Dirks RM - Search Results

1

Biomolecular simulation: a computational microscope for molecular biology.

Dror RO, Dirks RM, Grossman JP, Xu H, Shaw DE. Dror RO, et al. Among authors: dirks rm. Annu Rev Biophys. 2012;41:429-52. doi: 10.1146/annurev-biophys-042910-155245. Annu Rev Biophys. 2012. PMID: 22577825 Review.

2

Evaluating the effects of cutoffs and treatment of long-range electrostatics in protein folding simulations.

Piana S, Lindorff-Larsen K, Dirks RM, Salmon JK, Dror RO, Shaw DE. Piana S, et al. Among authors: dirks rm. PLoS One. 2012;7(6):e39918. doi: 10.1371/journal.pone.0039918. Epub 2012 Jun 29. PLoS One. 2012. PMID: 22768169 Free PMC article.

3

RNA force field with accuracy comparable to state-of-the-art protein force fields.

Tan D, Piana S, Dirks RM, Shaw DE. Tan D, et al. Among authors: dirks rm. Proc Natl Acad Sci U S A. 2018 Feb 13;115(7):E1346-E1355. doi: 10.1073/pnas.1713027115. Epub 2018 Jan 29. Proc Natl Acad Sci U S A. 2018. PMID: 29378935 Free PMC article.

4

The u-series: A separable decomposition for electrostatics computation with improved accuracy.

Predescu C, Lerer AK, Lippert RA, Towles B, Grossman JP, Dirks RM, Shaw DE. Predescu C, et al. Among authors: dirks rm. J Chem Phys. 2020 Feb 28;152(8):084113. doi: 10.1063/1.5129393. J Chem Phys. 2020. PMID: 32113352

5

Improving Sampling by Exchanging Hamiltonians with Efficiently Configured Nonequilibrium Simulations.

Dirks RM, Xu H, Shaw DE. Dirks RM, et al. J Chem Theory Comput. 2012 Jan 10;8(1):162-71. doi: 10.1021/ct200464v. Epub 2011 Dec 13. J Chem Theory Comput. 2012. PMID: 26592879

6

Triggered amplification by hybridization chain reaction.

Dirks RM, Pierce NA. Dirks RM, et al. Proc Natl Acad Sci U S A. 2004 Oct 26;101(43):15275-8. doi: 10.1073/pnas.0407024101. Epub 2004 Oct 18. Proc Natl Acad Sci U S A. 2004. PMID: 15492210 Free PMC article.

7

Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering.

Wolfe BR, Porubsky NJ, Zadeh JN, Dirks RM, Pierce NA. Wolfe BR, et al. Among authors: dirks rm. J Am Chem Soc. 2017 Mar 1;139(8):3134-3144. doi: 10.1021/jacs.6b12693. Epub 2017 Feb 13. J Am Chem Soc. 2017. PMID: 28191938 Free article.

8

Selective cell death mediated by small conditional RNAs.

Venkataraman S, Dirks RM, Ueda CT, Pierce NA. Venkataraman S, et al. Among authors: dirks rm. Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16777-82. doi: 10.1073/pnas.1006377107. Epub 2010 Sep 7. Proc Natl Acad Sci U S A. 2010. PMID: 20823260 Free PMC article. Retracted.

9

An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots.

Dirks RM, Pierce NA. Dirks RM, et al. J Comput Chem. 2004 Jul 30;25(10):1295-304. doi: 10.1002/jcc.20057. J Comput Chem. 2004. PMID: 15139042

10

An autonomous polymerization motor powered by DNA hybridization.

Venkataraman S, Dirks RM, Rothemund PW, Winfree E, Pierce NA. Venkataraman S, et al. Among authors: dirks rm. Nat Nanotechnol. 2007 Aug;2(8):490-4. doi: 10.1038/nnano.2007.225. Epub 2007 Jul 29. Nat Nanotechnol. 2007. PMID: 18654346

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