Mathews DH - Search Results

1

Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA.

Aytenfisu AH, Spasic A, Seetin MG, Serafini J, Mathews DH. Aytenfisu AH, et al. Among authors: mathews dh. J Chem Theory Comput. 2014 Mar 11;10(3):1292-1301. doi: 10.1021/ct400861g. Epub 2014 Jan 22. J Chem Theory Comput. 2014. PMID: 24803859 Free PMC article.

2

Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization.

Mathews DH. Mathews DH. RNA. 2004 Aug;10(8):1178-90. doi: 10.1261/rna.7650904. RNA. 2004. PMID: 15272118 Free PMC article.

3

Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pair.

Mathews DH, Case DA. Mathews DH, et al. J Mol Biol. 2006 Apr 14;357(5):1683-93. doi: 10.1016/j.jmb.2006.01.054. Epub 2006 Feb 3. J Mol Biol. 2006. PMID: 16487974

4

Prediction of RNA secondary structure by free energy minimization.

Mathews DH, Turner DH. Mathews DH, et al. Curr Opin Struct Biol. 2006 Jun;16(3):270-8. doi: 10.1016/j.sbi.2006.05.010. Epub 2006 May 19. Curr Opin Struct Biol. 2006. PMID: 16713706 Review.

5

Interpreting oligonucleotide microarray data to determine RNA secondary structure: application to the 3' end of Bombyx mori R2 RNA.

Duan S, Mathews DH, Turner DH. Duan S, et al. Among authors: mathews dh. Biochemistry. 2006 Aug 15;45(32):9819-32. doi: 10.1021/bi052618x. Biochemistry. 2006. PMID: 16893182

6

A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation.

Lu ZJ, Turner DH, Mathews DH. Lu ZJ, et al. Among authors: mathews dh. Nucleic Acids Res. 2006;34(17):4912-24. doi: 10.1093/nar/gkl472. Epub 2006 Sep 18. Nucleic Acids Res. 2006. PMID: 16982646 Free PMC article.

7

Predicting helical coaxial stacking in RNA multibranch loops.

Tyagi R, Mathews DH. Tyagi R, et al. Among authors: mathews dh. RNA. 2007 Jul;13(7):939-51. doi: 10.1261/rna.305307. Epub 2007 May 16. RNA. 2007. PMID: 17507661 Free PMC article.

8

NMR reveals the absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA.

Shankar N, Xia T, Kennedy SD, Krugh TR, Mathews DH, Turner DH. Shankar N, et al. Among authors: mathews dh. Biochemistry. 2007 Nov 6;46(44):12665-78. doi: 10.1021/bi700802s. Epub 2007 Oct 11. Biochemistry. 2007. PMID: 17929882

9

RNA secondary structure prediction.

Mathews DH, Turner DH, Zuker M. Mathews DH, et al. Curr Protoc Nucleic Acid Chem. 2007 Mar;Chapter 11:Unit 11.2. doi: 10.1002/0471142700.nc1102s28. Curr Protoc Nucleic Acid Chem. 2007. PMID: 18428968 Free PMC article.

10

NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon.

Hart JM, Kennedy SD, Mathews DH, Turner DH. Hart JM, et al. Among authors: mathews dh. J Am Chem Soc. 2008 Aug 6;130(31):10233-9. doi: 10.1021/ja8026696. Epub 2008 Jul 10. J Am Chem Soc. 2008. PMID: 18613678 Free PMC article.

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