{"id":"https://openalex.org/W4396801812","doi":"https://doi.org/10.3390/computation12050094","title":"To Bind or Not to Bind? A Comprehensive Characterization of TIR1 and Auxins Using Consensus In Silico Approaches","display_name":"To Bind or Not to Bind? A Comprehensive Characterization of TIR1 and Auxins Using Consensus In Silico Approaches","publication_year":2024,"publication_date":"2024-05-09","ids":{"openalex":"https://openalex.org/W4396801812","doi":"https://doi.org/10.3390/computation12050094"},"language":"en","primary_location":{"id":"doi:10.3390/computation12050094","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation12050094","pdf_url":"https://www.mdpi.com/2079-3197/12/5/94/pdf?version=1715258740","source":{"id":"https://openalex.org/S2738402919","display_name":"Computation","issn_l":"2079-3197","issn":["2079-3197"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computation","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2079-3197/12/5/94/pdf?version=1715258740","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004654043","display_name":"Fernando D. Prieto\u2010Mart\u00ednez","orcid":"https://orcid.org/0000-0002-0054-0862"},"institutions":[{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":true,"raw_author_name":"Fernando D. Prieto-Mart\u00ednez","raw_affiliation_strings":["Instituto de Qu\u00edmica Unidad M\u00e9rida, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Carretera M\u00e9rida-Tetiz, Km. 4.5, Uc\u00fa 97357, Mexico"],"raw_orcid":"https://orcid.org/0000-0002-0054-0862","affiliations":[{"raw_affiliation_string":"Instituto de Qu\u00edmica Unidad M\u00e9rida, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Carretera M\u00e9rida-Tetiz, Km. 4.5, Uc\u00fa 97357, Mexico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5094358686","display_name":"Jennifer Mendoza-Ca\u00f1as","orcid":"https://orcid.org/0009-0002-0041-891X"},"institutions":[{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Jennifer Mendoza-Ca\u00f1as","raw_affiliation_strings":["Facultad de Qu\u00edmica, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Avenida Universidad 3000, Mexico City 04510, Mexico"],"raw_orcid":"https://orcid.org/0009-0002-0041-891X","affiliations":[{"raw_affiliation_string":"Facultad de Qu\u00edmica, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Avenida Universidad 3000, Mexico City 04510, Mexico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057869875","display_name":"Karina Mart\u00ednez\u2010Mayorga","orcid":"https://orcid.org/0000-0002-6974-7941"},"institutions":[{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Karina Mart\u00ednez-Mayorga","raw_affiliation_strings":["Instituto de Investigaciones en Matem\u00e1ticas Aplicadas y en Sistemas, Unidad M\u00e9rida, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Sierra Papacal, M\u00e9rida 97302, Mexico","Instituto de Qu\u00edmica Unidad M\u00e9rida, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Carretera M\u00e9rida-Tetiz, Km. 4.5, Uc\u00fa 97357, Mexico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Instituto de Investigaciones en Matem\u00e1ticas Aplicadas y en Sistemas, Unidad M\u00e9rida, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Sierra Papacal, M\u00e9rida 97302, Mexico","institution_ids":["https://openalex.org/I8961855"]},{"raw_affiliation_string":"Instituto de Qu\u00edmica Unidad M\u00e9rida, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Carretera M\u00e9rida-Tetiz, Km. 4.5, Uc\u00fa 97357, Mexico","institution_ids":["https://openalex.org/I8961855"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5004654043"],"corresponding_institution_ids":["https://openalex.org/I8961855"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.06873415,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"12","issue":"5","first_page":"94","last_page":"94"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11745","display_name":"Potato Plant Research","score":0.4657000005245209,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11745","display_name":"Potato Plant Research","score":0.4657000005245209,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.40849998593330383,"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/T12215","display_name":"Phytochemical Studies and Bioactivities","score":0.40720000863075256,"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":0.9079311490058899},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6512987613677979},{"id":"https://openalex.org/keywords/characterization","display_name":"Characterization (materials science)","score":0.5790761709213257},{"id":"https://openalex.org/keywords/auxin","display_name":"Auxin","score":0.4746946692466736},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3571137487888336},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31255993247032166},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.25399309396743774},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.1430392861366272},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.06447300314903259},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.05550089478492737}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.9079311490058899},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6512987613677979},{"id":"https://openalex.org/C2780841128","wikidata":"https://www.wikidata.org/wiki/Q5073781","display_name":"Characterization (materials science)","level":2,"score":0.5790761709213257},{"id":"https://openalex.org/C207778908","wikidata":"https://www.wikidata.org/wiki/Q190022","display_name":"Auxin","level":3,"score":0.4746946692466736},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3571137487888336},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31255993247032166},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.25399309396743774},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.1430392861366272},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.06447300314903259},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.05550089478492737}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.3390/computation12050094","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation12050094","pdf_url":"https://www.mdpi.com/2079-3197/12/5/94/pdf?version=1715258740","source":{"id":"https://openalex.org/S2738402919","display_name":"Computation","issn_l":"2079-3197","issn":["2079-3197"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computation","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:a8f9ffed59034cadb6821991970acb9c","is_oa":true,"landing_page_url":"https://doaj.org/article/a8f9ffed59034cadb6821991970acb9c","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computation, Vol 