{"id":"https://openalex.org/W4382010728","doi":"https://doi.org/10.1021/acs.jpcb.3c01486","title":"Molecular Dynamics Force Field Parameters for the EGFP Chromophore and Some of Its Analogues","display_name":"Molecular Dynamics Force Field Parameters for the EGFP Chromophore and Some of Its Analogues","publication_year":2023,"publication_date":"2023-06-26","ids":{"openalex":"https://openalex.org/W4382010728","doi":"https://doi.org/10.1021/acs.jpcb.3c01486","pmid":"https://pubmed.ncbi.nlm.nih.gov/37357785","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/10331734"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jpcb.3c01486","doi":"https://doi.org/10.1021/acs.jpcb.3c01486","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jpcb.3c01486","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.3c01486","source":{"id":"https://openalex.org/S185621672","display_name":"The Journal of Physical Chemistry B","issn_l":"1520-5207","issn":["1520-5207","1520-6106"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-140","russia-white-list-2","vabb-shw"],"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":"The Journal of Physical Chemistry B","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.3c01486","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5117771512","display_name":"Kimberly L. Breyfogle","orcid":"https://orcid.org/0009-0005-7574-771X","observed_orcids":["https://orcid.org/0009-0005-7574-771X"]},"institutions":[{"id":"https://openalex.org/I145402516","display_name":"Hope College","ror":"https://ror.org/03chnr738","country_code":"US","type":"education","lineage":["https://openalex.org/I145402516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kimberly L. Breyfogle","raw_affiliation_strings":["Hope College Department of Chemistry, Holland, Michigan 49423, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hope College Department of Chemistry, Holland, Michigan 49423, United States","institution_ids":["https://openalex.org/I145402516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008699974","display_name":"Dalton L. Blood","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I145402516","display_name":"Hope College","ror":"https://ror.org/03chnr738","country_code":"US","type":"education","lineage":["https://openalex.org/I145402516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dalton L. Blood","raw_affiliation_strings":["Hope College Department of Chemistry, Holland, Michigan 49423, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hope College Department of Chemistry, Holland, Michigan 49423, United States","institution_ids":["https://openalex.org/I145402516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022900085","display_name":"Andreana M. Rosnik","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I145402516","display_name":"Hope College","ror":"https://ror.org/03chnr738","country_code":"US","type":"education","lineage":["https://openalex.org/I145402516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andreana M. Rosnik","raw_affiliation_strings":["Hope College Department of Chemistry, Holland, Michigan 49423, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hope College Department of Chemistry, Holland, Michigan 49423, United States","institution_ids":["https://openalex.org/I145402516"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085210707","display_name":"Brent P. Krueger","orcid":"https://orcid.org/0009-0005-1845-5358","observed_orcids":["https://orcid.org/0009-0005-1845-5358"]},"institutions":[{"id":"https://openalex.org/I145402516","display_name":"Hope College","ror":"https://ror.org/03chnr738","country_code":"US","type":"education","lineage":["https://openalex.org/I145402516"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Brent P. Krueger","raw_affiliation_strings":["Hope College Department of Chemistry, Holland, Michigan 49423, United States"],"raw_orcid":"https://orcid.org/0009-0005-1845-5358","affiliations":[{"raw_affiliation_string":"Hope College Department of Chemistry, Holland, Michigan 49423, United States","institution_ids":["https://openalex.org/I145402516"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5085210707"],"corresponding_institution_ids":["https://openalex.org/I145402516"],"apc_list":null,"apc_paid":null,"fwci":0.713,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.62765947,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":98},"biblio":{"volume":"127","issue":"26","first_page":"5772","last_page":"5788"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.850600004196167,"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":0.850600004196167,"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/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.04800000041723251,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T10002","display_name":"Advanced