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Improving RNA secondary structure prediction with structure mapping data.
Sloma MF, Mathews DH. Sloma MF, et al. Methods Enzymol. 2015;553:91-114. doi: 10.1016/bs.mie.2014.10.053. Epub 2015 Feb 3. Methods Enzymol. 2015. PMID: 25726462
Thermodynamics of three-way multibranch loops in RNA.
Diamond JM, Turner DH, Mathews DH. Diamond JM, et al. Biochemistry. 2001 Jun 12;40(23):6971-81. doi: 10.1021/bi0029548. Biochemistry. 2001. PMID: 11389613
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.
Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH. Mathews DH, et al. Proc Natl Acad Sci U S A. 2004 May 11;101(19):7287-92. doi: 10.1073/pnas.0401799101. Epub 2004 May 3. Proc Natl Acad Sci U S A. 2004. PMID: 15123812 Free PMC article.
Secondary structure models of the 3' untranslated regions of diverse R2 RNAs.
Ruschak AM, Mathews DH, Bibillo A, Spinelli SL, Childs JL, Eickbush TH, Turner DH. Ruschak AM, et al. RNA. 2004 Jun;10(6):978-87. doi: 10.1261/rna.5216204. RNA. 2004. PMID: 15146081 Free PMC article.
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