{"id":"https://openalex.org/W4385638396","doi":"https://doi.org/10.1093/bioinformatics/btad476","title":"TALAIA: a 3D visual dictionary for protein structures","display_name":"TALAIA: a 3D visual dictionary for protein structures","publication_year":2023,"publication_date":"2023-08-01","ids":{"openalex":"https://openalex.org/W4385638396","doi":"https://doi.org/10.1093/bioinformatics/btad476"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad476","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad476","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad476/51048009/btad476.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"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad476/51048009/btad476.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068828108","display_name":"Merc\u00e8 Alemany\u2010Chavarria","orcid":"https://orcid.org/0000-0002-3990-1215"},"institutions":[{"id":"https://openalex.org/I123044942","display_name":"Universitat Aut\u00f2noma de Barcelona","ror":"https://ror.org/052g8jq94","country_code":"ES","type":"education","lineage":["https://openalex.org/I123044942"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Merc\u00e8 Alemany-Chavarria","raw_affiliation_strings":["Insilichem, Department of chemistry, Universitat Aut\u00f2noma de Barcelona , Bellaterra 08193, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Insilichem, Department of chemistry, Universitat Aut\u00f2noma de Barcelona , Bellaterra 08193, Barcelona, Spain","institution_ids":["https://openalex.org/I123044942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101741282","display_name":"Jaime Rodr\u0131\u0301guez-Guerra","orcid":"https://orcid.org/0000-0001-8974-1566"},"institutions":[{"id":"https://openalex.org/I123044942","display_name":"Universitat Aut\u00f2noma de Barcelona","ror":"https://ror.org/052g8jq94","country_code":"ES","type":"education","lineage":["https://openalex.org/I123044942"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jaime Rodr\u00edguez-Guerra","raw_affiliation_strings":["Insilichem, Department of chemistry, Universitat Aut\u00f2noma de Barcelona , Bellaterra 08193, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Insilichem, Department of chemistry, Universitat Aut\u00f2noma de Barcelona , Bellaterra 08193, Barcelona, Spain","institution_ids":["https://openalex.org/I123044942"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076914476","display_name":"Jean\u2010Didier Mar\u00e9chal","orcid":"https://orcid.org/0000-0002-8344-9043"},"institutions":[{"id":"https://openalex.org/I123044942","display_name":"Universitat Aut\u00f2noma de Barcelona","ror":"https://ror.org/052g8jq94","country_code":"ES","type":"education","lineage":["https://openalex.org/I123044942"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jean-Didier Mar\u00e9chal","raw_affiliation_strings":["Insilichem, Department of chemistry, Universitat Aut\u00f2noma de Barcelona , Bellaterra 08193, Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Insilichem, Department of chemistry, Universitat Aut\u00f2noma de Barcelona , Bellaterra 08193, Barcelona, Spain","institution_ids":["https://openalex.org/I123044942"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5068828108"],"corresponding_institution_ids":["https://openalex.org/I123044942"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.159,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.58813153,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"39","issue":"8","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.996399998664856,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.996399998664856,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9914000034332275,"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/T11445","display_name":"Origins and Evolution of Life","score":0.9459999799728394,"subfield":{"id":"https://openalex.org/subfields/3103","display_name":"Astronomy and Astrophysics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7175529599189758},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.6544643640518188},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.5889750123023987},{"id":"https://openalex.org/keywords/grasp","display_name":"GRASP","score":0.5778017640113831},{"id":"https://openalex.org/keywords/depiction","display_name":"Depiction","score":0.5772358775138855},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.39576733112335205},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3265169858932495},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.22121134400367737},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11010047793388367}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7175529599189758},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6544643640518188},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.5889750123023987},{"id":"https://openalex.org/C171268870","wikidata":"https://www.wikidata.org/wiki/Q1486676","display_name":"GRASP","level":2,"score":0.5778017640113831},{"id":"https://openalex.org/C2779702343","wikidata":"https://www.wikidata.org/wiki/Q1166770","display_name":"Depiction","level":2,"score":0.5772358775138855},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39576733112335205},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3265169858932495},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.22121134400367737},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11010047793388367},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad476","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad476","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad476/51048009/btad476.