Silva DA - Search Results

1

Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue.

Da LT, Pardo-Avila F, Xu L, Silva DA, Zhang L, Gao X, Wang D, Huang X. Da LT, et al. Among authors: silva da. Nat Commun. 2016 Apr 19;7:11244. doi: 10.1038/ncomms11244. Nat Commun. 2016. PMID: 27091704 Free PMC article.

2

Simulating the T-jump-triggered unfolding dynamics of trpzip2 peptide and its time-resolved IR and two-dimensional IR signals using the Markov state model approach.

Zhuang W, Cui RZ, Silva DA, Huang X. Zhuang W, et al. Among authors: silva da. J Phys Chem B. 2011 May 12;115(18):5415-24. doi: 10.1021/jp109592b. Epub 2011 Mar 9. J Phys Chem B. 2011. PMID: 21388153

3

A role for both conformational selection and induced fit in ligand binding by the LAO protein.

Silva DA, Bowman GR, Sosa-Peinado A, Huang X. Silva DA, et al. PLoS Comput Biol. 2011 May;7(5):e1002054. doi: 10.1371/journal.pcbi.1002054. Epub 2011 May 26. PLoS Comput Biol. 2011. PMID: 21637799 Free PMC article.

4

Initiation complex structure and promoter proofreading.

Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD. Liu X, et al. Among authors: silva da. Science. 2011 Jul 29;333(6042):633-7. doi: 10.1126/science.1206629. Science. 2011. PMID: 21798951 Free PMC article.

5

Monitoring and inhibition of insulin fibrillation by a small organic fluorogen with aggregation-induced emission characteristics.

Hong Y, Meng L, Chen S, Leung CW, Da LT, Faisal M, Silva DA, Liu J, Lam JW, Huang X, Tang BZ. Hong Y, et al. Among authors: silva da, da lt. J Am Chem Soc. 2012 Jan 25;134(3):1680-9. doi: 10.1021/ja208720a. Epub 2012 Jan 10. J Am Chem Soc. 2012. PMID: 22191699

6

Force field development for cofactors in the photosystem II.

Zhang L, Silva DA, Yan Y, Huang X. Zhang L, et al. Among authors: silva da. J Comput Chem. 2012 Sep 30;33(25):1969-80. doi: 10.1002/jcc.23016. Epub 2012 Jun 8. J Comput Chem. 2012. PMID: 22685077

7

Hierarchical Nyström methods for constructing Markov state models for conformational dynamics.

Yao Y, Cui RZ, Bowman GR, Silva DA, Sun J, Huang X. Yao Y, et al. Among authors: silva da. J Chem Phys. 2013 May 7;138(17):174106. doi: 10.1063/1.4802007. J Chem Phys. 2013. PMID: 23656113

8

Application of Markov State Models to simulate long timescale dynamics of biological macromolecules.

Da LT, Sheong FK, Silva DA, Huang X. Da LT, et al. Among authors: silva da. Adv Exp Med Biol. 2014;805:29-66. doi: 10.1007/978-3-319-02970-2_2. Adv Exp Med Biol. 2014. PMID: 24446356

9

Millisecond dynamics of RNA polymerase II translocation at atomic resolution.

Silva DA, Weiss DR, Pardo Avila F, Da LT, Levitt M, Wang D, Huang X. Silva DA, et al. Among authors: da lt. Proc Natl Acad Sci U S A. 2014 May 27;111(21):7665-70. doi: 10.1073/pnas.1315751111. Epub 2014 Apr 21. Proc Natl Acad Sci U S A. 2014. PMID: 24753580 Free PMC article.

10

Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centre.

Zhang L, Silva DA, Zhang H, Yue A, Yan Y, Huang X. Zhang L, et al. Among authors: silva da. Nat Commun. 2014 Jun 23;5:4170. doi: 10.1038/ncomms5170. Nat Commun. 2014. PMID: 24954746 Free PMC article.

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