Chemical Physics Studies","score":0.043699998408555984,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"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/force-field-parameterization","display_name":"force field parameterization","score":0.7229999899864197},{"id":"https://openalex.org/keywords/enhanced-green-fluorescent-protein","display_name":"enhanced green fluorescent protein","score":0.6439999938011169},{"id":"https://openalex.org/keywords/eyfp","display_name":"eYFP","score":0.9760000109672546},{"id":"https://openalex.org/keywords/extended-connectivity-fingerprints","display_name":"ECFP","score":0.9980000257492065},{"id":"https://openalex.org/keywords/mcherry","display_name":"mCherry","score":1.0},{"id":"https://openalex.org/keywords/dsred","display_name":"DsRed","score":1.0},{"id":"https://openalex.org/keywords/amber-force-field","display_name":"AMBER force field","score":0.7799999713897705},{"id":"https://openalex.org/keywords/solvent-dielectric-constant","display_name":"solvent dielectric constant","score":0.8289999961853027},{"id":"https://openalex.org/keywords/atomic-charges","display_name":"atomic charges","score":0.9509999752044678}],"concepts":[{"id":"https://openalex.org/C192468462","wikidata":"https://www.wikidata.org/wiki/Q533543","display_name":"Chromophore","level":2,"score":0.9279772043228149},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7964359521865845},{"id":"https://openalex.org/C142613039","wikidata":"https://www.wikidata.org/wiki/Q272983","display_name":"Green fluorescent protein","level":3,"score":0.6690506935119629},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.5972418189048767},{"id":"https://openalex.org/C91881484","wikidata":"https://www.wikidata.org/wiki/Q191807","display_name":"Fluorescence","level":2,"score":0.5499942302703857},{"id":"https://openalex.org/C2779260011","wikidata":"https://www.wikidata.org/wiki/Q412287","display_name":"mCherry","level":4,"score":0.544163703918457},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.4938400387763977},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.45182886719703674},{"id":"https://openalex.org/C3019336641","wikidata":"https://www.wikidata.org/wiki/Q55643886","display_name":"Fluorescent protein","level":4,"score":0.43026119470596313},{"id":"https://openalex.org/C61272859","wikidata":"https://www.wikidata.org/wiki/Q7834031","display_name":"Transferability","level":3,"score":0.42249882221221924},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3931909203529358},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.36082595586776733},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.3223920464515686},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.309642493724823},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.30367252230644226},{"id":"https://openalex.org/C75473681","wikidata":"https://www.wikidata.org/wiki/Q188651","display_name":"Photochemistry","level":1,"score":0.130680114030838},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0793982744216919},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C140331021","wikidata":"https://www.wikidata.org/wiki/Q1868104","display_name":"Logit","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jpcb.3c01486","doi":"https://doi.org/10.1021/acs.jpcb.3c01486","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jpcb.3c01486","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.3c01486","source":{"id":"https://openalex.org/S185621672","display_name":"The Journal of Physical Chemistry B","issn_l":"1520-5207","issn":["1520-5207","1520-6106"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-140","russia-white-list-2","vabb-shw"],"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":"The Journal of Physical Chemistry B","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10331734","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10331734","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10331734/pdf/jp3c01486.