Whitford PC - Search Results

1

Capturing transition paths and transition states for conformational rearrangements in the ribosome.

Noel JK, Chahine J, Leite VBP, Whitford PC. Noel JK, et al. Among authors: whitford pc. Biophys J. 2014 Dec 16;107(12):2881-2890. doi: 10.1016/j.bpj.2014.10.022. Biophys J. 2014. PMID: 25517153 Free PMC article.

2

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

Whitford PC, Noel JK, Gosavi S, Schug A, Sanbonmatsu KY, Onuchic JN. Whitford PC, et al. Proteins. 2009 May 1;75(2):430-41. doi: 10.1002/prot.22253. Proteins. 2009. PMID: 18837035 Free PMC article.

3

Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways.

Whitford PC, Geggier P, Altman RB, Blanchard SC, Onuchic JN, Sanbonmatsu KY. Whitford PC, et al. RNA. 2010 Jun;16(6):1196-204. doi: 10.1261/rna.2035410. Epub 2010 Apr 28. RNA. 2010. PMID: 20427512 Free PMC article.

4

Coordinate and time-dependent diffusion dynamics in protein folding.

Oliveira RJ, Whitford PC, Chahine J, Leite VB, Wang J. Oliveira RJ, et al. Among authors: whitford pc. Methods. 2010 Sep;52(1):91-8. doi: 10.1016/j.ymeth.2010.04.016. Epub 2010 May 11. Methods. 2010. PMID: 20438841 Review.

5

SMOG@ctbp: simplified deployment of structure-based models in GROMACS.

Noel JK, Whitford PC, Sanbonmatsu KY, Onuchic JN. Noel JK, et al. Among authors: whitford pc. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W657-61. doi: 10.1093/nar/gkq498. Epub 2010 Jun 4. Nucleic Acids Res. 2010. PMID: 20525782 Free PMC article.

6

The origin of nonmonotonic complex behavior and the effects of nonnative interactions on the diffusive properties of protein folding.

Oliveira RJ, Whitford PC, Chahine J, Wang J, Onuchic JN, Leite VB. Oliveira RJ, et al. Among authors: whitford pc. Biophys J. 2010 Jul 21;99(2):600-8. doi: 10.1016/j.bpj.2010.04.041. Biophys J. 2010. PMID: 20643080 Free PMC article.

7

Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome.

Whitford PC, Onuchic JN, Sanbonmatsu KY. Whitford PC, et al. J Am Chem Soc. 2010 Sep 29;132(38):13170-1. doi: 10.1021/ja1061399. J Am Chem Soc. 2010. PMID: 20806913 Free PMC article.

8

Excited states of ribosome translocation revealed through integrative molecular modeling.

Whitford PC, Ahmed A, Yu Y, Hennelly SP, Tama F, Spahn CM, Onuchic JN, Sanbonmatsu KY. Whitford PC, et al. Proc Natl Acad Sci U S A. 2011 Nov 22;108(47):18943-8. doi: 10.1073/pnas.1108363108. Epub 2011 Nov 11. Proc Natl Acad Sci U S A. 2011. PMID: 22080606 Free PMC article.

9

The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function.

Noel JK, Whitford PC, Onuchic JN. Noel JK, et al. Among authors: whitford pc. J Phys Chem B. 2012 Jul 26;116(29):8692-702. doi: 10.1021/jp300852d. Epub 2012 May 11. J Phys Chem B. 2012. PMID: 22536820 Free PMC article.

10

Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch.

Hayes RL, Noel JK, Mohanty U, Whitford PC, Hennelly SP, Onuchic JN, Sanbonmatsu KY. Hayes RL, et al. Among authors: whitford pc. J Am Chem Soc. 2012 Jul 25;134(29):12043-53. doi: 10.1021/ja301454u. Epub 2012 Jul 16. J Am Chem Soc. 2012. PMID: 22612276 Free PMC article.

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