871342693","display_name":null,"funder_award_id":"24589","funder_id":"https://openalex.org/F4320323054","funder_display_name":"Associazione Italiana per la Ricerca sul Cancro"}],"funders":[{"id":"https://openalex.org/F4320317988","display_name":"Artificial Intelligence Research Center","ror":null},{"id":"https://openalex.org/F4320320894","display_name":"Abdus Salam International Centre for Theoretical Physics","ror":"https://ror.org/009gyvm78"},{"id":"https://openalex.org/F4320321047","display_name":"Partnership for Advanced Computing in Europe AISBL","ror":"https://ror.org/038j4hz26"},{"id":"https://openalex.org/F4320323054","display_name":"Associazione Italiana per la Ricerca sul Cancro","ror":"https://ror.org/02g2x7380"},{"id":"https://openalex.org/F4320323641","display_name":"Vedeck\u00e1 Grantov\u00e1 Agent\u00fara M\u0160VVa\u0160 SR a SAV","ror":"https://ror.org/044gwpv05"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W2071200955","https://openalex.org/W2103325328","https://openalex.org/W2565789529","https://openalex.org/W2744172477","https://openalex.org/W2782624750","https://openalex.org/W2896148359","https://openalex.org/W2951122824","https://openalex.org/W2953176058","https://openalex.org/W2982376098","https://openalex.org/W3023697740","https://openalex.org/W3156522942","https://openalex.org/W3202287440","https://openalex.org/W3214888383","https://openalex.org/W4214886481","https://openalex.org/W4296021807","https://openalex.org/W4308450127","https://openalex.org/W4316126743","https://openalex.org/W4366823175","https://openalex.org/W4383877908","https://openalex.org/W4384298552","https://openalex.org/W4392509499"],"related_works":["https://openalex.org/W2912862995","https://openalex.org/W3129816939","https://openalex.org/W2985427592","https://openalex.org/W2101501829","https://openalex.org/W2400569965","https://openalex.org/W2060263731","https://openalex.org/W2003194288","https://openalex.org/W391093122","https://openalex.org/W1521239975","https://openalex.org/W4361305867"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"Engineering":[2],"high-affinity":[3],"binders":[4,67],"targeting":[5],"specific":[6],"antigenic":[7],"determinants":[8],"remains":[9],"a":[10,60,76],"challenging":[11],"and":[12,31,40,47,83,94,136,145],"often":[13],"daunting":[14],"task,":[15],"requiring":[16],"extensive":[17],"experimental":[18],"screening.":[19],"Computational":[20],"methods":[21],"have":[22],"the":[23,102,123],"potential":[24],"to":[25,55,88,130],"accelerate":[26],"this":[27,153],"process,":[28],"reducing":[29],"costs":[30],"time,":[32],"but":[33],"only":[34],"if":[35],"they":[36],"demonstrate":[37],"broad":[38],"applicability":[39],"efficiency":[41],"in":[42,112],"exploring":[43],"mutations,":[44],"evaluating":[45],"affinity,":[46],"pruning":[48],"unproductive":[49],"mutation":[50,81,95,109],"paths.":[51],"Results":[52],"In":[53],"response":[54],"these":[56],"challenges,":[57],"we":[58],"introduce":[59],"new":[61],"computational":[62],"platform":[63,72,103,124],"for":[64],"optimizing":[65],"protein":[66],"towards":[68],"their":[69,132],"targets.":[70],"The":[71,138,150],"is":[73,125,141,147],"organized":[74],"as":[75],"series":[77],"of":[78,107],"modules,":[79],"performing":[80],"selection":[82],"application,":[84],"molecular":[85],"dynamics":[86],"simulations":[87],"sample":[89],"conformations":[90],"around":[91],"interaction":[92],"poses,":[93],"prioritization":[96],"using":[97],"suitable":[98],"scoring":[99],"functions.":[100],"Notably,":[101],"supports":[104],"parallel":[105],"exploration":[106],"different":[108],"streams,":[110],"enabling":[111],"silico":[113],"high-throughput":[114],"screening":[115],"on":[116],"High":[117],"Performance":[118],"Computing":[119],"(HPC)":[120],"systems.":[121],"Furthermore,":[122],"highly":[126],"customizable,":[127],"allowing":[128],"users":[129],"implement":[131],"own":[133],"protocols.":[134],"Availability":[135],"implementation":[137],"source":[139],"code":[140],"available":[142,156],"at":[143,148,157],"https://github.com/pgbarletta/locuaz":[144],"documentation":[146],"https://locuaz.readthedocs.io/.":[149],"data":[151],"underlying":[152],"article":[154],"are":[155],"https://github.com/pgbarletta/suppl_info_locuaz":[158]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2024-08-08T00:00:00"}