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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Phys Chem B","raw_type":"Text"},{"id":"pmid:37357785","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37357785","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,"listed_in":[],"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":"The journal of physical chemistry. B","raw_type":"Journal Article"},{"id":"pmh:oai:digitalcommons.hope.edu:faculty_publications-2758","doi":null,"is_oa":false,"landing_page_url":"https://digitalcommons.hope.edu/faculty_publications/1636","pdf_url":null,"source":{"id":"https://openalex.org/S4306402446","display_name":"Hope College Digital Commons (Hope College)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I145402516","host_organization_name":"Hope College","host_organization_lineage":["https://openalex.org/I145402516"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Publications","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1021/acs.jpcb.3c01486","doi":"https://doi.org/10.1021/acs.jpcb.3c01486","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jpcb.3c01486","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jpcb.3c01486","source":{"id":"https://openalex.org/S185621672","display_name":"The Journal of Physical Chemistry B","issn_l":"1520-5207","issn":["1520-5207","1520-6106"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-140","russia-white-list-2","vabb-shw"],"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":"The Journal of Physical Chemistry B","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1104651672","display_name":null,"funder_award_id":"CHE 1039925","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"},{"id":"https://openalex.org/G1438443317","display_name":null,"funder_award_id":"1039925","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"},{"id":"https://openalex.org/G4033530544","display_name":"RUI: Quantifying Fluorescent Probe Dynamics in FRET Experiments by Combining Single-Molecule and Bulk Spectroscopies with Molecular Dynamics and Quantum Mechanics Simulations","funder_award_id":"1058981","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4257795037","display_name":null,"funder_award_id":"1919571","funder_id":"https://openalex.org/F4320337563","funder_display_name":"Division of Advanced Cyberinfrastructure"},{"id":"https://openalex.org/G467220805","display_name":"MRI: Acquisition of a High Performance Computing Cluster for Undergraduate Chemistry Research and Teaching by the Midwest Undergraduate Computational Chemistry Consortium (MU3C)","funder_award_id":"1919571","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4755640387","display_name":"MRI: Acquisition of a Computer Cluster for Undergraduate Chemistry Research and Teaching by the Midwest Undergraduate Computational Chemistry Consortium (MU3C)","funder_award_id":"1039925","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6688081928","display_name":null,"funder_award_id":"1919571","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"},{"id":"https://openalex.org/G812778616","display_name":null,"funder_award_id":"1058981","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337393","display_name":"Division of Chemistry","ror":"https://ror.org/01ar8dr59"},{"id":"https://openalex.org/F4320337563","display_name":"Division of Advanced Cyberinfrastructure","ror":"https://ror.org/04nh1dc89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4382010728.pdf","grobid_xml":"https://content.openalex.org/works/W4382010728.grobid-xml"},"referenced_works_count":99,"referenced_works":["https://openalex.org/W1967568579","https://openalex.org/W1970572417","https://openalex.org/W1973501174","https://openalex.org/W1976161355","https://openalex.org/W1981225934","https://openalex.org/W1999100572","https://openalex.org/W1999923843","https://openalex.org/W2002360833","https://openalex.org/W2007608151","https://openalex.org/W2009447971","https://openalex.org/W2009765812","https://openalex.org/W2011215428","https://openalex.org/W2014245863","https://openalex.org/W2023271753","https://openalex.org/W2029381257","https://openalex.org/W2030693318","https://openalex.org/W2032579724","https://openalex.org/W2034546870","https://openalex.org/W2035199159","https://openalex.org/W2036742051","https://openalex.org/W2038533471","https://openalex.org/W2038756774","https://openalex.org/W2044025325","https://openalex.org/W2050485933","https://openalex.org/W2055757537","https://openalex.org/W2058653824","https://openalex.org/W2061104342","https://openalex.org/W2061831940","https://openalex.org/W2062963396","https://openalex.org/W2066690664","https://openalex.org/W2067174909","https://openalex.org/W2067677265","https://openalex.org/W2072332843","https://openalex.org/W2076202230","https://openalex.org/W2077045286","https://openalex.org/W2077591905","https://openalex.org/W2079473982","https://openalex.org/W2080518134","https://openalex.org/W2084312697","https://openalex.org/W2091522880","https://openalex.org/W2093015919","https://openalex.org/W2093398469","https://openalex.org/W2104951509","https://openalex.org/W2106140689","https://openalex.org/W2109813678","https://openalex.org/W2117458899","https://openalex.org/W2118233996","https://openalex.org/W2120153949","https://openalex.org/W2122199548","https://openalex.org/W2124259497","