{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,9,11]],"date-time":"2023-09-11T01:50:38Z","timestamp":1694397038682},"reference-count":80,"publisher":"Springer Science and Business Media LLC","issue":"5","license":[{"start":{"date-parts":[[2011,9,22]],"date-time":"2011-09-22T00:00:00Z","timestamp":1316649600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Mol Model"],"published-print":{"date-parts":[[2012,5]]},"DOI":"10.1007\/s00894-011-1228-8","type":"journal-article","created":{"date-parts":[[2011,9,21]],"date-time":"2011-09-21T12:35:15Z","timestamp":1316608515000},"page":"2117-2133","source":"Crossref","is-referenced-by-count":10,"title":["Structural insights into human GPCR protein OA1: a computational perspective"],"prefix":"10.1007","volume":"18","author":[{"given":"Anirban","family":"Ghosh","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Uddhavesh","family":"Sonavane","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sai Krishna","family":"Andhirka","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gopala Krishna","family":"Aradhyam","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rajendra","family":"Joshi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,9,22]]},"reference":[{"key":"1228_CR1","first-page":"143","volume":"144","author":"T Sch\u00f6neberg","year":"2002","unstructured":"Sch\u00f6neberg T, Schulz A, Gudermann T (2002) The structural basis of G-protein-coupled receptor function and dysfunction in human diseases. Rev Physiol Biochem Pharmacol 144:143\u2013227","journal-title":"Rev Physiol Biochem Pharmacol"},{"key":"1228_CR2","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1007\/978-1-60327-317-6_4","volume":"552","author":"K Lundstrom","year":"2009","unstructured":"Lundstrom K (2009) An overview on GPCRs and drug discovery: structure-based drug design and structural biology on GPCRs. Methods Mol Biol 552:51\u201366","journal-title":"Methods Mol Biol"},{"key":"1228_CR3","first-page":"105","volume":"17","author":"S Wilson","year":"2000","unstructured":"Wilson S, Bergsma D (2000) Orphan G-protein coupled receptors: novel drug targets for the pharmaceutical industry. Drug Des Discov 17:105\u2013114","journal-title":"Drug Des Discov"},{"key":"1228_CR4","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1038\/nrd2199","volume":"5","author":"JP Overington","year":"2006","unstructured":"Overington JP, Al-Lazikani B, Hopkins AL (2006) How many drug targets are there? Nat Rev Drug Discov 5:993\u2013996","journal-title":"Nat Rev Drug Discov"},{"key":"1228_CR5","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1126\/science.289.5480.739","volume":"289","author":"K Palczewski","year":"2000","unstructured":"Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H et al (2000) Crystal structure of rhodopsin: a G protein-coupled receptor. Science 289:739\u2013745","journal-title":"Science"},{"key":"1228_CR6","first-page":"561","volume":"4","author":"J Ballesteros","year":"2001","unstructured":"Ballesteros J, Palczewski K (2001) G protein-coupled receptor drug discovery: implications from the crystal structure of rhodopsin. Curr Opin Drug Discov Dev 4:561\u2013574","journal-title":"Curr Opin Drug Discov Dev"},{"key":"1228_CR7","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1038\/nature06325","volume":"450","author":"SG Rasmussen","year":"2007","unstructured":"Rasmussen SG, Choi HJ, Rosenbaum DM, Kobilka TS, Thian FS et al (2007) Crystal structure of the human beta2 adrenergic G-protein-coupled receptor. Nature 450:383\u2013387","journal-title":"Nature"},{"key":"1228_CR8","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1038\/nature09648","volume":"469","author":"SG Rasmussen","year":"2011","unstructured":"Rasmussen