{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T16:07:46Z","timestamp":1778602066846,"version":"3.51.4"},"publisher-location":"New York, NY","reference-count":53,"publisher":"Springer US","isbn-type":[{"value":"9781071650912","type":"print"},{"value":"9781071650929","type":"electronic"}],"license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026]]},"DOI":"10.1007\/978-1-0716-5092-9_10","type":"book-chapter","created":{"date-parts":[[2026,1,2]],"date-time":"2026-01-02T00:59:06Z","timestamp":1767315546000},"page":"147-182","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Methods and Guidelines for Analyzing the Conformational Dynamics of Proteins in the Antigen Presentation Pathway"],"prefix":"10.1007","author":[{"given":"Athanasios","family":"Papakyriakou","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2026,1,2]]},"reference":[{"issue":"1","key":"10_CR1","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/j.bbapap.2004.09.011","volume":"1751","author":"M Tsujimoto","year":"2005","unstructured":"Tsujimoto M, Hattori A (2005) The oxytocinase subfamily of M1 aminopeptidases. Biochim Biophys Acta 1751(1):9\u201318. https:\/\/doi.org\/10.1016\/j.bbapap.2004.09.011","journal-title":"Biochim Biophys Acta"},{"issue":"31","key":"10_CR2","doi-asserted-by":"publisher","first-page":"3656","DOI":"10.2174\/138161209789271816","volume":"15","author":"I Evnouchidou","year":"2009","unstructured":"Evnouchidou I, Papakyriakou A, Stratikos E (2009) A new role for Zn(II) aminopeptidases: antigenic peptide generation and destruction. Curr Pharm Des 15(31):3656\u20133670. https:\/\/doi.org\/10.2174\/138161209789271816","journal-title":"Curr Pharm Des"},{"issue":"5937","key":"10_CR3","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1126\/science.1172845","volume":"325","author":"L Saveanu","year":"2009","unstructured":"Saveanu L, Carroll O, Weimershaus M, Guermonprez P, Firat E, Lindo V, Greer F, Davoust J, Kratzer R, Keller SR, Niedermann G, van Endert P (2009) IRAP identifies an endosomal compartment required for MHC class I cross-presentation. Science 325(5937):213\u2013217. https:\/\/doi.org\/10.1126\/science.1172845","journal-title":"Science"},{"issue":"19","key":"10_CR4","doi-asserted-by":"publisher","first-page":"7745","DOI":"10.1073\/pnas.1101262108","volume":"108","author":"G Kochan","year":"2011","unstructured":"Kochan G, Krojer T, Harvey D, Fischer R, Chen L, Vollmar M, von Delft F, Kavanagh KL, Brown MA, Bowness P, Wordsworth P, Kessler BM, Oppermann U (2011) Crystal structures of the endoplasmic reticulum aminopeptidase-1 (ERAP1) reveal the molecular basis for N-terminal peptide trimming. Proc Natl Acad Sci USA 108(19):7745\u20137750. https:\/\/doi.org\/10.1073\/pnas.1101262108","journal-title":"Proc Natl Acad Sci USA"},{"issue":"5","key":"10_CR5","doi-asserted-by":"publisher","first-page":"604","DOI":"10.1038\/nsmb.2021","volume":"18","author":"TT Nguyen","year":"2011","unstructured":"Nguyen TT, Chang SC, Evnouchidou I, York IA, Zikos C, Rock KL, Goldberg AL, Stratikos E, Stern LJ (2011) Structural basis for antigenic peptide precursor processing by the endoplasmic reticulum aminopeptidase ERAP1. Nat Struct Mol Biol 18(5):604\u2013613. https:\/\/doi.org\/10.1038\/nsmb.2021","journal-title":"Nat Struct Mol Biol"},{"issue":"6","key":"10_CR6","doi-asserted-by":"publisher","first-page":"2842","DOI":"10.4049\/jimmunol.1501103","volume":"195","author":"A Mpakali","year":"2015","unstructured":"Mpakali A, Saridakis E, Harlos K, Zhao Y, Papakyriakou A, Kokkala P, Georgiadis D, Stratikos E (2015) Crystal structure of insulin-regulated aminopeptidase with bound substrate analogue provides insight on antigenic epitope precursor recognition