000877528 001__ 877528
000877528 005__ 20230815122837.0
000877528 0247_ $$2doi$$a10.1063/5.0007630
000877528 0247_ $$2ISSN$$a0021-9606
000877528 0247_ $$2ISSN$$a1089-7690
000877528 0247_ $$2ISSN$$a1520-9032
000877528 0247_ $$2Handle$$a2128/25090
000877528 0247_ $$2pmid$$apmid:32534525
000877528 0247_ $$2WOS$$aWOS:000541908200002
000877528 0247_ $$2altmetric$$aaltmetric:84063593
000877528 037__ $$aFZJ-2020-02264
000877528 082__ $$a540
000877528 1001_ $$0P:(DE-HGF)0$$aSchepers, Bastian$$b0
000877528 245__ $$aAMBER-DYES in AMBER: Implementation of fluorophore and linker parameters into AmberTools
000877528 260__ $$aWoodbury, NY$$bAmerican Institute of Physics$$c2020
000877528 264_1 $$2Crossref$$3print$$bAIP Publishing$$c2020-06-14
000877528 264_1 $$2Crossref$$3print$$bAIP Publishing$$c2020-06-14
000877528 3367_ $$2DRIVER$$aarticle
000877528 3367_ $$2DataCite$$aOutput Types/Journal article
000877528 3367_ $$0PUB:(DE-HGF)16$$2PUB:(DE-HGF)$$aJournal Article$$bjournal$$mjournal$$s1592462538_13936
000877528 3367_ $$2BibTeX$$aARTICLE
000877528 3367_ $$2ORCID$$aJOURNAL_ARTICLE
000877528 3367_ $$00$$2EndNote$$aJournal Article
000877528 520__ $$aMolecular dynamics (MD) simulations of explicit representations of fluorescent dyes attached via a linker to a protein allow, e.g., probing commonly used approximations for dye localization and/or orientation or modeling Förster resonance energy transfer. However, setting up and performing such MD simulations with the AMBER suite of biomolecular simulation programs has remained challenging due to the unavailability of an easy-to-use set of parameters within AMBER. Here, we adapted the AMBER-DYES parameter set derived by Graen et al. [J. Chem. Theory Comput. 10, 5505 (2014)] into “AMBER-DYES in AMBER” to generate a force field applicable within AMBER for commonly used fluorescent dyes and linkers attached to a protein. In particular, the computationally efficient graphics processing unit (GPU) implementation of the AMBER MD engine can now be exploited to overcome sampling issues of dye movements. The implementation is compatible with state-of-the-art force fields such as GAFF, GAFF2, ff99SB, ff14SB, lipid17, and GLYCAM_06j, which allows simulating post-translationally modified proteins and/or protein–ligand complexes and/or proteins in membrane environments. It is applicable with frequently used water models such as TIP3P, TIP4P, TIP4P-Ew, and OPC. For ease of use, a LEaP-based workflow was created, which allows attaching (multiple) dye/linker combinations to a protein prior to further system preparation steps. Following the parameter development described by Graen et al. [J. Chem. Theory Comput. 10, 5505 (2014)] and the adaptation steps described here, AMBER-DYES in AMBER can be extended by additional linkers and fluorescent molecules.
000877528 536__ $$0G:(DE-HGF)POF3-511$$a511 - Computational Science and Mathematical Methods (POF3-511)$$cPOF3-511$$fPOF III$$x0
000877528 536__ $$0G:(DE-Juel1)hkf7_20170501$$aForschergruppe Gohlke (hkf7_20170501)$$chkf7_20170501$$fForschergruppe Gohlke$$x1
000877528 536__ $$0G:(GEPRIS)267205415$$aDFG project 267205415 - SFB 1208: Identität und Dynamik von Membransystemen - von Molekülen bis zu zellulären Funktionen $$c267205415$$x2
000877528 588__ $$aDataset connected to CrossRef
000877528 7001_ $$0P:(DE-Juel1)172663$$aGohlke, Holger$$b1$$eCorresponding author
000877528 77318 $$2Crossref$$3journal-article$$a10.1063/5.0007630$$bAIP Publishing$$d2020-06-14$$n22$$p221103$$tThe Journal of Chemical Physics$$v152$$x0021-9606$$y2020
000877528 773__ $$0PERI:(DE-600)1473050-9$$a10.1063/5.0007630$$gVol. 152, no. 22, p. 221103 -$$n22$$p221103$$tThe journal of chemical physics$$v152$$x0021-9606$$y2020
000877528 8564_ $$uhttps://juser.fz-juelich.de/record/877528/files/5.0007630.pdf$$yPublished on 2020-06-12. Available in OpenAccess from 2021-06-12.
000877528 8564_ $$uhttps://juser.fz-juelich.de/record/877528/files/JCP20-CM-CLMD2020-00910.pdf$$yPublished on 2020-06-12. Available in OpenAccess from 2021-06-12.
000877528 8564_ $$uhttps://juser.fz-juelich.de/record/877528/files/JCP20-CM-CLMD2020-00910.pdf?subformat=pdfa$$xpdfa$$yPublished on 2020-06-12. Available in OpenAccess from 2021-06-12.