SG, Choi HJ, Fung JJ, Pardon E, Casarosa P et al (2011) Structure of a nanobody-stabilized active state of the \u03b2(2) adrenoceptor. Nature 469:175\u2013180","journal-title":"Nature"},{"key":"1228_CR9","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1038\/nature09665","volume":"469","author":"DM Rosenbaum","year":"2011","unstructured":"Rosenbaum DM, Zhang C, Lyons JA, Holl R, Aragao D et al (2011) Structure and function of an irreversible agonist-\u03b2(2) adrenoceptor complex. Nature 469:236\u2013240","journal-title":"Nature"},{"key":"1228_CR10","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1126\/science.1164772","volume":"322","author":"VP Jaakola","year":"2008","unstructured":"Jaakola VP, Griffith MT, Hanson MA, Cherezov V, Chien EY et al (2008) The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science 322:1211\u20131217","journal-title":"Science"},{"key":"1228_CR11","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/nature06925","volume":"453","author":"M Murakami","year":"2008","unstructured":"Murakami M, Kouyama T (2008) Crystal structure of squid rhodopsin. Nature 453:363\u2013367","journal-title":"Nature"},{"key":"1228_CR12","doi-asserted-by":"crossref","first-page":"1066","DOI":"10.1126\/science.1194396","volume":"330","author":"B Wu","year":"2010","unstructured":"Wu B, Chien EY, Mol CD, Fenalti G, Liu W et al (2010) Structures of the CXCR4 chemokine GPCR with small molecule and cyclic peptide antagonists. Science 330:1066\u20131071","journal-title":"Science"},{"key":"1228_CR13","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1038\/nature09789","volume":"471","author":"HW Choe","year":"2011","unstructured":"Choe HW, Kim YJ, Park JH, Morizumi T, Pai EF et al (2011) Crystal structure of metarhodopsin II. Nature 471:651\u2013655","journal-title":"Nature"},{"key":"1228_CR14","doi-asserted-by":"crossref","first-page":"1667","DOI":"10.2174\/092986706777442002","volume":"13","author":"A Patny","year":"2006","unstructured":"Patny A, Desai PV, Avery MA (2006) Homology modelling of G-protein coupled receptors and implications in drug design. Curr Med Chem 13:1667\u20131691","journal-title":"Curr Med Chem"},{"key":"1228_CR15","doi-asserted-by":"crossref","first-page":"1877","DOI":"10.1039\/b906391a","volume":"5","author":"K Kanagarajadurai","year":"2009","unstructured":"Kanagarajadurai K, Malini M, Bhattacharya A, Panicker M, Sowdhamini R (2009) Molecular modeling and docking studies of human 5-hydroxytryptamine 2A (5-HT2A) receptor for the identification of hotspots for ligand binding. Mol BioSys 5:1877\u20131888","journal-title":"Mol BioSys"},{"key":"1228_CR16","doi-asserted-by":"crossref","first-page":"7254","DOI":"10.1074\/jbc.M307191200","volume":"279","author":"SU Miedlich","year":"2004","unstructured":"Miedlich SU, Gama L, Seuwen K, Wolf RM, Breitwieser GE (2004) Homology modeling of the transmembrane domain of the human calcium sensing receptor and localization of an allosteric binding site. J Biol Chem 279:7254\u20137263","journal-title":"J Biol Chem"},{"key":"1228_CR17","doi-asserted-by":"crossref","first-page":"S14","DOI":"10.1186\/1471-2105-9-S1-S14","volume":"9","author":"S Dastmalchi","year":"2008","unstructured":"Dastmalchi S, Church WB, Morris MB (2008) Modelling the structures of G protein-coupled receptors aided by three-dimensional validation. BMC Bioinforma 9:S14","journal-title":"BMC Bioinforma"},{"key":"1228_CR18","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1007\/s10822-006-9061-3","volume":"20","author":"MY Niv","year":"2006","unstructured":"Niv MY, Skrabanek L, Filizola M, Weinstein H (2006) Modeling activated states of GPCRs: the rhodopsin template. J Comput