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| Hauptseite > Publikationsdatenbank > AMBER-DYES in AMBER: Implementation of fluorophore and linker parameters into AmberTools > print |
| Hauptseite > Publikationsdatenbank > AMBER-DYES in AMBER: Implementation of fluorophore and linker parameters into AmberTools > print |
| 001 | 877528 | ||
| 005 | 20230815122837.0 | ||
| 024 | 7 | _ | |a 10.1063/5.0007630 |2 doi |
| 024 | 7 | _ | |a 0021-9606 |2 ISSN |
| 024 | 7 | _ | |a 1089-7690 |2 ISSN |
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| 037 | _ | _ | |a FZJ-2020-02264 |
| 082 | _ | _ | |a 540 |
| 100 | 1 | _ | |a Schepers, Bastian |0 P:(DE-HGF)0 |b 0 |
| 245 | _ | _ | |a AMBER-DYES in AMBER: Implementation of fluorophore and linker parameters into AmberTools |
| 260 | _ | _ | |a Woodbury, NY |c 2020 |b American Institute of Physics |
| 264 | _ | 1 | |3 print |2 Crossref |b AIP Publishing |c 2020-06-14 |
| 264 | _ | 1 | |3 print |2 Crossref |b AIP Publishing |c 2020-06-14 |
| 336 | 7 | _ | |a article |2 DRIVER |
| 336 | 7 | _ | |a Output Types/Journal article |2 DataCite |
| 336 | 7 | _ | |a Journal Article |b journal |m journal |0 PUB:(DE-HGF)16 |s 1592462538_13936 |2 PUB:(DE-HGF) |
| 336 | 7 | _ | |a ARTICLE |2 BibTeX |
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| 336 | 7 | _ | |a Journal Article |0 0 |2 EndNote |
| 520 | _ | _ | |a Molecular 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. |
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| 700 | 1 | _ | |a Gohlke, Holger |0 P:(DE-Juel1)172663 |b 1 |e Corresponding author |
| 773 | 1 | 8 | |a 10.1063/5.0007630 |b AIP Publishing |d 2020-06-14 |n 22 |p 221103 |3 journal-article |2 Crossref |t The Journal of Chemical Physics |v 152 |y 2020 |x 0021-9606 |
| 773 | _ | _ | |a 10.1063/5.0007630 |g Vol. 152, no. 22, p. 221103 - |0 PERI:(DE-600)1473050-9 |n 22 |p 221103 |t The journal of chemical physics |v 152 |y 2020 |x 0021-9606 |
| 856 | 4 | _ | |y Published on 2020-06-12. Available in OpenAccess from 2021-06-12. |u https://juser.fz-juelich.de/record/877528/files/5.0007630.pdf |
| 856 | 4 | _ | |y Published on 2020-06-12. Available in OpenAccess from 2021-06-12. |u https://juser.fz-juelich.de/record/877528/files/JCP20-CM-CLMD2020-00910.pdf |
| 856 | 4 | _ | |y Published on 2020-06-12. Available in OpenAccess from 2021-06-12. |x pdfa |u https://juser.fz-juelich.de/record/877528/files/JCP20-CM-CLMD2020-00910.pdf?subformat=pdfa |
| 856 | 4 | _ | |y Published on 2020-06-12. Available in OpenAccess from 2021-06-12. |x pdfa |u https://juser.fz-juelich.de/record/877528/files/5.0007630.pdf?subformat=pdfa |
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| 999 | C | 5 | |a 10.1021/ct500869p |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1016/j.sbi.2016.11.012 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1038/s41467-020-14886-w |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1126/science.283.5408.1676 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1016/j.sbi.2012.10.008 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1073/pnas.0408164102 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1038/nmeth.2222 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1016/j.jsb.2010.09.004 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1371/journal.pone.0039492 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1021/ja105725e |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1039/c4cp01222d |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1515/zna-1949-0501 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1002/andp.19484370105 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1016/j.bpj.2015.04.038 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1073/pnas.58.2.719 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1039/c0cp02058c |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1021/jp311071y |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.3390/molecules191219269 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1073/pnas.0709567104 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1002/prot.21123 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1021/acs.jctc.5b00255 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1021/ct700301q |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1002/jcc.20291 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1021/ct200909j |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1021/ct400314y |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |2 Crossref |u I. 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). |
| 999 | C | 5 | |1 Vandrunen R. |y 1995 |2 Crossref |o Vandrunen R. 1995 |
| 999 | C | 5 | |a 10.1007/s10822-016-9977-1 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |2 Crossref |u R. 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). |
| 999 | C | 5 | |a 10.1002/jcc.20035 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1021/acs.jpcb.5b00689 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |1 Simmerling C. |y 2015 |2 Crossref |o Simmerling C. 2015 |
| 999 | C | 5 | |1 Case D. |y 2014 |2 Crossref |o Case D. 2014 |
| 999 | C | 5 | |a 10.1021/ct4010307 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1002/jcc.20820 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1016/j.bpj.2017.12.025 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1021/j100142a004 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |2 Crossref |u M. J. Frisch et al., Gaussian 16 (Gaussian, Inc., Wallingford, CT, 2016). |
| 999 | C | 5 | |2 Crossref |u I. 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). |
| 999 | C | 5 | |a 10.1063/1.464397 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1016/0010-4655(91)90105-t |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1021/acs.jpcb.6b05754 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |1 Horn H. W. |y 2005 |2 Crossref |o Horn H. W. 2005 |
| 999 | C | 5 | |a 10.1063/1.2085031 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1063/1.1683075 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1021/jz501780a |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1021/ct500569b |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1063/1.1329346 |9 -- missing cx lookup -- |2 Crossref |
| 999 | C | 5 | |a 10.1063/1.481505 |9 -- missing cx lookup -- |2 Crossref |
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