and processing. J Immunol 195(6):2842\u20132851. https:\/\/doi.org\/10.4049\/jimmunol.1501103","journal-title":"J Immunol"},{"issue":"2","key":"10_CR7","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1002\/pro.2604","volume":"24","author":"SJ Hermans","year":"2015","unstructured":"Hermans SJ, Ascher DB, Hancock NC, Holien JK, Michell BJ, Chai SY, Morton CJ, Parker MW (2015) Crystal structure of human insulin-regulated aminopeptidase with specificity for cyclic peptides. Protein Sci Publ Protein Soc 24(2):190\u2013199. https:\/\/doi.org\/10.1002\/pro.2604","journal-title":"Protein Sci Publ Protein Soc"},{"issue":"7","key":"10_CR8","doi-asserted-by":"publisher","first-page":"2963","DOI":"10.1021\/acs.jmedchem.6b01890","volume":"60","author":"A Mpakali","year":"2017","unstructured":"Mpakali A, Saridakis E, Harlos K, Zhao Y, Kokkala P, Georgiadis D, Giastas P, Papakyriakou A, Stratikos E (2017) Ligand-induced conformational change of insulin-regulated aminopeptidase: insights on catalytic mechanism and active site plasticity. J Med Chem 60(7):2963\u20132972. https:\/\/doi.org\/10.1021\/acs.jmedchem.6b01890","journal-title":"J Med Chem"},{"issue":"5","key":"10_CR9","doi-asserted-by":"publisher","first-page":"708","DOI":"10.1021\/acsmedchemlett.9b00002","volume":"10","author":"P Giastas","year":"2019","unstructured":"Giastas P, Neu M, Rowland P, Stratikos E (2019) High-resolution crystal structure of endoplasmic reticulum aminopeptidase 1 with bound Phosphinic transition-state analogue inhibitor. ACS Med Chem Lett 10(5):708\u2013713. https:\/\/doi.org\/10.1021\/acsmedchemlett.9b00002","journal-title":"ACS Med Chem Lett"},{"issue":"1","key":"10_CR10","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-25564-w","volume":"12","author":"Z Maben","year":"2021","unstructured":"Maben Z, Arya R, Georgiadis D, Stratikos E, Stern LJ (2021) Conformational dynamics linked to domain closure and substrate binding explain the ERAP1 allosteric regulation mechanism. Nat Commun 12(1):5302. https:\/\/doi.org\/10.1038\/s41467-021-25564-w","journal-title":"Nat Commun"},{"issue":"14","key":"10_CR11","doi-asserted-by":"publisher","first-page":"10098","DOI":"10.1021\/acs.jmedchem.2c00904","volume":"65","author":"D Vourloumis","year":"2022","unstructured":"Vourloumis D, Mavridis I, Athanasoulis A, Temponeras I, Koumantou D, Giastas P, Mpakali A, Magrioti V, Leib J, van Endert P, Stratikos E, Papakyriakou A (2022) Discovery of selective Nanomolar inhibitors for insulin-regulated aminopeptidase based on alpha-Hydroxy-beta-amino acid derivatives of Bestatin. J Med Chem 65(14):10098\u201310117. https:\/\/doi.org\/10.1021\/acs.jmedchem.2c00904","journal-title":"J Med Chem"},{"issue":"1","key":"10_CR12","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1021\/bi201230p","volume":"51","author":"JR Birtley","year":"2012","unstructured":"Birtley JR, Saridakis E, Stratikos E, Mavridis IM (2012) The crystal structure of human endoplasmic reticulum aminopeptidase 2 reveals the atomic basis for distinct roles in antigen processing. Biochemistry 51(1):286\u2013295. https:\/\/doi.org\/10.1021\/bi201230p","journal-title":"Biochemistry"},{"issue":"5","key":"10_CR13","doi-asserted-by":"publisher","first-page":"2383","DOI":"10.4049\/jimmunol.1200918","volume":"189","author":"I Evnouchidou","year":"2012","unstructured":"Evnouchidou I, Birtley J, Seregin S, Papakyriakou A, Zervoudi E, Samiotaki M, Panayotou G, Giastas P, Petrakis O, Georgiadis D, Amalfitano A, Saridakis E, Mavridis IM, Stratikos E (2012) A common single nucleotide polymorphism in endoplasmic reticulum aminopeptidase 2 induces a specificity switch that leads to altered antigen processing. J Immunol 