Aided Mol Des 20:437\u2013448","journal-title":"J Comput Aided Mol Des"},{"key":"1228_CR19","doi-asserted-by":"crossref","first-page":"2907","DOI":"10.1021\/jm800044k","volume":"51","author":"S Costanzi","year":"2008","unstructured":"Costanzi S (2008) On the applicability of GPCR homology models to computer-aided drug discovery: a comparison between in silico and crystal structures of the \u03b22-adrenergic receptor. J Med Chem 51:2907\u20132914","journal-title":"J Med Chem"},{"key":"1228_CR20","doi-asserted-by":"crossref","first-page":"2480","DOI":"10.1021\/jm049110x","volume":"48","author":"A Lavecchia","year":"2005","unstructured":"Lavecchia A, Cosconati S, Novellino E (2005) Architecture of the human urotensin II receptor: comparison of the binding domains of peptide and non-peptide urotensin II agonists. J Med Chem 48:2480\u20132492","journal-title":"J Med Chem"},{"key":"1228_CR21","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1023\/A:1023845015343","volume":"16","author":"X Periole","year":"2002","unstructured":"Periole X, Weinstein H (2002) Key issues in computational simulation of GPCR function. J Comput Aided Mol Des 16:841\u2013853","journal-title":"J Comput Aided Mol Des"},{"key":"1228_CR22","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1007\/s00249-007-0225-4","volume":"37","author":"A Ivetac","year":"2008","unstructured":"Ivetac A, Sansom MS (2008) Molecular dynamics simulations and membrane protein structure quality. Eur Biophys J 37:403\u2013409","journal-title":"Eur Biophys J"},{"key":"1228_CR23","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1110\/ps.03381404","volume":"13","author":"H Fan","year":"2004","unstructured":"Fan H, Mark AE (2004) Refinement of homology-based protein structures by molecular dynamics simulation techniques. Protein Sci 13:211\u2013220","journal-title":"Protein Sci"},{"key":"1228_CR24","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.tips.2007.11.009","volume":"29","author":"B Kobilka","year":"2008","unstructured":"Kobilka B, Schertler GF (2008) New G-protein-coupled receptor crystal structures: insights and limitations. Trends Pharmacol Sci 29:79\u201383","journal-title":"Trends Pharmacol Sci"},{"key":"1228_CR25","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1002\/1439-7633(20021004)3:10<981::AID-CBIC981>3.0.CO;2-9","volume":"3","author":"J Klein-Seetharaman","year":"2002","unstructured":"Klein-Seetharaman J (2002) Dynamics in rhodopsin. ChemBioChem 3:981\u2013986","journal-title":"ChemBioChem"},{"key":"1228_CR26","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1038\/nbt838","volume":"21","author":"JP Vilardaga","year":"2003","unstructured":"Vilardaga JP, B\u00fcnemann M, Krasel C, Castro M, Lohse MJ (2003) Measurement of the millisecond activation switch of G protein-coupled receptors in living cells. Nat Biotechnol 21:807\u2013812","journal-title":"Nat Biotechnol"},{"key":"1228_CR27","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1034\/j.1600-0749.2001.140403.x","volume":"14","author":"B Shen","year":"2001","unstructured":"Shen B, Samaraweera P, Rosenberg B, Orlow SJ (2001) Ocular albenism type I: more than meets the eye. Pigment Cell Res 14:243\u2013248","journal-title":"Pigment Cell Res"},{"key":"1228_CR28","doi-asserted-by":"crossref","first-page":"2781","DOI":"10.1093\/hmg\/9.19.2781","volume":"9","author":"B Incerti","year":"2000","unstructured":"Incerti B, Cortese K, Pizzigoni A, Surace EM, Varani S et al (2000) Oa1 knock-out: new insights on the pathogenesis of ocular albinism type I. Hum Mol Genet 9:2781\u20132788","journal-title":"Hum Mol Genet"},{"key":"1228_CR29","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1038\/ng0595-13","volume":"10","author":"MV