{"id":"https://openalex.org/W4405826268","doi":"https://doi.org/10.1021/acs.jcim.4c01478","title":"Ranking Single Fluorescent Protein-Based Calcium Biosensor Performance by Molecular Dynamics Simulations","display_name":"Ranking Single Fluorescent Protein-Based Calcium Biosensor Performance by Molecular Dynamics Simulations","publication_year":2024,"publication_date":"2024-12-27","ids":{"openalex":"https://openalex.org/W4405826268","doi":"https://doi.org/10.1021/acs.jcim.4c01478","pmid":"https://pubmed.ncbi.nlm.nih.gov/39726324"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c01478","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01478","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1021/acs.jcim.4c01478","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027899977","display_name":"Melike Berks\u00f6z","orcid":"https://orcid.org/0000-0003-1774-2193"},"institutions":[{"id":"https://openalex.org/I134235054","display_name":"Sabanc\u0131 \u00dcniversitesi","ror":"https://ror.org/049asqa32","country_code":"TR","type":"education","lineage":["https://openalex.org/I134235054"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Melike Berksoz","raw_affiliation_strings":["Faculty of Engineering and Natural Sciences","Sabanci University","Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey"],"affiliations":[{"raw_affiliation_string":"Faculty of Engineering and Natural Sciences","institution_ids":[]},{"raw_affiliation_string":"Sabanci University","institution_ids":["https://openalex.org/I134235054"]},{"raw_affiliation_string":"Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey","institution_ids":["https://openalex.org/I134235054"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054767162","display_name":"Canan At\u0131lgan","orcid":"https://orcid.org/0000-0003-0557-6044"},"institutions":[{"id":"https://openalex.org/I134235054","display_name":"Sabanc\u0131 \u00dcniversitesi","ror":"https://ror.org/049asqa32","country_code":"TR","type":"education","lineage":["https://openalex.org/I134235054"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Canan Atilgan","raw_affiliation_strings":["Faculty of Engineering and Natural Sciences","Sabanci University","Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey"],"affiliations":[{"raw_affiliation_string":"Faculty of Engineering and Natural Sciences","institution_ids":[]},{"raw_affiliation_string":"Sabanci University","institution_ids":["https://openalex.org/I134235054"]},{"raw_affiliation_string":"Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul 34956, Turkey","institution_ids":["https://openalex.org/I134235054"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5054767162"],"corresponding_institution_ids":["https://openalex.org/I134235054"],"apc_list":null,"apc_paid":null,"fwci":0.6826,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.71391664,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"65","issue":"1","first_page":"338","last_page":"350"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9973999857902527,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9973999857902527,"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/T13127","display_name":"Biotin and Related Studies","score":0.9973000288009644,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.9947999715805054,"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/fluorescence","display_name":"Fluorescence","score":0.6644375920295715},{"id":"https://openalex.org/keywords/biosensor","display_name":"Biosensor","score":0.6634368896484375},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.6535191535949707},{"id":"https://openalex.org/keywords/fluorescent-protein","display_name":"Fluorescent protein","score":0.6092033982276917},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5102741718292236},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4672033190727234},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.45356863737106323},{"id":"https://openalex.org/keywords/calcium","display_name":"Calcium","score":0.42000406980514526},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.37116891145706177},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3607216775417328},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.359647661447525},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.33017605543136597},{"id":"https://openalex.org/keywords/green-fluorescent-protein","display_name":"Green fluorescent protein","score":0.28049319982528687},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.24116969108581543},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.21966004371643066},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21169966459274292},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.12979251146316528},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.1155068576335907},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10856541991233826},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.060901910066604614}],"concepts":[{"id":"https://openalex.org/C91881484","wikidata":"https://www.wikidata.org/wiki/Q191807","display_name":"Fluorescence","level":2,"score":0.6644375920295715},{"id":"https://openalex.org/C160756335","wikidata":"https://www.wikidata.org/wiki/Q669391","display_name":"Biosensor","level":2,"score":0.6634368896484375},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.6535191535949707},{"id":"https://openalex.org/C3019336641","wikidata":"https://www.wikidata.org/wiki/Q55643886","display_name":"Fluorescent