{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T13:31:13Z","timestamp":1790343073853,"version":"4.1.0"},"reference-count":34,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Molecular Graphics and Modelling"],"published-print":{"date-parts":[[2019,1]]},"DOI":"10.1016\/j.jmgm.2018.10.022","type":"journal-article","created":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T08:38:07Z","timestamp":1540283887000},"page":"199-208","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":15,"special_numbering":"C","title":["The effect of different alcohols on the Asp23-Lys28 and Asp23-Ala42 salt bridges of the most effective peptide in Alzheimer's disease: Molecular dynamics viewpoints"],"prefix":"10.1016","volume":"86","author":[{"given":"Farnaz","family":"Jahanbin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8651-9289","authenticated-orcid":false,"given":"Mohammad Reza","family":"Bozorgmehr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ali","family":"Morsali","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9616-8550","authenticated-orcid":false,"given":"S. Ali","family":"Beyramabadi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"5707","key":"10.1016\/j.jmgm.2018.10.022_bib1","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1126\/science.1105850","article-title":"Self-propagating, molecular-level polymorphism in Alzheimer's \u00df-amyloid fibrils","volume":"307","author":"Petkova","year":"2005","journal-title":"Science"},{"issue":"3","key":"10.1016\/j.jmgm.2018.10.022_bib2","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1046\/j.1471-4159.2003.02018.x","article-title":"Amyloid \u03b2-protein (A\u03b2) 1\u201340 protects neurons from damage induced by A\u03b21\u201342 in culture and in rat brain","volume":"87","author":"Zou","year":"2003","journal-title":"J.\u00a0Neurochem."},{"issue":"3","key":"10.1016\/j.jmgm.2018.10.022_bib3","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1016\/j.jmb.2008.11.005","article-title":"A\u03b2 (1-40) fibril polymorphism implies diverse interaction patterns in amyloid fibrils","volume":"386","author":"Meinhardt","year":"2009","journal-title":"J.\u00a0Mol. Biol."},{"issue":"34","key":"10.1016\/j.jmgm.2018.10.022_bib4","doi-asserted-by":"crossref","first-page":"14339","DOI":"10.1073\/pnas.0907821106","article-title":"Measurement of amyloid fibril mass-per-length by tilted-beam transmission electron microscopy","volume":"106","author":"Chen","year":"2009","journal-title":"Proc. Natl. Acad. Sci. Unit. States Am."},{"issue":"1","key":"10.1016\/j.jmgm.2018.10.022_bib5","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/j.ymeth.2004.03.012","article-title":"Techniques to study amyloid fibril formation in\u00a0vitro","volume":"34","author":"Nilsson","year":"2004","journal-title":"Methods"},{"issue":"5","key":"10.1016\/j.jmgm.2018.10.022_bib6","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1016\/S0006-3495(91)82154-3","article-title":"pH-dependent structural transitions of Alzheimer amyloid peptides","volume":"60","author":"Fraser","year":"1991","journal-title":"Biophys. J."},{"key":"10.1016\/j.jmgm.2018.10.022_bib7","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.jinorgbio.2012.07.007","article-title":"Dual role of Cu2+ ions on the aggregation and degradation of soluble A\u03b2 oligomers and protofibrils investigated by fluorescence spectroscopy and AFM","volume":"116","author":"Garc\u00eda","year":"2012","journal-title":"J.\u00a0Inorg. Biochem."},{"issue":"3","key":"10.1016\/j.jmgm.2018.10.022_bib8","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1006\/jmbi.1997.1348","article-title":"Common core structure of amyloid fibrils by synchrotron X-ray diffraction1","volume":"273","author":"Sunde","year":"1997","journal-title":"J.\u00a0Mol. Biol."},{"issue":"11","key":"10.1016\/j.jmgm.2018.10.022_bib9","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1177\/16.11.673","article-title":"X-ray diffraction studies on amyloid filaments","volume":"16","author":"Eanes","year":"1968","journal-title":"J.\u00a0Histochem. Cytochem."},{"issue":"43","key":"10.1016\/j.jmgm.2018.10.022_bib10","doi-asserted-by":"crossref","first-page":"40810","DOI":"10.1074\/jbc.M205659200","article-title":"Structural and dynamic features of Alzheimer's A\u03b2 peptide in amyloid fibrils studied by site-directed spin labeling","volume":"277","author":"T\u00f6r\u00f6k","year":"2002","journal-title":"J.