000877528 8564_ $$uhttps://juser.fz-juelich.de/record/877528/files/5.0007630.pdf?subformat=pdfa$$xpdfa$$yPublished on 2020-06-12. Available in OpenAccess from 2021-06-12.
000877528 909CO $$ooai:juser.fz-juelich.de:877528$$pdnbdelivery$$pdriver$$pVDB$$popen_access$$popenaire
000877528 9101_ $$0I:(DE-588b)5008462-8$$6P:(DE-Juel1)172663$$aForschungszentrum Jülich$$b1$$kFZJ
000877528 9131_ $$0G:(DE-HGF)POF3-511$$1G:(DE-HGF)POF3-510$$2G:(DE-HGF)POF3-500$$3G:(DE-HGF)POF3$$4G:(DE-HGF)POF$$aDE-HGF$$bKey Technologies$$lSupercomputing & Big Data$$vComputational Science and Mathematical Methods$$x0
000877528 9141_ $$y2020
000877528 915__ $$0StatID:(DE-HGF)0530$$2StatID$$aEmbargoed OpenAccess
000877528 920__ $$lyes
000877528 9201_ $$0I:(DE-Juel1)NIC-20090406$$kNIC$$lJohn von Neumann - Institut für Computing$$x0
000877528 9201_ $$0I:(DE-Juel1)JSC-20090406$$kJSC$$lJülich Supercomputing Center$$x1
000877528 9201_ $$0I:(DE-Juel1)IBI-7-20200312$$kIBI-7$$lStrukturbiochemie$$x2
000877528 980__ $$ajournal
000877528 980__ $$aVDB
000877528 980__ $$aUNRESTRICTED
000877528 980__ $$aI:(DE-Juel1)NIC-20090406
000877528 980__ $$aI:(DE-Juel1)JSC-20090406
000877528 980__ $$aI:(DE-Juel1)IBI-7-20200312
000877528 9801_ $$aFullTexts
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1021/ct500869p
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1016/j.sbi.2016.11.012
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1038/s41467-020-14886-w
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1126/science.283.5408.1676
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1016/j.sbi.2012.10.008
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1073/pnas.0408164102
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1038/nmeth.2222
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1016/j.jsb.2010.09.004
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1371/journal.pone.0039492
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1021/ja105725e
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1039/c4cp01222d
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1515/zna-1949-0501
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1002/andp.19484370105
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1016/j.bpj.2015.04.038
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1073/pnas.58.2.719
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1039/c0cp02058c
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1021/jp311071y
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.3390/molecules191219269
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1073/pnas.0709567104
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1002/prot.21123
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1021/acs.jctc.5b00255
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1021/ct700301q
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1002/jcc.20291
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1021/ct200909j
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1021/ct400314y
000877528 999C5 $$2Crossref$$uI. Y. B.S. D. A. Case, S. R. Brozell, D. S. Cerutti, T. E. Cheatham III, V. W. D. Cruzeiro, T. A. Darden et al., AMBER 2018 (University of California, San Francisco, 2018).
000877528 999C5 $$1Vandrunen R.$$2Crossref$$oVandrunen R. 1995$$y1995
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1007/s10822-016-9977-1
000877528 999C5 $$2Crossref$$uR. M. B. D. A. Case, D. S. Cerutti, T. E. Cheatham III, T. A. Darden, R. E. Duke, T. J. Giese, H. Gohlke, A. W. Goetz, N. Homeyer, S. Izadi, P. Janowski, J. Kaus, A. Kovalenko, T. S. Lee, S. LeGrand, P. Li, C. Lin, T. Lunchko, R. Luo, B. Madej, D. Mermelstein, K. M. Merz, G. Monard, H. Nguyen, H. T. Nguyen, I. Omelyan, A. Onufriev, D. R. Roe, A. Roitberg, C. Sagui, C. L. Simmerling, W. M. Botello-Smith, J. Swails, R. C. Walker, J. Wang, R. M. Wolf, X. Wu, L. Xiao, and P. A. Kollmann, Amber 2016 (University of California, San Francisco, 2016).
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1002/jcc.20035
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1021/acs.jpcb.5b00689
000877528 999C5 $$1Simmerling C.$$2Crossref$$oSimmerling C. 2015$$y2015
000877528 999C5 $$1Case D.$$2Crossref$$oCase D. 2014$$y2014
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1021/ct4010307
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1002/jcc.20820
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1016/j.bpj.2017.12.025
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1021/j100142a004
000877528 999C5 $$2Crossref$$uM. J. Frisch et al., Gaussian 16 (Gaussian, Inc., Wallingford, CT, 2016).
000877528 999C5 $$2Crossref$$uI. Y. B.S. D. A. Case, S. R. Brozell, D. S. Cerutti, T. E. Cheatham III, V. W. D. Cruzeiro, T. A. Darden et al., AMBER 2019 (University of California, San Francisco, 2019).
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1063/1.464397
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1016/0010-4655(91)90105-t
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1021/acs.jpcb.6b05754
000877528 999C5 $$1Horn H. W.$$2Crossref$$oHorn H. W. 2005$$y2005
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1063/1.2085031
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1063/1.1683075
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1021/jz501780a
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1021/ct500569b
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1063/1.1329346
000877528 999C5 $$2Crossref$$9-- missing cx lookup --$$a10.1063/1.481505