protein","level":4,"score":0.6092033982276917},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5102741718292236},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4672033190727234},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.45356863737106323},{"id":"https://openalex.org/C519063684","wikidata":"https://www.wikidata.org/wiki/Q706","display_name":"Calcium","level":2,"score":0.42000406980514526},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.37116891145706177},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3607216775417328},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.359647661447525},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.33017605543136597},{"id":"https://openalex.org/C142613039","wikidata":"https://www.wikidata.org/wiki/Q272983","display_name":"Green fluorescent protein","level":3,"score":0.28049319982528687},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.24116969108581543},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.21966004371643066},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21169966459274292},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.12979251146316528},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.1155068576335907},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10856541991233826},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.060901910066604614},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002118","descriptor_name":"Calcium","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D002118","descriptor_name":"Calcium","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D002118","descriptor_name":"Calcium","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002118","descriptor_name":"Calcium","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002118","descriptor_name":"Calcium","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002118","descriptor_name":"Calcium","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002118","descriptor_name":"Calcium","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002118","descriptor_name":"Calcium","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002147","descriptor_name":"Calmodulin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002147","descriptor_name":"Calmodulin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002147","descriptor_name":"Calmodulin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002147","descriptor_name":"Calmodulin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002147","descriptor_name":"Calmodulin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002147","descriptor_name":"Calmodulin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D002147","descriptor_name":"Calmodulin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002147","descriptor_name":"Calmodulin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002147","descriptor_name":"Calmodulin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002147","descriptor_name":"Calmodulin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002147","descriptor_name":"Calmodulin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002147","descriptor_name":"Calmodulin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008164","descriptor_name":"Luminescent Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008164","descriptor_name":"Luminescent Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008164","descriptor_name":"Luminescent Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008164","descriptor_name":"Luminescent Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008164","descriptor_name":"Luminescent Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008164","descriptor_name":"Luminescent Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008164","descriptor_name":"Luminescent Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008164","descriptor_name":"Luminescent Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015374","descriptor_name":"Biosensing Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D015374","descriptor_name":"Biosensing Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D015374","descriptor_name":"Biosensing Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D015374","descriptor_name":"Biosensing Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D015374","descriptor_name":"Biosensing Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D015374","descriptor_name":"Biosensing Techniques","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.4c01478","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01478","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:39726324","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39726324","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":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11733952","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11733952","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11733952/pdf/ci4c01478.