{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T12:33:56Z","timestamp":1770899636712,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1005974","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,2,5]],"date-time":"2018-02-05T00:00:00Z","timestamp":1517788800000}}],"reference-count":48,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2018,1,24]],"date-time":"2018-01-24T00:00:00Z","timestamp":1516752000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["P20 GM104420"],"award-info":[{"award-number":["P20 GM104420"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000053","name":"National Eye Institute","doi-asserted-by":"publisher","award":["R01 EY012146"],"award-info":[{"award-number":["R01 EY012146"]}],"id":[{"id":"10.13039\/100000053","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1005974","type":"journal-article","created":{"date-parts":[[2018,1,24]],"date-time":"2018-01-24T18:25:18Z","timestamp":1516818318000},"page":"e1005974","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":20,"title":["Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations"],"prefix":"10.1371","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4999-5347","authenticated-orcid":true,"given":"Jagdish Suresh","family":"Patel","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Celeste J.","family":"Brown","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"F. Marty","family":"Ytreberg","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5005-802X","authenticated-orcid":true,"given":"Deborah L.","family":"Stenkamp","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2018,1,24]]},"reference":[{"issue":"11","key":"ref1","doi-asserted-by":"crossref","first-page":"1359","DOI":"10.1016\/0042-6989(94)90134-1","article-title":"An analysis of two spectral properties of vertebrate visual pigments","volume":"34","author":"FI Harosi","year":"1994","journal-title":"Vision Research"},{"issue":"17","key":"ref2","doi-asserted-by":"crossref","first-page":"2241","DOI":"10.1016\/S0042-6989(00)00101-2","article-title":"Visual pigment reconstitution in intact goldfish retina using synthetic retinaldehyde isomers","volume":"40","author":"JW Parry","year":"2000","journal-title":"Vision Research"},{"issue":"4","key":"ref3","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1016\/S1350-9462(00)00002-1","article-title":"Molecular evolution of vertebrate visual pigments","volume":"19","author":"S Yokoyama","year":"2000","journal-title":"Progress in retinal and eye research"},{"issue":"1","key":"ref4","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1002\/bies.201300094","article-title":"The photochemical determinants of color vision: revealing how opsins tune their chromophore's absorption wavelength","volume":"36","author":"W Wang","year":"2014","journal-title":"Bioessays"},{"issue":"4","key":"ref5","doi-asserted-by":"crossref","first-page":"e2001627","DOI":"10.1371\/journal.pbio.2001627","article-title":"Convergent evolution of SWS2 opsin facilitates adaptive radiation of threespine stickleback into different light environments","volume":"15","author":"DA Marques","year":"2017","journal-title":"PLoS biology"},{"issue":"1798","key":"ref6","doi-asserted-by":"crossref","first-page":"20142321","DOI":"10.1098\/rspb.2014.2321","article-title":"Evolution of opsin expression in birds driven by sexual selection and habitat","volume":"282","author":"NI Bloch","year":"2015","journal-title":"Proceedings Biological sciences \/ The Royal Society"},{"key":"ref7","article-title":"Rapid adaptation to a novel light environment: The importance of ontogeny and phenotypic plasticity in shaping the visual system of Nicaraguan Midas cichlid fish (Amphilophus citrinellus spp.)","author":"A Harer","year":"2017","journal-title":"Molecular ecology"},{"issue":"2","key":"ref8","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1007\/s00239-010-9426-z","article-title":"Gene duplication and divergence of long wavelength-sensitive opsin genes in the guppy, Poecilia reticulata","volume":"72","author":"CT Watson","year":"2011","journal-title":"Journal of molecular evolution"},{"issue":"4747","key":"ref9","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1126\/science.2937147","article-title":"Molecular-Genetics of Human Color-Vision\u2014the Genes Encoding Blue, Green, and Red Pigments","volume":"232","author":"J Nathans","year":"1986","journal-title":"Science (New York, NY"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/1471-2148-13-238","article-title":"The vertebrate ancestral repertoire of visual opsins, transducin alpha subunits and oxytocin\/vasopressin receptors was established by duplication of their shared genomic region in the two rounds of early vertebrate genome duplications","volume":"13","author":"D Lagman","year":"2013","journal-title":"BMC evolutionary biology"},{"issue":"2","key":"ref11","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/S0896-6273(00)80845-4","article-title":"The evolution and physiology of human color vision: insights from molecular genetic studies of visual pigments","volume":"24","author":"J Nathans","year":"1999","journal-title":"Neuron"},{"issue":"6","key":"ref12","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1093\/icb\/icp079","article-title":"Gene duplication and differential gene expression play an important role in the diversification of visual pigments in fish","volume":"49","author":"CM Hofmann","year":"2009","journal-title":"Integrative and comparative