Bassi","year":"1995","unstructured":"Bassi MV, Schiaffino MV, Renieri A, De Nigris F, Galli L et al (1995) Cloning of the gene for ocular albinism type I from the distal short arm of the X chromosome. Nat Genet 10:13\u201319","journal-title":"Nat Genet"},{"key":"1228_CR30","doi-asserted-by":"crossref","first-page":"2319","DOI":"10.1093\/hmg\/4.12.2319","volume":"4","author":"MV Schiaffino","year":"1995","unstructured":"Schiaffino MV, Bassi MV, Galli L, Renieri A, Bruttini M et al (1995) Analysis of the OA1 gene reveals mutations in only one-third of the patients with X linked ocular albinism. Hum Mol Genet 4:2319\u20132325","journal-title":"Hum Mol Genet"},{"key":"1228_CR31","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1038\/12715","volume":"23","author":"MV Schiaffino","year":"1999","unstructured":"Schiaffino MV, d\u2019Addio M, Alloni A, Baschirotto C, Valetti C et al (1999) Ocular albinism: evidence for a defect in an intracellular signal transduction system. Nat Genet 23:108\u2013112","journal-title":"Nat Genet"},{"key":"1228_CR32","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1111\/j.1600-0749.2005.00240.x","volume":"18","author":"MV Schiaffino","year":"2005","unstructured":"Schiaffino MV, Tacchetti C (2005) The Ocular Albinism type I (OA1) protein and the evidence for an intracellular signal transduction system involved in melanosome biogenesis. Pigment Cell Res 18:227\u2013233","journal-title":"Pigment Cell Res"},{"key":"1228_CR33","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1111\/j.1600-0749.2006.00292.x","volume":"19","author":"G Innamorati","year":"2006","unstructured":"Innamorati G, Piccirillo R, Bagnato P, Palmisano I, Schiaffino MV (2006) The melanosome\/lysosomal protein OA1 has properties of a G protein coupled receptor. Pigment Cell Res 19:125\u2013135","journal-title":"Pigment Cell Res"},{"key":"1228_CR34","doi-asserted-by":"crossref","first-page":"3011","DOI":"10.1093\/hmg\/9.20.3011","volume":"9","author":"M d\u2019Addio","year":"2000","unstructured":"d\u2019Addio M, Pizzigoni A, Bassi MT, Baschirotto C, Valetti C et al (2000) Defective intracellular transport and processing of OA1 is a major cause of ocular albinism type 1. Human Mol Genet 9:3011\u20133018","journal-title":"Human Mol Genet"},{"key":"1228_CR35","doi-asserted-by":"crossref","first-page":"3487","DOI":"10.1093\/hmg\/ddn241","volume":"17","author":"I Palmisano","year":"2008","unstructured":"Palmisano I, Bagnato P, Palmigiano A, Innamorati G, Rotondo G et al (2008) The ocular albinism type 1 protein, an intracellular G protein coupled receptor, regulates melanosome transport in pigment cells. Human Mol Genet 17:3487\u20133501","journal-title":"Human Mol Genet"},{"key":"1228_CR36","doi-asserted-by":"crossref","first-page":"e236","DOI":"10.1371\/journal.pbio.0060236","volume":"6","author":"VM Lopez","year":"2008","unstructured":"Lopez VM, Decatur CL, Stamer WD, Lynch RM, MacKay BS (2008) l-DOPA is an endogenous ligand for OA1. PLoS Biol 6:e236","journal-title":"PLoS Biol"},{"key":"1228_CR37","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1093\/nar\/26.1.38","volume":"26","author":"A Bairoch","year":"1998","unstructured":"Bairoch A, Apweiler R (1998) The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Res 26:38\u201342","journal-title":"Nucleic Acids Res"},{"key":"1228_CR38","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1093\/nar\/gkh121","volume":"32","author":"A Bateman","year":"2004","unstructured":"Bateman A, Coin L, Durbin R, Finn RD, Hollich V et al (2004) The Pfam protein families database. Nucleic Acids Res 32:138\u2013141","journal-title":"Nucleic Acids Res"},{"key":"1228_CR39","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul SF, Madden TL, Sch\u00e4ffer AA (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389\u20133402","journal-title":"Nucleic Acids Res"},{"key":"1228_CR40","doi-asserted-by":"crossref","first-page":"2947","DOI":"10.1093\/bioinformatics\/btm404","volume":"23","author":"MA Larkin","year":"2007","unstructured":"Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947\u20132948","journal-title":"Bioinformatics"},{"key":"1228_CR41","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","volume":"305","author":"A Krogh","year":"2001","unstructured":"Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. J Mol Biol 305:567\u2013580","journal-title":"J Mol Biol"},{"key":"1228_CR42","doi-asserted-by":"crossref","first-page":"W321","DOI":"10.1093\/nar\/gkh377","volume":"32","author":"B Rost","year":"2004","unstructured":"Rost B, Yachdav G, Liu J (2004) The PredictProtein Server. Nucleic Acids Res 32:W321\u2013W326","journal-title":"Nucleic Acids Res"},{"key":"1228_CR43","doi-asserted-by":"crossref","first-page":"1258","DOI":"10.1126\/science.1150577","volume":"318","author":"V Cherezov","year":"2007","unstructured":"Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SGF, Thian FS et al (2007) High-resolution crystal structure of an engineered human \u03b22-adrenergic G protein-coupled receptor. Science 318:1258\u20131265","journal-title":"Science"},{"key":"1228_CR44","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1016\/j.jmb.2004.07.044","volume":"342","author":"T Okada","year":"2004","unstructured":"Okada T, Sugihara M, Bondar AN, Elstner M, Entel P et al (2004) The retinal conformation and its environment in rhodopsin in light of a new 2.2\u00a0\u00c5 crystal structure. J Mol Biol 342:571\u2013583","journal-title":"J Mol Biol"},{"key":"1228_CR45","first-page":"95","volume":"41","author":"TA Hall","year":"1999","unstructured":"Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95\/98\/NT. Nucleic Acids Symp Series 41:95\u201398","journal-title":"Nucleic Acids Symp Series"},{"key":"1228_CR46","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1006\/jmbi.1993.1626","volume":"234","author":"A \u0160ali","year":"1993","unstructured":"\u0160ali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779\u2013815","journal-title":"J Mol Biol"},{"key":"1228_CR47","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1107\/S0021889892009944","volume":"26","author":"RA Laskowski","year":"1993","unstructured":"Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26:283\u2013291","journal-title":"J Appl Cryst"},{"key":"1228_CR48","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1016\/S0076-6879(97)77022-8","volume":"277","author":"D Eisenberg","year":"1997","unstructured":"Eisenberg D, L\u00fcthy R, Bowie JU (1997) VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 277:396\u2013404","journal-title":"Methods Enzymol"},{"key":"1228_CR49","unstructured":"Schr\u00f6dinger Suite (2009) QM-polarized ligand docking protocol; Glide version 5.5; Jaguar version 7.6; QSite version 5.5. Schr\u00f6dinger, LLC, New York, NY"},{"key":"1228_CR50","doi-asserted-by":"crossref","first-page":"2382","DOI":"10.1021\/ci900231p","volume":"49","author":"JY Chung","year":"2009","unstructured":"Chung JY, Hah JM, Cho AE (2009) Correlation between performance of QM\/MM docking and simple classification of binding sites. J Chem Inf Model 49:2382\u20132387","journal-title":"J Chem Inf Model"},{"key":"1228_CR51","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1021\/ct700301q","volume":"4","author":"B Hess","year":"2008","unstructured":"Hess B, Kutzner C, van der Spoel D, Lindahl EJ (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. Chem Theor