189(5):2383\u20132392. https:\/\/doi.org\/10.4049\/jimmunol.1200918","journal-title":"J Immunol"},{"issue":"43","key":"10_CR14","doi-asserted-by":"publisher","first-page":"26021","DOI":"10.1074\/jbc.M115.685909","volume":"290","author":"A Mpakali","year":"2015","unstructured":"Mpakali A, Giastas P, Mathioudakis N, Mavridis IM, Saridakis E, Stratikos E (2015) Structural basis for antigenic peptide recognition and processing by endoplasmic reticulum (ER) aminopeptidase 2. J Biol Chem 290(43):26021\u201326032. https:\/\/doi.org\/10.1074\/jbc.M115.685909","journal-title":"J Biol Chem"},{"issue":"3","key":"10_CR15","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1021\/acsmedchemlett.6b00505","volume":"8","author":"A Mpakali","year":"2017","unstructured":"Mpakali A, Giastas P, Deprez-Poulain R, Papakyriakou A, Koumantou D, Gealageas R, Tsoukalidou S, Vourloumis D, Mavridis IM, Stratikos E, Saridakis E (2017) Crystal structures of ERAP2 complexed with inhibitors reveal pharmacophore requirements for optimizing inhibitor potency. ACS Med Chem Lett 8(3):333\u2013337. https:\/\/doi.org\/10.1021\/acsmedchemlett.6b00505","journal-title":"ACS Med Chem Lett"},{"issue":"39","key":"10_CR16","doi-asserted-by":"publisher","DOI":"10.1002\/anie.202203560","volume":"61","author":"V Camberlein","year":"2022","unstructured":"Camberlein V, Fleau C, Sierocki P, Li L, Gealageas R, Bosc D, Guillaume V, Warenghem S, Leroux F, Rosell M, Cheng K, Medve L, Prigent M, Decanter M, Piveteau C, Biela A, Eveque M, Dumont J, Mpakali A, Giastas P, Herledan A, Couturier C, Haupenthal J, Lesire L, Hirsch AKH, Deprez B, Stratikos E, Bouvier M, Deprez-Poulain R (2022) Discovery of the first selective Nanomolar inhibitors of ERAP2 by kinetic target-guided synthesis. Angew Chem Int Ed Engl 61(39):e202203560. https:\/\/doi.org\/10.1002\/anie.202203560","journal-title":"Angew Chem Int Ed Engl"},{"issue":"2","key":"10_CR17","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1021\/acsmedchemlett.1c00582","volume":"13","author":"A Mpakali","year":"2022","unstructured":"Mpakali A, Georgiadis D, Stratikos E, Giastas P (2022) Inhibitor-dependent usage of the S1' specificity pocket of ER aminopeptidase 2. ACS Med Chem Lett 13(2):218\u2013224. https:\/\/doi.org\/10.1021\/acsmedchemlett.1c00582","journal-title":"ACS Med Chem Lett"},{"issue":"12","key":"10_CR18","doi-asserted-by":"publisher","first-page":"1177","DOI":"10.1038\/ni860","volume":"3","author":"IA York","year":"2002","unstructured":"York IA, Chang SC, Saric T, Keys JA, Favreau JM, Goldberg AL, Rock KL (2002) The ER aminopeptidase ERAP1 enhances or limits antigen presentation by trimming epitopes to 8-9 residues. Nat Immunol 3(12):1177\u20131184. https:\/\/doi.org\/10.1038\/ni860","journal-title":"Nat Immunol"},{"issue":"47","key":"10_CR19","doi-asserted-by":"publisher","first-page":"17107","DOI":"10.1073\/pnas.0500721102","volume":"102","author":"SC Chang","year":"2005","unstructured":"Chang SC, Momburg F, Bhutani N, Goldberg AL (2005) The ER aminopeptidase, ERAP1, trims precursors to lengths of MHC class I peptides by a \"molecular ruler\" mechanism. Proc Natl Acad Sci USA 102(47):17107\u201317112. https:\/\/doi.org\/10.1073\/pnas.0500721102","journal-title":"Proc Natl Acad Sci USA"},{"issue":"52","key":"10_CR20","doi-asserted-by":"publisher","first-page":"26709","DOI":"10.1073\/pnas.1912070116","volume":"116","author":"P Giastas","year":"2019","unstructured":"Giastas P, Mpakali A, Papakyriakou A, Lelis A, Kokkala P, Neu M, Rowland P, Liddle J, Georgiadis D, Stratikos E (2019) Mechanism for antigenic peptide selection by endoplasmic reticulum aminopeptidase 1. Proc Natl Acad Sci USA 116(52):26709\u201326716. https:\/\/doi.org\/10.1073\/pnas.1912070116","journal-title":"Proc