biology"},{"issue":"4","key":"ref13","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1093\/molbev\/msi086","article-title":"Reconstitution of ancestral green visual pigments of zebrafish and molecular mechanism of their spectral differentiation","volume":"22","author":"A Chinen","year":"2005","journal-title":"Molecular biology and evolution"},{"issue":"7","key":"ref14","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1016\/j.visres.2010.12.002","article-title":"The genetics of normal and defective color vision","volume":"51","author":"J Neitz","year":"2011","journal-title":"Vision Research"},{"issue":"1","key":"ref15","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.ajhg.2010.05.019","article-title":"X-linked cone dystrophy caused by mutation of the red and green cone opsins","volume":"87","author":"JC Gardner","year":"2010","journal-title":"Am J Hum Genet"},{"issue":"2","key":"ref16","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1136\/bjo.2004.050773","article-title":"A detailed study of the phenotype of an autosomal dominant cone-rod dystrophy (CORD7) associated with mutation in the gene for RIM1","volume":"89","author":"M Michaelides","year":"2005","journal-title":"Br J Ophthalmol"},{"issue":"10","key":"ref17","doi-asserted-by":"crossref","first-page":"1790","DOI":"10.1002\/anie.200905061","article-title":"Probing and modeling the absorption of retinal protein chromophores in vacuo","volume":"49","author":"J Rajput","year":"2010","journal-title":"Angewandte Chemie (International ed"},{"issue":"1\u20132","key":"ref18","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1002\/anie.200603306","article-title":"Origin of spectral tuning in rhodopsin\u2014it is not the binding pocket","volume":"46","author":"S Sekharan","year":"2007","journal-title":"Angewandte Chemie (International ed"},{"issue":"4","key":"ref19","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1002\/prot.20744","article-title":"Electrostatic potential at the retinal of three archaeal rhodopsins: implications for their different absorption spectra","volume":"61","author":"E Kloppmann","year":"2005","journal-title":"Proteins"},{"issue":"4","key":"ref20","doi-asserted-by":"crossref","first-page":"1697","DOI":"10.1093\/genetics\/158.4.1697","article-title":"The molecular genetics and evolution of red and green color vision in vertebrates","volume":"158","author":"S Yokoyama","year":"2001","journal-title":"Genetics"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/j.visres.2016.06.013","article-title":"Spectral sensitivity of guppy visual pigments reconstituted in vitro to resolve association of opsins with cone cell types","volume":"127","author":"S Kawamura","year":"2016","journal-title":"Vision Research"},{"issue":"5","key":"ref22","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1093\/oxfordjournals.molbev.a025956","article-title":"The "five-sites" rule and the evolution of red and green color vision in mammals","volume":"15","author":"S Yokoyama","year":"1998","journal-title":"Molecular biology and evolution"},{"key":"ref23","first-page":"646","article-title":"Molecular dynamics simulations of biomolecules","volume":"9","author":"M Karplus","year":"2002"},{"issue":"2","key":"ref24","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1016\/j.jmb.2004.07.044","article-title":"The Retinal Conformation and its Environment in Rhodopsin in Light of a New 2.2\u00c5 Crystal Structure\u2020\u2020This paper is dedicated to Dr Yoshimasa Kyogoku","volume":"342","author":"T Okada","year":"2004","journal-title":"J Mol Biol"},{"issue":"5480","key":"ref25","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1126\/science.289.5480.739","article-title":"Crystal structure of rhodopsin: A G protein-coupled receptor","volume":"289","author":"K Palczewski","year":"2000","journal-title":"Science (New York, NY"},{"issue":"2","key":"ref26","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1093\/genetics\/163.2.663","article-title":"Gene duplication and spectral diversification of cone visual pigments of zebrafish","volume":"163","author":"A Chinen","year":"2003","journal-title":"Genetics"},{"issue":"2","key":"ref27","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1016\/j.gene.2005.12.005","article-title":"Functional characterization of visual opsin repertoire in Medaka (Oryzias latipes)","volume":"371","author":"Y Matsumoto","year":"2006","journal-title":"Gene"},{"issue":"19","key":"ref28","doi-asserted-by":"crossref","first-page":"1734","DOI":"10.1016\/j.cub.2005.08.010","article-title":"Mix and match color vision: tuning spectral sensitivity by differential opsin gene expression in Lake Malawi cichlids","volume":"15","author":"JW Parry","year":"2005","journal-title":"Current biology: CB"},{"issue":"5","key":"ref29","doi-asserted-by":"crossref","first-page":"854","DOI":"10.1002\/jcc.21663","article-title":"The opsin shift and mechanism of spectral tuning in rhodopsin","volume":"32","author":"R Rajamani","year":"2011","journal-title":"J Comput Chem"},{"issue":"2","key":"ref30","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1016\/S0005-2736(02)00567-9","article-title":"Crystal structure of rhodopsin: a template for cone visual pigments and other G protein-coupled receptors","volume":"1565","author":"RE Stenkamp","year":"2002","journal-title":"Biochim Biophys Acta"},{"issue":"5","key":"ref31","doi-asserted-by":"crossref","first-page":"1131","DOI":"10.1016\/0896-6273(94)90320-4","article-title":"Molecular determinants of human red\/green color discrimination","volume":"12","author":"AB