\u00a0Biol. Chem."},{"issue":"5580","key":"10.1016\/j.jmgm.2018.10.022_bib11","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1126\/science.1072994","article-title":"The amyloid hypothesis of Alzheimer's disease: progress and problems on the road to therapeutics","volume":"297","author":"Hardy","year":"2002","journal-title":"Science"},{"issue":"9","key":"10.1016\/j.jmgm.2018.10.022_bib12","doi-asserted-by":"crossref","first-page":"3518","DOI":"10.1021\/cr500638n","article-title":"Amyloid \u03b2 protein and Alzheimer's disease: when computer simulations complement experimental studies","volume":"115","author":"Nasica-Labouze","year":"2015","journal-title":"Chem. Rev."},{"issue":"5","key":"10.1016\/j.jmgm.2018.10.022_bib13","doi-asserted-by":"crossref","first-page":"1573","DOI":"10.1039\/C2CP23326F","article-title":"Atomic-level investigations on the amyloid-\u03b2 dimerization process and its driving forces in water","volume":"14","author":"Chong","year":"2012","journal-title":"Phys. Chem. Chem. Phys."},{"issue":"15","key":"10.1016\/j.jmgm.2018.10.022_bib14","doi-asserted-by":"crossref","first-page":"3993","DOI":"10.1021\/jp312573y","article-title":"Molecular mechanism of the inhibition of EGCG on the Alzheimer A\u03b21\u201342 dimer","volume":"117","author":"Zhang","year":"2013","journal-title":"J.\u00a0Phys. Chem. B"},{"issue":"29","key":"10.1016\/j.jmgm.2018.10.022_bib15","doi-asserted-by":"crossref","first-page":"8412","DOI":"10.1021\/jp2118778","article-title":"Structures of A\u03b217\u201342 trimers in isolation and with five small-molecule drugs using a hierarchical computational procedure","volume":"116","author":"Chebaro","year":"2012","journal-title":"J.\u00a0Phys. Chem. B"},{"issue":"6","key":"10.1016\/j.jmgm.2018.10.022_bib16","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/nsmb.2991","article-title":"A\u03b2 (1\u201342) fibril structure illuminates self-recognition and replication of amyloid in Alzheimer's disease","volume":"22","author":"Xiao","year":"2015","journal-title":"Nat. Struct. Mol. Biol."},{"issue":"1","key":"10.1016\/j.jmgm.2018.10.022_bib17","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.jalz.2012.12.006","article-title":"Changes in plasma amyloid beta in a longitudinal study of aging and Alzheimer's disease. Alzheimer's & dementia","volume":"10","author":"Rembach","year":"2014","journal-title":"J.\u00a0Alzheimer's Assoc."},{"issue":"48","key":"10.1016\/j.jmgm.2018.10.022_bib18","doi-asserted-by":"crossref","first-page":"17342","DOI":"10.1073\/pnas.0506723102","article-title":"3D structure of Alzheimer's amyloid-\u03b2 (1\u201342) fibrils","volume":"102","author":"L\u00fchrs","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"issue":"11","key":"10.1016\/j.jmgm.2018.10.022_bib19","doi-asserted-by":"crossref","first-page":"1446","DOI":"10.1021\/cn400110d","article-title":"Effect of the tottori familial disease mutation (D7N) on the monomers and dimers of A\u03b240 and A\u03b242","volume":"4","author":"Viet","year":"2013","journal-title":"ACS Chem. Neurosci."},{"issue":"10","key":"10.1016\/j.jmgm.2018.10.022_bib20","doi-asserted-by":"crossref","first-page":"2638","DOI":"10.1021\/jp412153s","article-title":"Alzheimer's A\u03b210\u201340 peptide binds and penetrates DMPC bilayer: an isobaric\u2013isothermal replica exchange molecular dynamics study","volume":"118","author":"Lockhart","year":"2014","journal-title":"J.\u00a0Phys. Chem. B"},{"issue":"49","key":"10.1016\/j.jmgm.2018.10.022_bib21","doi-asserted-by":"crossref","first-page":"17843","DOI":"10.1021\/ja905457d","article-title":"Structures of \u03b2-amyloid peptide 1\u2212 40, 1\u2212 42, and 1\u2212 55\u2212 the 672\u2212 726 fragment of APP- in a membrane environment with implications for interactions with \u03b3-secretase","volume":"131","author":"Miyashita","year":"2009","journal-title":"J.\u00a0Am. Chem. Soc."},{"key":"10.1016\/j.jmgm.2018.10.022_bib22","series-title":"The GROMACS Development Team, GROMACS User Manual Version 5.1. 2","author":"Abraham","year":"2016"},{"issue":"28","key":"10.1016\/j.jmgm.2018.10.022_bib23","doi-asserted-by":"crossref","first-page":"6474","DOI":"10.1021\/jp003919d","article-title":"Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides","volume":"105","author":"Kaminski","year":"2001","journal-title":"J.