Natl Acad Sci USA"},{"key":"10_CR21","doi-asserted-by":"publisher","first-page":"946","DOI":"10.3389\/fimmu.2017.00946","volume":"8","author":"A Papakyriakou","year":"2017","unstructured":"Papakyriakou A, Stratikos E (2017) The role of conformational dynamics in antigen trimming by intracellular aminopeptidases. Front Immunol 8:946. https:\/\/doi.org\/10.3389\/fimmu.2017.00946","journal-title":"Front Immunol"},{"issue":"2 Pt B","key":"10_CR22","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1016\/j.molimm.2015.07.010","volume":"67","author":"A Stamogiannos","year":"2015","unstructured":"Stamogiannos A, Koumantou D, Papakyriakou A, Stratikos E (2015) Effects of polymorphic variation on the mechanism of endoplasmic reticulum aminopeptidase 1. Mol Immunol 67(2 Pt B):426\u2013435. https:\/\/doi.org\/10.1016\/j.molimm.2015.07.010","journal-title":"Mol Immunol"},{"issue":"10","key":"10_CR23","doi-asserted-by":"publisher","first-page":"1546","DOI":"10.1021\/acs.biochem.6b01170","volume":"56","author":"A Stamogiannos","year":"2017","unstructured":"Stamogiannos A, Maben Z, Papakyriakou A, Mpakali A, Kokkala P, Georgiadis D, Stern LJ, Stratikos E (2017) Critical role of Interdomain interactions in the conformational change and catalytic mechanism of endoplasmic reticulum aminopeptidase 1. Biochemistry 56(10):1546\u20131558. https:\/\/doi.org\/10.1021\/acs.biochem.6b01170","journal-title":"Biochemistry"},{"issue":"2","key":"10_CR24","doi-asserted-by":"publisher","first-page":"901","DOI":"10.4049\/jimmunol.1302855","volume":"193","author":"I Evnouchidou","year":"2014","unstructured":"Evnouchidou I, Weimershaus M, Saveanu L, van Endert P (2014) ERAP1-ERAP2 dimerization increases peptide-trimming efficiency. J Immunol 193(2):901\u2013908. https:\/\/doi.org\/10.4049\/jimmunol.1302855","journal-title":"J Immunol"},{"key":"10_CR25","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.863529","volume":"13","author":"A Papakyriakou","year":"2022","unstructured":"Papakyriakou A, Mpakali A, Stratikos E (2022) Can ERAP1 and ERAP2 form functional heterodimers? A structural dynamics investigation. Front Immunol 13:863529. https:\/\/doi.org\/10.3389\/fimmu.2022.863529","journal-title":"Front Immunol"},{"issue":"2","key":"10_CR26","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1002\/wcms.1121","volume":"3","author":"R Salomon-Ferrer","year":"2013","unstructured":"Salomon-Ferrer R, Case DA, Walker RC (2013) An overview of the Amber biomolecular simulation package. WIREs Comput Mol Sci 3(2):198\u2013210. https:\/\/doi.org\/10.1002\/wcms.1121","journal-title":"WIREs Comput Mol Sci"},{"key":"10_CR27","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1007\/978-1-62703-017-5_6","volume":"924","author":"S Hug","year":"2013","unstructured":"Hug S (2013) Classical molecular dynamics in a nutshell. Methods Mol Biol 924:127\u2013152. https:\/\/doi.org\/10.1007\/978-1-62703-017-5_6","journal-title":"Methods Mol Biol"},{"key":"10_CR28","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1007\/978-1-62703-017-5_8","volume":"924","author":"L Monticelli","year":"2013","unstructured":"Monticelli L, Tieleman DP (2013) Force fields for classical molecular dynamics. Methods Mol Biol 924:197\u2013213. https:\/\/doi.org\/10.1007\/978-1-62703-017-5_8","journal-title":"Methods Mol Biol"},{"issue":"16","key":"10_CR29","doi-asserted-by":"publisher","first-page":"1668","DOI":"10.1002\/jcc.20290","volume":"26","author":"DA Case","year":"2005","unstructured":"Case DA, Cheatham TE III, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, Woods RJ (2005) The Amber biomolecular simulation programs. J Comput Chem 26(16):1668\u20131688. https:\/\/doi.org\/10.1002\/jcc.20290","journal-title":"J