Asenjo","year":"1994","journal-title":"Neuron"},{"issue":"5008","key":"ref32","doi-asserted-by":"crossref","first-page":"971","DOI":"10.1126\/science.1903559","article-title":"Spectral tuning of pigments underlying red-green color vision","volume":"252","author":"M Neitz","year":"1991","journal-title":"Science (New York, NY"},{"issue":"20","key":"ref33","doi-asserted-by":"crossref","first-page":"6025","DOI":"10.1021\/bi020629+","article-title":"Molecular basis of spectral tuning in the newt short wavelength sensitive visual pigment","volume":"42","author":"Y Takahashi","year":"2003","journal-title":"Biochemistry"},{"issue":"4","key":"ref34","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1002\/prot.20744","article-title":"Electrostatic potential at the retinal of three archaeal rhodopsins: Implications for their different absorption spectra","volume":"61","author":"E Kloppmann","year":"2005","journal-title":"Proteins: Structure, Function, and Bioinformatics"},{"issue":"27","key":"ref35","doi-asserted-by":"crossref","first-page":"7947","DOI":"10.1021\/ja00547a029","article-title":"Opsin shifts in bovine rhodopsin and bacteriorhodopsin. Comparison of two external point-charge models","volume":"102","author":"MG Motto","year":"1980","journal-title":"J Am Chem Soc"},{"issue":"27","key":"ref36","doi-asserted-by":"crossref","first-page":"7947","DOI":"10.1021\/ja00547a029","article-title":"Opsin Shifts in Bovine Rhodopsin and Bacteriorhodopsin\u2014Comparison of 2 External Point-Charge Models","volume":"102","author":"MG Motto","year":"1980","journal-title":"Journal of the American Chemical Society"},{"issue":"24","key":"ref37","doi-asserted-by":"crossref","first-page":"7549","DOI":"10.1021\/bi020007o","article-title":"Relative orientation between the beta-ionone ring and the polyene chain for the chromophore of rhodopsin in native membranes","volume":"41","author":"PJ Spooner","year":"2002","journal-title":"Biochemistry"},{"issue":"3","key":"ref38","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1021\/bi0515624","article-title":"Origin and consequences of steric strain in the rhodopsin binding pocket","volume":"45","author":"M Sugihara","year":"2006","journal-title":"Biochemistry"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"5.6.1","DOI":"10.1002\/cpbi.3","article-title":"Comparative Protein Structure Modeling Using MODELLER","volume":"54","author":"B Webb","year":"2016","journal-title":"Current protocols in bioinformatics"},{"issue":"24","key":"ref40","doi-asserted-by":"crossref","first-page":"11631","DOI":"10.1073\/pnas.91.24.11631","article-title":"Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer","volume":"91","author":"TB Woolf","year":"1994","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"25","key":"ref41","doi-asserted-by":"crossref","first-page":"2135","DOI":"10.1002\/jcc.23354","article-title":"CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data","volume":"34","author":"J Huang","year":"2013","journal-title":"J Comput Chem"},{"issue":"12","key":"ref42","doi-asserted-by":"crossref","first-page":"7182","DOI":"10.1063\/1.328693","article-title":"Polymorphic transitions in single crystals: A new molecular dynamics method","volume":"52","author":"M Parrinello","year":"1981","journal-title":"J Appl Phys"},{"issue":"8","key":"ref43","doi-asserted-by":"crossref","first-page":"4069","DOI":"10.1063\/1.449071","article-title":"The Nose\u2013Hoover thermostat","volume":"83","author":"DJ Evans","year":"1985","journal-title":"The Journal of Chemical Physics"},{"issue":"12","key":"ref44","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle mesh Ewald: An N\u22c5log(N) method for Ewald sums in large systems","volume":"98","author":"T Darden","year":"1993","journal-title":"J Chem Phys"},{"issue":"16","key":"ref45","doi-asserted-by":"crossref","first-page":"1701","DOI":"10.1002\/jcc.20291","article-title":"GROMACS: fast, flexible, and free","volume":"26","author":"D Van Der Spoel","year":"2005","journal-title":"J Comput Chem"},{"issue":"2","key":"ref46","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1016\/j.cpc.2013.09.018","article-title":"PLUMED 2: New feathers for an old bird","volume":"185","author":"GA Tribello","year":"2014","journal-title":"Comput Phys Commun"},{"issue":"1","key":"ref47","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: Visual molecular dynamics","volume":"14","author":"W Humphrey","year":"1996","journal-title":"J Mol Graphics"},{"issue":"2","key":"ref48","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1214\/aos\/1176344136","article-title":"Estimating Dimension of a Model","volume":"6","author":"G Schwarz","year":"1978","journal-title":"Ann Stat"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1005974","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,2,5]],"date-time":"2018-02-05T00:00:00Z","timestamp":1517788800000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005974","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,8,13]],"date-time":"2022-08-13T04:02:51Z","timestamp":1660363371000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005974"}},"subtitle":[],"editor":[{"given":"Alexander","family":"MacKerell","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,1,24]]},"references-count":48,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2018,1,24]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1005974","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1005974","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,1,24]]}}}