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":"pmh:oai:ddd.uab.cat:281919","is_oa":true,"landing_page_url":"https://ddd.uab.cat/record/281919","pdf_url":"https://ddd.uab.cat/pub/artpub/2023/281919/btad476.pdf","source":{"id":"https://openalex.org/S4306400380","display_name":"Dip\u00f2sit Digital de Documents de la UAB (Universitat Aut\u00f2noma de Barcelona)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I123044942","host_organization_name":"Universitat Aut\u00f2noma de Barcelona","host_organization_lineage":["https://openalex.org/I123044942"],"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":"","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10423020","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10423020","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10423020/pdf/btad476.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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad476","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad476","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad476/51048009/btad476.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/4","score":0.6299999952316284,"display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4385638396.pdf"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W1985982026","https://openalex.org/W2132629607","https://openalex.org/W2190199302","https://openalex.org/W2774987310","https://openalex.org/W2910708059","https://openalex.org/W3006781192"],"related_works":["https://openalex.org/W2354497654","https://openalex.org/W1521279281","https://openalex.org/W1925626449","https://openalex.org/W3012686786","https://openalex.org/W2375460546","https://openalex.org/W4239616774","https://openalex.org/W2112416132","https://openalex.org/W170685810","https://openalex.org/W2775654505","https://openalex.org/W2381432856"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"Graphical":[2],"analysis":[3],"of":[4,8,59,64,83,95,129,158,195,211],"the":[5,156,193],"molecular":[6,125],"structure":[7,175],"proteins":[9],"can":[10,28,153,213],"be":[11,29,36,43,214],"very":[12],"complex.":[13],"Full-atom":[14],"representations":[15,34,94],"retain":[16],"most":[17],"geometric":[18],"information":[19],"but":[20,42],"are":[21,143],"generally":[22],"crowded,":[23],"and":[24,103,113,147,151,173,176,190,200],"key":[25,133],"structural":[26,84,203],"patterns":[27],"challenging":[30],"to":[31,79,115,122],"identify.":[32],"Non-full-atom":[33],"could":[35],"more":[37],"instructive":[38],"on":[39],"physicochemical":[40,104,177],"aspects":[41,178],"insufficiently":[44],"detailed":[45],"regarding":[46],"shapes":[47,112],"(e.g.":[48,62],"entity":[49],"beans-like":[50],"models":[51],"in":[52,141,145],"coarse":[53],"grain":[54],"approaches)":[55],"or":[56,132],"simple":[57,93,181],"properties":[58],"amino":[60,96,117,130],"acids":[61,97,131],"representation":[63],"superficial":[65],"electrostatic":[66],"properties).":[67],"In":[68],"this":[69],"work,":[70],"we":[71],"present":[72],"TALAIA":[73,86,142,160,165,212],"a":[74,88,167,180],"visual":[75,89,182],"dictionary":[76],"that":[77,91,169],"aims":[78],"provide":[80],"another":[81],"layer":[82],"representations.":[85],"offers":[87],"grammar":[90],"combines":[92],"while":[98],"retaining":[99],"their":[100],"general":[101],"geometry":[102],"properties.":[105],"It":[106,119],"uses":[107],"unique":[108],"objects,":[109],"with":[110],"differentiated":[111],"colors":[114],"represent":[116],"acids.":[118],"makes":[120],"easier":[121],"spot":[123],"crucial":[124],"information,":[126],"including":[127],"patches":[128],"interactions":[134],"between":[135],"side":[136],"chains.":[137],"Most":[138],"conventions":[139],"used":[140],"standard":[144],"chemistry":[146],"biochemistry,":[148],"so":[149],"experimentalists":[150],"modelers":[152],"rapidly":[154],"grasp":[155],"meaning":[157],"any":[159],"depiction.":[161],"Results":[162],"We":[163],"propose":[164],"as":[166,179],"tool":[168],"renders":[170],"protein":[171],"structures":[172],"encodes":[174],"grammar.":[183],"The":[184,208],"approach":[185],"is":[186],"fast,":[187],"highly":[188],"informative,":[189],"intuitive,":[191],"allowing":[192],"identification":[194],"possible":[196],"interactions,":[197],"hydrophobic":[198],"patches,":[199],"other":[201],"characteristic":[202],"features":[204],"at":[205,216],"first":[206,209],"glance.":[207],"implementation":[210],"found":[215],"https://github.com/insilichem/talaia.":[217]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2025-12-25T23:11:45.687758","created_date":"2025-10-10T00:00:00"}