Comput Chem"},{"issue":"9","key":"10_CR30","doi-asserted-by":"publisher","first-page":"3878","DOI":"10.1021\/ct400314y","volume":"9","author":"R Salomon-Ferrer","year":"2013","unstructured":"Salomon-Ferrer R, Gotz AW, Poole D, Le Grand S, Walker RC (2013) Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle mesh Ewald. J Chem Theory Comput 9(9):3878\u20133888. https:\/\/doi.org\/10.1021\/ct400314y","journal-title":"J Chem Theory Comput"},{"issue":"20","key":"10_CR31","doi-asserted-by":"publisher","first-page":"6183","DOI":"10.1021\/acs.jcim.3c01153","volume":"63","author":"DA Case","year":"2023","unstructured":"Case DA, Aktulga HM, Belfon K, Cerutti DS, Cisneros GA, Cruzeiro VWD, Forouzesh N, Giese TJ, Gotz AW, Gohlke H, Izadi S, Kasavajhala K, Kaymak MC, King E, Kurtzman T, Lee TS, Li P, Liu J, Luchko T, Luo R, Manathunga M, Machado MR, Nguyen HM, O'Hearn KA, Onufriev AV, Pan F, Pantano S, Qi R, Rahnamoun A, Risheh A, Schott-Verdugo S, Shajan A, Swails J, Wang J, Wei H, Wu X, Wu Y, Zhang S, Zhao S, Zhu Q, Cheatham TE 3rd, Roe DR, Roitberg A, Simmerling C, York DM, Nagan MC, Merz KM Jr (2023) AmberTools. J Chem Inf Model 63(20):6183\u20136191. https:\/\/doi.org\/10.1021\/acs.jcim.3c01153","journal-title":"J Chem Inf Model"},{"issue":"9","key":"10_CR32","doi-asserted-by":"publisher","first-page":"1753","DOI":"10.1110\/ps.9.9.1753","volume":"9","author":"A Fiser","year":"2000","unstructured":"Fiser A, Do RK, Sali A (2000) Modeling of loops in protein structures. Protein science: a publication of the Protein Society 9(9):1753\u20131773. https:\/\/doi.org\/10.1110\/ps.9.9.1753","journal-title":"Protein science: a publication of the Protein Society"},{"issue":"1","key":"10_CR33","doi-asserted-by":"publisher","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 Model 14(1):33\u201338. https:\/\/doi.org\/10.1016\/0263-7855(96)00018-5","journal-title":"J Mol Graph Model"},{"issue":"Web Server issu","key":"10_CR34","doi-asserted-by":"publisher","first-page":"W368","DOI":"10.1093\/nar\/gki464","volume":"33","author":"JC Gordon","year":"2005","unstructured":"Gordon JC, Myers JB, Folta T, Shoja V, Heath LS, Onufriev A (2005) H++: a server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Res 33(Web Server issue):W368\u2013W371. https:\/\/doi.org\/10.1093\/nar\/gki464","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"10_CR35","doi-asserted-by":"publisher","DOI":"10.1002\/pro.5151","volume":"33","author":"A Mpakali","year":"2024","unstructured":"Mpakali A, Georgaki G, Buson A, Findlay AD, Foot JS, Mauvais FX, van Endert P, Giastas P, Hamprecht DW, Stratikos E (2024) Stabilization of the open conformation omicronf insulin-regulated aminopeptidase by a novel substrate-selective small-molecule inhibitor. Protein science: a publication of the Protein Society 33(9):e5151. https:\/\/doi.org\/10.1002\/pro.5151","journal-title":"Protein science: a publication of the Protein Society"},{"issue":"44","key":"10_CR36","doi-asserted-by":"publisher","first-page":"17966","DOI":"10.1073\/pnas.1210123109","volume":"109","author":"L Chen","year":"2012","unstructured":"Chen L, Lin YL, Peng G, Li F (2012) Structural basis for multifunctional roles of mammalian aminopeptidase N. Proc Natl Acad Sci USA 109(44):17966\u201317971. https:\/\/doi.org\/10.1073\/pnas.1210123109","journal-title":"Proc Natl Acad Sci USA"},{"issue":"4","key":"10_CR37","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1016\/j.jmb.2005.03.070","volume":"349","author":"OJ Kyrieleis","year":"2005","unstructured":"Kyrieleis OJ, Goettig P, Kiefersauer R, Huber R, Brandstetter H (2005) Crystal structures of the tricorn interacting factor F3 from Thermoplasma acidophilum, a zinc