Comput 4:435\u2013447","journal-title":"Chem Theor Comput"},{"key":"1228_CR52","first-page":"1355","volume":"D60","author":"AW Schuettelkopf","year":"2004","unstructured":"Schuettelkopf AW, van Aalten DMF (2004) PRODRG\u2014a tool for high-throughput crystallography of protein\u2013ligand complexes. Acta Crystallographica D60:1355\u20131363","journal-title":"Acta Crystallographica"},{"key":"1228_CR53","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1016\/j.ymeth.2006.08.006","volume":"41","author":"C Kandt","year":"2007","unstructured":"Kandt C, Ash WL, Tieleman DP (2007) Setting up and running molecular dynamics simulations of membrane proteins. Methods 41:475\u2013488","journal-title":"Methods"},{"key":"1228_CR54","doi-asserted-by":"crossref","first-page":"014101","DOI":"10.1063\/1.2408420","volume":"126","author":"G Bussi","year":"2007","unstructured":"Bussi G, Donadio D, Parrinello M (2007) Canonical sampling through velocity rescaling. J Chem Phys 126:014101","journal-title":"J Chem Phys"},{"key":"1228_CR55","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1021\/ct700200b","volume":"4","author":"B Hess","year":"2008","unstructured":"Hess B (2008) P-LINCS: a parallel linear constraint solver for molecular simulations. J Chem Theor Comput 4:116\u2013122","journal-title":"J Chem Theor Comput"},{"key":"1228_CR56","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1093\/protein\/8.2.127","volume":"8","author":"AC Wallace","year":"1995","unstructured":"Wallace AC, Laskowski RA, Thornton JM (1995) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Prot Eng 8:127\u2013134","journal-title":"Prot Eng"},{"key":"1228_CR57","unstructured":"XMGRACE: http:\/\/plasma-gate.weizmann.ac.il\/Grace\/"},{"key":"1228_CR58","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","volume":"14","author":"W Humphrey","year":"1996","unstructured":"Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33\u201338","journal-title":"J Mol Graph"},{"key":"1228_CR59","volume-title":"The PyMOL Molecular Graphics System","author":"WL DeLano","year":"2003","unstructured":"DeLano WL (2003) The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA"},{"key":"1228_CR60","doi-asserted-by":"crossref","first-page":"800","DOI":"10.1086\/301776","volume":"62","author":"RE Schnur","year":"1998","unstructured":"Schnur RE, Gao M, Wick PA, Keller M, Benke PJ et al (1998) OA1 mutations and deletions in X-linked ocular albinism. Am J Hum Genet 62:800\u2013809","journal-title":"Am J Hum Genet"},{"key":"1228_CR61","doi-asserted-by":"crossref","first-page":"16341","DOI":"10.1074\/jbc.M109.094870","volume":"285","author":"H Unal","year":"2010","unstructured":"Unal H, Jagannathan R, Bhat MB, Karnik SS (2010) Ligand-specific conformation of extracellular loop-2 in the angiotensin II type 1 receptor. J Biol Chem 285:16341\u201316350","journal-title":"J Biol Chem"},{"key":"1228_CR62","doi-asserted-by":"crossref","first-page":"17405","DOI":"10.1074\/jbc.M702151200","volume":"282","author":"M Conner","year":"2007","unstructured":"Conner M, Hawtin SR, Simms J, Wootten D, Lawson Z et al (2007) Systematic analysis of the entire second extracellular loop of the V(1a) vasopressin receptor: key residues, conserved throughout a G-protein-coupled receptor family, identified. J Biol Chem 282:17405\u201317412","journal-title":"J Biol Chem"},{"key":"1228_CR63","doi-asserted-by":"crossref","first-page":"1683","DOI":"10.1074\/jbc.274.3.1683","volume":"274","author":"TD Dunham","year":"1999","unstructured":"Dunham TD, Farrens DL (1999) Conformational changes in rhodopsin. Movement of helix f detected by site-specific chemical labeling and fluorescence spectroscopy. J Biol Chem 274:1683\u20131690","journal-title":"J