\u00a0Phys. Chem. B"},{"issue":"4","key":"10.1016\/j.jmgm.2018.10.022_bib24","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1016\/j.jmb.2003.11.046","article-title":"Two types of Alzheimer's \u03b2-amyloid (1\u201340) peptide membrane interactions: aggregation preventing transmembrane anchoring versus accelerated surface fibril formation","volume":"335","author":"Bokvist","year":"2004","journal-title":"J.\u00a0Mol. Biol."},{"key":"10.1016\/j.jmgm.2018.10.022_bib25","volume":"vol. 2","author":"Luenberger","year":"1984"},{"issue":"19","key":"10.1016\/j.jmgm.2018.10.022_bib26","doi-asserted-by":"crossref","first-page":"8577","DOI":"10.1063\/1.470117","article-title":"A\u00a0smooth particle mesh Ewald method","volume":"103","author":"Essmann","year":"1995","journal-title":"J.\u00a0Chem. Phys."},{"issue":"12","key":"10.1016\/j.jmgm.2018.10.022_bib27","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H","article-title":"LINCS: a linear constraint solver for molecular simulations","volume":"18","author":"Hess","year":"1997","journal-title":"J.\u00a0Comput. Chem."},{"issue":"8","key":"10.1016\/j.jmgm.2018.10.022_bib28","doi-asserted-by":"crossref","first-page":"952","DOI":"10.1002\/jcc.540130805","article-title":"Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models","volume":"13","author":"Miyamoto","year":"1992","journal-title":"J.\u00a0Comput. Chem."},{"key":"10.1016\/j.jmgm.2018.10.022_bib29","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/j.jtbi.2014.09.015","article-title":"Molecular crowding effects on conformation and stability of G-quadruplex DNA structure: insights from molecular dynamics simulation","volume":"364","author":"Doghaei","year":"2015","journal-title":"J.\u00a0Theor. Biol."},{"issue":"23","key":"10.1016\/j.jmgm.2018.10.022_bib30","doi-asserted-by":"crossref","first-page":"5042","DOI":"10.1021\/jp050836u","article-title":"Interior and interfacial aqueous solvation of benzene dicarboxylate dianions and their methylated analogues: a combined molecular dynamics and photoelectron spectroscopy study","volume":"109","author":"Minofar","year":"2005","journal-title":"J.\u00a0Phys. Chem."},{"issue":"7","key":"10.1016\/j.jmgm.2018.10.022_bib31","doi-asserted-by":"crossref","first-page":"890","DOI":"10.1002\/cbic.201200733","article-title":"Expansion of access tunnels and active-site cavities influence activity of haloalkane dehalogenases in organic cosolvents","volume":"14","author":"Stepankova","year":"2013","journal-title":"Chembiochem"},{"key":"10.1016\/j.jmgm.2018.10.022_bib32","volume":"vol. 1","author":"Frenkel","year":"2001"},{"issue":"50","key":"10.1016\/j.jmgm.2018.10.022_bib33","doi-asserted-by":"crossref","first-page":"16159","DOI":"10.1021\/ja064872y","article-title":"Dynamics of Asp23\u2212 Lys28 salt-bridge formation in a\u03b210-35 monomers","volume":"128","author":"Tarus","year":"2006","journal-title":"J.\u00a0Am. Chem. Soc."},{"key":"10.1016\/j.jmgm.2018.10.022_bib34","series-title":"Foreword by David Chandler","first-page":"288","article-title":"Introduction to modern statistical mechanics. Introduction to modern statistical mechanics","author":"Chandler","year":"1987"}],"container-title":["Journal of Molecular Graphics and Modelling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1093326318304765?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1093326318304765?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T21:00:32Z","timestamp":1761080432000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1093326318304765"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,1]]},"references-count":34,"alternative-id":["S1093326318304765"],"URL":"https:\/\/doi.org\/10.1016\/j.jmgm.2018.10.022","relation":{},"ISSN":["1093-3263"],"issn-type":[{"value":"1093-3263","type":"print"}],"subject":[],"published":{"date-parts":[[2019,1]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"The effect of different alcohols on the Asp23-Lys28 and Asp23-Ala42 salt bridges of the most effective peptide in Alzheimer's disease: Molecular dynamics viewpoints","name":"articletitle","label":"Article Title"},{"value":"Journal of Molecular Graphics and Modelling","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jmgm.2018.10.022","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2018 Elsevier Inc. All rights reserved.","name":"copyright","label":"Copyright"}]}}