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":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.4c01478","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01478","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.6700000166893005}],"awards":[{"id":"https://openalex.org/G7144264676","display_name":null,"funder_award_id":"121Z329","funder_id":"https://openalex.org/F4320322626","funder_display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu"}],"funders":[{"id":"https://openalex.org/F4320322626","display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu","ror":"https://ror.org/04w9kkr77"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W159300978","https://openalex.org/W1964605826","https://openalex.org/W1967642375","https://openalex.org/W1982738875","https://openalex.org/W2010694064","https://openalex.org/W2020188049","https://openalex.org/W2029667189","https://openalex.org/W2030693318","https://openalex.org/W2035879549","https://openalex.org/W2041794187","https://openalex.org/W2052592051","https://openalex.org/W2057806291","https://openalex.org/W2069518737","https://openalex.org/W2070753604","https://openalex.org/W2071333655","https://openalex.org/W2080145954","https://openalex.org/W2087045046","https://openalex.org/W2115202121","https://openalex.org/W2132262459","https://openalex.org/W2140387095","https://openalex.org/W2150981663","https://openalex.org/W2151228364","https://openalex.org/W2158957954","https://openalex.org/W2160919229","https://openalex.org/W2164548935","https://openalex.org/W2325171366","https://openalex.org/W2330799739","https://openalex.org/W2332712348","https://openalex.org/W2413987655","https://openalex.org/W2521101013","https://openalex.org/W2550167580","https://openalex.org/W2781779907","https://openalex.org/W2802723872","https://openalex.org/W2811334205","https://openalex.org/W2901329901","https://openalex.org/W2903827925","https://openalex.org/W2938370601","https://openalex.org/W2952425397","https://openalex.org/W2965956202","https://openalex.org/W2981948585","https://openalex.org/W3009290538","https://openalex.org/W3042082711","https://openalex.org/W3095308972","https://openalex.org/W3109218211","https://openalex.org/W3122236753","https://openalex.org/W3127757890","https://openalex.org/W3177828909","https://openalex.org/W3202879383","https://openalex.org/W4220692195","https://openalex.org/W4220735552","https://openalex.org/W4220973994","https://openalex.org/W4221110791","https://openalex.org/W4226293383","https://openalex.org/W4281790889","https://openalex.org/W4283023183","https://openalex.org/W4292358539","https://openalex.org/W4324344199","https://openalex.org/W4385263737","https://openalex.org/W4388622554","https://openalex.org/W4393942395"],"related_works":["https://openalex.org/W2046430340","https://openalex.org/W2383021773","https://openalex.org/W2322026400","https://openalex.org/W4206515393","https://openalex.org/W1990396141","https://openalex.org/W1929958295","https://openalex.org/W2226641048","https://openalex.org/W3016076744","https://openalex.org/W3086218413","https://openalex.org/W2473022915"],"abstract_inverted_index":{"Genetically":[0],"encoded":[1],"fluorescent":[2,43,62],"biosensors":[3],"(GEFBs)":[4],"have":[5],"become":[6],"indispensable":[7],"tools":[8],"for":[9,99],"visualizing":[10],"biological":[11],"processes":[12],"<i>in":[13],"vivo.</i>":[14],"A":[15],"typical":[16],"GEFB":[17],"is":[18,38],"composed":[19],"of":[20,67,109,143,146,159,176],"a":[21,27,42,65,70,96,144],"sensory":[22],"domain":[23],"(SD)":[24],"that":[25,167],"undergoes":[26],"conformational":[28,124],"change":[29,125],"upon":[30],"ligand":[31],"binding":[32],"or":[33],"enzymatic":[34],"reaction;":[35],"the":[36,49,53,104,112,120,127,140,180,189],"SD":[37,50],"genetically":[39],"fused":[40],"with":[41,151],"protein":[44],"(FP).":[45],"The":[46],"changes":[47],"in":[48,79,126,184],"allosterically":[51],"modulate":[52],"chromophore":[54,121,181],"environment":[55],"whose":[56],"spectral":[57],"properties":[58,142],"are":[59,75],"changed.":[60],"Single":[61],"(FP)-based":[63],"biosensors,":[64,149],"subclass":[66],"GEFBs,":[68],"offer":[69],"simple":[71,85],"experimental":[72],"setup;":[73],"they":[74,94],"easy":[76],"to":[77,86,89,123,138],"produce":[78],"living":[80],"cells,":[81],"structurally":[82],"stable,":[83],"and":[84,106,114,156,182,191],"use":[87,133],"due":[88],"their":[90],"single-wavelength":[91],"operation.":[92],"However,":[93],"pose":[95],"significant":[97],"challenge":[98],"structure":[100],"optimization,":[101],"especially":[102],"concerning":[103],"length":[105],"residue":[107],"content":[108],"linkers":[110],"between":[111,188],"FP":[113],"SD,":[115],"which":[116],"affect":[117],"how":[118],"well":[119],"responds":[122],"SD.":[128],"In":[129],"this":[130],"work,":[131],"we":[132],"all-atom":[134],"molecular":[135],"dynamics":[136],"simulations":[137],"analyze":[139],"dynamic":[141],"series":[145],"calmodulin-based":[147],"calcium":[148,160],"all":[150],"different":[152],"FP-SD":[153],"interaction":[154],"interfaces":[155],"varying":[157],"degrees":[158],"binding-dependent":[161],"fluorescence":[162],"change.":[163],"Our":[164],"results":[165],"indicate":[166],"biosensor":[168],"performance":[169],"can":[170],"be":[171],"predicted":[172],"based":[173],"on":[174],"distribution":[175],"water":[177],"molecules":[178],"around":[179],"shifts":[183],"hydrogen":[185],"bond":[186],"occupancies":[187],"ligand-bound":[190],"ligand-free":[192],"sensor":[193],"structures.":[194]},"counts_by_year":[{"year":2025,"cited_by_count":3}],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2025-10-10T00:00:00"}