Biol Chem"},{"key":"1228_CR64","doi-asserted-by":"crossref","first-page":"20290","DOI":"10.1073\/pnas.0710393104","volume":"104","author":"B Knierim","year":"2007","unstructured":"Knierim B, Hofmann KP, Ernst OP, Hubbell WL (2007) Sequence of late molecular events in the activation of rhodopsin. Proc Natl Acad Sci USA 104:20290\u201320295","journal-title":"Proc Natl Acad Sci USA"},{"key":"1228_CR65","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1016\/j.bbamem.2006.10.021","volume":"1768","author":"BK Kobilka","year":"2007","unstructured":"Kobilka BK (2007) G protein coupled receptor structure and activation. Biochim Biophys Acta 1768:794\u2013807","journal-title":"Biochim Biophys Acta"},{"key":"1228_CR66","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1034\/j.1399-3011.2002.21062.x","volume":"60","author":"BK Kobilka","year":"2002","unstructured":"Kobilka BK (2002) Agonist-induced conformational changes in the beta2 adrenergic receptor. J Pept Res 60:317\u2013321","journal-title":"J Pept Res"},{"key":"1228_CR67","doi-asserted-by":"crossref","first-page":"40989","DOI":"10.1074\/jbc.M206801200","volume":"277","author":"L Shi","year":"2002","unstructured":"Shi L, Liapakis G, Xu R, Guarnieri F, Ballesteros JA et al (2002) Beta2 adrenergic receptor activation. Modulation of the proline kink in transmembrane 6 by a rotamer toggle switch. J Biol Chem 277:40989\u201340996","journal-title":"J Biol Chem"},{"key":"1228_CR68","first-page":"2027","volume":"94","author":"S Bhattacharya","year":"2008","unstructured":"Bhattacharya S, Hall SE, Li H, Vaidehi N (2008) Ligand-stabilized conformational states of human \u03b22 adrenergic receptor: insight into G-protein-coupled receptor activation. Bio Phys J 94:2027\u20132042","journal-title":"Bio Phys J"},{"key":"1228_CR69","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1016\/j.jmb.2008.06.084","volume":"382","author":"S Bhattacharya","year":"2008","unstructured":"Bhattacharya S, Hall SE, Vaidehi N (2008) Agonist-induced conformational changes in bovine rhodopsin: insight into activation of G-protein-coupled receptors. J Mol Biol 382:539\u2013555","journal-title":"J Mol Biol"},{"key":"1228_CR70","doi-asserted-by":"crossref","first-page":"1416","DOI":"10.1126\/science.8248781","volume":"262","author":"ZT Farahbakhsh","year":"1993","unstructured":"Farahbakhsh ZT, Hideg K, Hubbell WL (1993) Photoactivated conformational-changes in rhodopsin\u2014a time-resolved spin-label study. Science 262:1416\u20131419","journal-title":"Science"},{"key":"1228_CR71","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1038\/78956","volume":"7","author":"WL Hubbell","year":"2000","unstructured":"Hubbell WL, Cafiso D, Altenbach C (2000) Identifying conformational changes with site-directed spin labeling. Nature Struct Biol 7:735\u2013739","journal-title":"Nature Struct Biol"},{"key":"1228_CR72","doi-asserted-by":"crossref","first-page":"7918","DOI":"10.1021\/bi990010g","volume":"38","author":"R Langen","year":"1999","unstructured":"Langen R, Cai K, Altenbach C, Khorana HG, Hubbell WL (1999) Structural features of the C-terminal domain of bovine rhodopsin: a site directed spin-labeling study. Biochemistry 38:7918\u20137924","journal-title":"Biochemistry"},{"key":"1228_CR73","doi-asserted-by":"crossref","first-page":"768","DOI":"10.1126\/science.274.5288.768","volume":"274","author":"D Farrens","year":"1996","unstructured":"Farrens D, Altenbach C, Yang K, Hubbell WL, Khorana HG (1996) Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin. Science 274:768\u2013770","journal-title":"Science"},{"key":"1228_CR74","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1016\/j.jmb.2003.08.045","volume":"333","author":"PS