12, Iss 5, p 94 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3390/computation12050094","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation12050094","pdf_url":"https://www.mdpi.com/2079-3197/12/5/94/pdf?version=1715258740","source":{"id":"https://openalex.org/S2738402919","display_name":"Computation","issn_l":"2079-3197","issn":["2079-3197"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computation","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/6","score":0.800000011920929,"display_name":"Clean water and sanitation"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4396801812.pdf"},"referenced_works_count":80,"referenced_works":["https://openalex.org/W194228989","https://openalex.org/W1183155069","https://openalex.org/W1966950894","https://openalex.org/W1967291128","https://openalex.org/W1971849220","https://openalex.org/W1982900536","https://openalex.org/W1987198662","https://openalex.org/W1988437166","https://openalex.org/W1990621581","https://openalex.org/W2021295492","https://openalex.org/W2027247295","https://openalex.org/W2034453871","https://openalex.org/W2039127550","https://openalex.org/W2039609876","https://openalex.org/W2042129725","https://openalex.org/W2049185580","https://openalex.org/W2050992606","https://openalex.org/W2080661991","https://openalex.org/W2084550263","https://openalex.org/W2093414812","https://openalex.org/W2101234009","https://openalex.org/W2116211618","https://openalex.org/W2123566274","https://openalex.org/W2135732933","https://openalex.org/W2141528038","https://openalex.org/W2153387948","https://openalex.org/W2156091491","https://openalex.org/W2156665896","https://openalex.org/W2160648204","https://openalex.org/W2162825164","https://openalex.org/W2169527365","https://openalex.org/W2265028324","https://openalex.org/W2281410876","https://openalex.org/W2295598076","https://openalex.org/W2340782621","https://openalex.org/W2347697584","https://openalex.org/W2483704935","https://openalex.org/W2751974217","https://openalex.org/W2755682685","https://openalex.org/W2765889348","https://openalex.org/W2773035064","https://openalex.org/W2791355014","https://openalex.org/W2796288304","https://openalex.org/W2803653576","https://openalex.org/W2883458601","https://openalex.org/W2883470891","https://openalex.org/W2883886126","https://openalex.org/W2888137448","https://openalex.org/W2891800472","https://openalex.org/W2943623664","https://openalex.org/W2952463638","https://openalex.org/W2961010564","https://openalex.org/W2970175280","https://openalex.org/W2982145277","https://openalex.org/W2988682892","https://openalex.org/W2996385237","https://openalex.org/W3010340553","https://openalex.org/W3010891266","https://openalex.org/W3023189783","https://openalex.org/W3047924539","https://openalex.org/W3069883202","https://openalex.org/W3080868448","https://openalex.org/W3112440833","https://openalex.org/W3113720224","https://openalex.org/W3126031592","https://openalex.org/W3128405656","https://openalex.org/W3132468014","https://openalex.org/W3149078497","https://openalex.org/W3187833099","https://openalex.org/W3200016416","https://openalex.org/W4200335476","https://openalex.org/W4210860040","https://openalex.org/W4211166631","https://openalex.org/W4309391087","https://openalex.org/W4310602620","https://openalex.org/W4388446710","https://openalex.org/W6638899461","https://openalex.org/W6675354045","https://openalex.org/W6743332088","https://openalex.org/W6912327399"],"related_works":["https://openalex.org/W2003194288","https://openalex.org/W2513589746","https://openalex.org/W2153919606","https://openalex.org/W2213189664","https://openalex.org/W2074002899","https://openalex.org/W2062254828","https://openalex.org/W4237480606","https://openalex.org/W2936968863","https://openalex.org/W2941821699","https://openalex.org/W1971792277"],"abstract_inverted_index":{"Auxins":[0],"are":[1,70],"chemical":[2],"compounds":[3],"of":[4,36,43,64,86,121,140,148],"wide":[5],"interest,":[6],"mostly":[7],"due":[8],"to":[9,54],"their":[10,37,56],"role":[11,57],"in":[12,32,51,58,80],"plant":[13,59],"metabolism":[14],"and":[15,29,45,67,124],"development.":[16],"Synthetic":[17],"auxins":[18,47],"have":[19,48],"been":[20,49],"used":[21],"as":[22],"herbicides":[23],"for":[24,83],"more":[25],"than":[26],"75":[27],"years":[28],"low":[30],"toxicity":[31],"humans":[33],"is":[34,145],"one":[35],"most":[38],"advantageous":[39],"features.":[40],"Extensive":[41],"studies":[42,131],"natural":[44],"synthetic":[46,134],"made":[50],"an":[52,72],"effort":[53],"understand":[55],"growth.":[60],"However,":[61],"molecular":[62],"details":[63],"the":[65,84,100,138,146],"binding":[66,101],"recognition":[68],"process":[69],"still":[71],"open":[73],"question.":[74],"Herein,":[75],"we":[76,117],"present":[77],"a":[78,119],"comprehensive":[79],"silico":[81],"pipeline":[82],"assessment":[85],"TIR1":[87],"ligands":[88,123],"using":[89],"several":[90],"structure-based":[91],"methods.":[92],"Our":[93],"results":[94],"suggest":[95],"that":[96,110],"subtle":[97],"dynamics":[98],"within":[99],"pocket":[102],"arise":[103],"from":[104],"water\u2013ligand":[105],"interactions.":[106],"We":[107],"also":[108],"show":[109],"this":[111,143],"trait":[112],"distinguishes":[113],"effective":[114],"binders.":[115],"Finally,":[116],"construct":[118],"database":[120],"putative":[122],"decoy":[125],"compounds,":[126],"which":[127],"can":[128],"aid":[129],"further":[130],"focusing":[132,151],"on":[133,152],"auxin":[135],"design.":[136],"To":[137],"best":[139],"our":[141],"knowledge,":[142],"study":[144],"first":[147],"its":[149],"kind":[150],"TIR1.":[153]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