aminopeptidase in three different conformations. J Mol Biol 349(4):787\u2013800. https:\/\/doi.org\/10.1016\/j.jmb.2005.03.070","journal-title":"J Mol Biol"},{"issue":"12","key":"10_CR38","doi-asserted-by":"publisher","first-page":"1228","DOI":"10.1021\/acsptsci.2c00183","volume":"5","author":"D Georgiadis","year":"2022","unstructured":"Georgiadis D, Skoulikas N, Papakyriakou A, Stratikos E (2022) Phosphinic peptides as tool compounds for the study of pharmacologically relevant Zn-metalloproteases. ACS Pharmacol Transl Sci 5(12):1228\u20131253. https:\/\/doi.org\/10.1021\/acsptsci.2c00183","journal-title":"ACS Pharmacol Transl Sci"},{"key":"10_CR39","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2021.100443","volume":"296","author":"JP Hutchinson","year":"2021","unstructured":"Hutchinson JP, Temponeras I, Kuiper J, Cortes A, Korczynska J, Kitchen S, Stratikos E (2021) Common allotypes of ER aminopeptidase 1 have substrate-dependent and highly variable enzymatic properties. J Biol Chem 296:100443. https:\/\/doi.org\/10.1016\/j.jbc.2021.100443","journal-title":"J Biol Chem"},{"issue":"16","key":"10_CR40","doi-asserted-by":"publisher","first-page":"1623","DOI":"10.1002\/jcc.10128","volume":"23","author":"A Jakalian","year":"2002","unstructured":"Jakalian A, Jack DB, Bayly CI (2002) Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J Comput Chem 23(16):1623\u20131641. https:\/\/doi.org\/10.1002\/jcc.10128","journal-title":"J Comput Chem"},{"issue":"9","key":"10_CR41","doi-asserted-by":"publisher","first-page":"1157","DOI":"10.1002\/jcc.20035","volume":"25","author":"J Wang","year":"2004","unstructured":"Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 25(9):1157\u20131174. https:\/\/doi.org\/10.1002\/jcc.20035","journal-title":"J Comput Chem"},{"issue":"22","key":"10_CR42","doi-asserted-by":"publisher","first-page":"8262","DOI":"10.1021\/Ja00022a010","volume":"113","author":"SC Hoops","year":"1991","unstructured":"Hoops SC, Anderson KW, Merz KM (1991) Force-field Design for Metalloproteins. J Am Chem Soc 113(22):8262\u20138270. https:\/\/doi.org\/10.1021\/Ja00022a010","journal-title":"J Am Chem Soc"},{"issue":"8","key":"10_CR43","doi-asserted-by":"publisher","first-page":"3696","DOI":"10.1021\/acs.jctc.5b00255","volume":"11","author":"JA Maier","year":"2015","unstructured":"Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C (2015) ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J Chem Theory Comput 11(8):3696\u20133713. https:\/\/doi.org\/10.1021\/acs.jctc.5b00255","journal-title":"J Chem Theory Comput"},{"issue":"2","key":"10_CR44","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1063\/1.445869","volume":"79","author":"WL Jorgensen","year":"1983","unstructured":"Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79(2):926\u2013935. https:\/\/doi.org\/10.1063\/1.445869","journal-title":"J Chem Phys"},{"issue":"30","key":"10_CR45","doi-asserted-by":"publisher","first-page":"9020","DOI":"10.1021\/jp8001614","volume":"112","author":"IS Joung","year":"2008","unstructured":"Joung IS, Cheatham TE III (2008) Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J Phys Chem B 112(30):9020\u20139041. https:\/\/doi.org\/10.1021\/jp8001614","journal-title":"J Phys Chem B"},{"issue":"4","key":"10_CR46","doi-asserted-by":"publisher","first-page":"1864","DOI":"10.1021\/ct5010406","volume":"11","author":"CW Hopkins","year":"2015","unstructured":"Hopkins CW, Le Grand S, Walker RC, Roitberg AE (2015) Long-time-step molecular dynamics through hydrogen mass repartitioning. J Chem Theory Comput 11(4):1864\u20131874. https:\/\/doi.org\/10.1021\/ct5010406","journal-title":"J Chem Theory