https://openalex.org/W2127068865","https://openalex.org/W2127336290","https://openalex.org/W2128276019","https://openalex.org/W2130479394","https://openalex.org/W2131713387","https://openalex.org/W2132629607","https://openalex.org/W2141322976","https://openalex.org/W2143094150","https://openalex.org/W2143981217","https://openalex.org/W2144288821","https://openalex.org/W2144489999","https://openalex.org/W2147993766","https://openalex.org/W2148284063","https://openalex.org/W2149263899","https://openalex.org/W2151228364","https://openalex.org/W2155358697","https://openalex.org/W2156073913","https://openalex.org/W2156495637","https://openalex.org/W2156777159","https://openalex.org/W2159010139","https://openalex.org/W2161996750","https://openalex.org/W2167098582","https://openalex.org/W2168240189","https://openalex.org/W2316949674","https://openalex.org/W2325171366","https://openalex.org/W2327411526","https://openalex.org/W2332689400","https://openalex.org/W2332712348","https://openalex.org/W2404280981","https://openalex.org/W2408012444","https://openalex.org/W2411216911","https://openalex.org/W2510867035","https://openalex.org/W2531689781","https://openalex.org/W2550167580","https://openalex.org/W2556522674","https://openalex.org/W2708924763","https://openalex.org/W2801696982","https://openalex.org/W2899110998","https://openalex.org/W2900908302","https://openalex.org/W2989052455","https://openalex.org/W3004055520","https://openalex.org/W3004465863","https://openalex.org/W3004651336","https://openalex.org/W3035248921","https://openalex.org/W3127970744","https://openalex.org/W3135184975","https://openalex.org/W3153296807","https://openalex.org/W3172300021","https://openalex.org/W4283023183"],"related_works":["https://openalex.org/W2592898504","https://openalex.org/W7051408612","https://openalex.org/W1973501174","https://openalex.org/W1509050043","https://openalex.org/W1992988788","https://openalex.org/W3108635639","https://openalex.org/W2093398469","https://openalex.org/W7099255081","https://openalex.org/W2150332823","https://openalex.org/W3035248921"],"abstract_inverted_index":{"High":[0],"Resolution":[1],"Image":[2],"Download":[3],"MS":[4],"PowerPoint":[5],"Slide":[6],"Fluorescent":[7],"proteins":[8],"(FPs)":[9],"have":[10,41],"had":[11],"an":[12],"enormous":[13],"impact":[14,135],"on":[15,140,162],"molecular":[16,30,43],"and":[17,20,32,90,115,132,165],"cellular":[18],"biology":[19],"are":[21,216],"employed":[22],"in":[23,151],"a":[24,36,54,69,119,160],"wide":[25,55,120],"range":[26,56,121],"of":[27,29,39,53,57,65,71,109,122,136,185,211],"studies":[28],"structure":[31],"dynamics.":[33],"Yet,":[34],"only":[35],"modest":[37],"number":[38],"papers":[40],"published":[42],"dynamics":[44],"(MD)":[45],"parameters":[46,67,79,172,204,223],"describing":[47,80],"FPs.":[48,72],"And":[49],"despite":[50],"the":[51,95,128,134,137,141,186,190,220],"development":[52,64],"FPs,":[58],"there":[59],"has":[60],"been":[61],"no":[62],"careful":[63],"MD":[66,78,180,214,222],"across":[68],"series":[70],"In":[73],"this":[74,199],"work,":[75],"we":[76,153],"present":[77,147],"six":[81,156,187],"fluorescent":[82,207],"protein":[83],"chromophores":[84,157],"(EGFP,":[85],"EBFP,":[86],"EYFP,":[87],"ECFP,":[88],"mCherry,":[89],"DsRed)":[91],"for":[92,126,195,205],"use":[93],"with":[94,159,167,231],"Cornell":[96],"et":[97],"al":[98],".":[99],"(":[100],"J.":[101],"Am.":[102],"Chem.":[103],"Soc.":[104],"1995,":[105],"117,":[106],"5179\u22125197)":[107],"family":[108],"AMBER":[110],"force":[111,169],"fields,":[112],"including":[113],"ff14SB":[114],"ff19SB.":[116],"We":[117,145],"explore":[118],"solvent":[123,139],"dielectric":[124],"constants":[125],"determining":[127],"chromophore":[129,225],"equilibrium":[130],"geometry":[131],"evaluate":[133],"modeled":[138],"final":[142],"atomic":[143],"charges.":[144],"also":[146],"our":[148,212],"methodological":[149],"approach":[150],"which":[152],"considered":[154],"all":[155],"together":[158],"focus":[161],"modularity,":[163],"transferability,":[164],"balance":[166],"existing":[168],"fields.":[170],"The":[171,209],"given":[173],"here":[174],"make":[175],"it":[176,193],"easy":[177,194],"to":[178,182,197,201],"employ":[179],"simulations":[181,215],"study":[183],"any":[184],"systems,":[188],"whereas":[189],"methodology":[191],"makes":[192],"anyone":[196],"extend":[198],"work":[200],"develop":[202],"consistent":[203],"additional":[206],"proteins.":[208],"results":[210],"own":[213],"presented,":[217],"showing":[218],"that":[219,228],"classical":[221],"yield":[224],"structural":[226],"distributions":[227],"compare":[229],"well":[230],"QM/MM":[232],"simulations.":[233]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2023-06-27T00:00:00"}