Crozier","year":"2003","unstructured":"Crozier PS, Stevens MJ, Forrest LR, Woolf TB (2003) Molecular dynamics simulations of dark-adapted rhodopsin in an explicit membrane bilayer: coupling between local retinal and larger scale conformational change. J Mol Biol 333:493\u2013514","journal-title":"J Mol Biol"},{"key":"1228_CR75","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1016\/j.jmb.2008.05.022","volume":"380","author":"R Vogel","year":"2008","unstructured":"Vogel R, Mahalingam M, L\u00fcdeke S, Huber T, Siebert F et al (2008) Functional role of the \u201cIonic Lock\u201d\u2014an interhelical hydrogen-bond network in family a heptahelical receptors. J Mol Biol 380:648\u2013655","journal-title":"J Mol Biol"},{"key":"1228_CR76","doi-asserted-by":"crossref","first-page":"29171","DOI":"10.1074\/jbc.M103747200","volume":"276","author":"JA Ballesteros","year":"2001","unstructured":"Ballesteros JA, Jensen AD, Liapakis G, Rasmussen SGF, Shi L et al (2001) Activation of the \u03b22-adrenergic receptor involves disruption of an ionic lock between cytoplasmic ends of transmembrane segments 3 and 6. J Biol Chem 276:29171\u201329177","journal-title":"J Biol Chem"},{"key":"1228_CR77","doi-asserted-by":"crossref","first-page":"4689","DOI":"10.1073\/pnas.0811065106","volume":"106","author":"RO Dror","year":"2009","unstructured":"Dror RO, Arlow DH, Borhani DW, Jensen M\u00d8, Piana S et al (2009) Identification of two distinct inactive conformations of the beta2-adrenergic receptor reconciles structural and biochemical observations. Proc Natl Acad Sci USA 106:4689\u20134694","journal-title":"Proc Natl Acad Sci USA"},{"key":"1228_CR78","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/j.bpj.2009.09.046","volume":"98","author":"TD Romo","year":"2010","unstructured":"Romo TD, Grossfield A, Pitman MC (2010) Concerted interconversion between ionic lock substates of the beta(2) adrenergic receptor revealed by microsecond timescale molecular dynamics. Biophys J 98:76\u201384","journal-title":"Biophys J"},{"key":"1228_CR79","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.jmb.2010.02.032","volume":"398","author":"NG Sgourakis","year":"2010","unstructured":"Sgourakis NG, Garcia AE (2010) The membrane complex between transducin and dark-state rhodopsin exhibits large-amplitude interface dynamics on the sub-microsecond timescale: insights from all-atom MD simulations. J Mol Biol 398:161\u2013173","journal-title":"J Mol Biol"},{"key":"1228_CR80","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1007\/s10822-006-9064-0","volume":"20","author":"F Fanelli","year":"2006","unstructured":"Fanelli F, De Benedetti PG (2006) Inactive and active states and supramolecular organization of GPCRs: insights from computational modeling. J Comput Aided Mol Des 20:449\u2013461","journal-title":"J Comput Aided Mol Des"}],"container-title":["Journal of Molecular Modeling"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00894-011-1228-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s00894-011-1228-8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00894-011-1228-8","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,29]],"date-time":"2019-05-29T06:52:13Z","timestamp":1559112733000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s00894-011-1228-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,9,22]]},"references-count":80,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2012,5]]}},"alternative-id":["1228"],"URL":"https:\/\/doi.org\/10.1007\/s00894-011-1228-8","relation":{},"ISSN":["1610-2940","0948-5023"],"issn-type":[{"value":"1610-2940","type":"print"},{"value":"0948-5023","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,9,22]]}}}