Comput"},{"issue":"9","key":"10_CR47","doi-asserted-by":"publisher","first-page":"2997","DOI":"10.1021\/ct300284c","volume":"8","author":"LC Pierce","year":"2012","unstructured":"Pierce LC, Salomon-Ferrer R, Augusto FOC, McCammon JA, Walker RC (2012) Routine access to millisecond time scale events with accelerated molecular dynamics. J Chem Theory Comput 8(9):2997\u20133002. https:\/\/doi.org\/10.1021\/ct300284c","journal-title":"J Chem Theory Comput"},{"key":"10_CR48","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1007\/978-1-4939-1465-4_12","volume":"1215","author":"PC Gedeon","year":"2015","unstructured":"Gedeon PC, Thomas JR, Madura JD (2015) Accelerated molecular dynamics and protein conformational change: a theoretical and practical guide using a membrane embedded model neurotransmitter transporter. Methods Mol Biol 1215:253\u2013287. https:\/\/doi.org\/10.1007\/978-1-4939-1465-4_12","journal-title":"Methods Mol Biol"},{"issue":"7","key":"10_CR49","doi-asserted-by":"publisher","first-page":"3084","DOI":"10.1021\/ct400341p","volume":"9","author":"DR Roe","year":"2013","unstructured":"Roe DR, Cheatham TE III (2013) PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J Chem Theory Comput 9(7):3084\u20133095. https:\/\/doi.org\/10.1021\/ct400341p","journal-title":"J Chem Theory Comput"},{"issue":"11","key":"10_CR50","doi-asserted-by":"publisher","first-page":"1575","DOI":"10.1093\/bioinformatics\/btr168","volume":"27","author":"A Bakan","year":"2011","unstructured":"Bakan A, Meireles LM, Bahar I (2011) ProDy: protein dynamics inferred from theory and experiments. Bioinformatics 27(11):1575\u20131577. https:\/\/doi.org\/10.1093\/bioinformatics\/btr168","journal-title":"Bioinformatics"},{"issue":"11","key":"10_CR51","doi-asserted-by":"publisher","DOI":"10.1063\/5.0019056","volume":"153","author":"X He","year":"2020","unstructured":"He X, Man VH, Yang W, Lee TS, Wang J (2020) A fast and high-quality charge model for the next generation general AMBER force field. J Chem Phys 153(11):114502. https:\/\/doi.org\/10.1063\/5.0019056","journal-title":"J Chem Phys"},{"issue":"1","key":"10_CR52","doi-asserted-by":"publisher","first-page":"528","DOI":"10.1021\/acs.jctc.9b00591","volume":"16","author":"C Tian","year":"2020","unstructured":"Tian C, Kasavajhala K, Belfon KAA, Raguette L, Huang H, Migues AN, Bickel J, Wang Y, Pincay J, Wu Q, Simmerling C (2020) ff19SB: amino-acid-specific protein backbone parameters trained against quantum mechanics energy surfaces in solution. J Chem Theory Comput 16(1):528\u2013552. https:\/\/doi.org\/10.1021\/acs.jctc.9b00591","journal-title":"J Chem Theory Comput"},{"issue":"21","key":"10_CR53","doi-asserted-by":"publisher","first-page":"3863","DOI":"10.1021\/jz501780a","volume":"5","author":"S Izadi","year":"2014","unstructured":"Izadi S, Anandakrishnan R, Onufriev AV (2014) Building water models: a different approach. J Phys Chem Lett 5(21):3863\u20133871. https:\/\/doi.org\/10.1021\/jz501780a","journal-title":"J Phys Chem Lett"}],"container-title":["Methods in Molecular Biology","Antigen Processing and Presentation"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-0716-5092-9_10","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T15:09:01Z","timestamp":1778598541000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-1-0716-5092-9_10"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"ISBN":["9781071650912","9781071650929"],"references-count":53,"URL":"https:\/\/doi.org\/10.1007\/978-1-0716-5092-9_10","relation":{},"ISSN":["1064-3745","1940-6029"],"issn-type":[{"value":"1064-3745","type":"print"},{"value":"1940-6029","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026]]},"assertion":[{"value":"2 January 2026","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}