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RNA Secondary Structure Prediction.
Mathews DH, Turner DH, Watson RM. Mathews DH, et al. Curr Protoc Nucleic Acid Chem. 2016 Dec 1;67:11.2.1-11.2.19. doi: 10.1002/cpnc.19. Curr Protoc Nucleic Acid Chem. 2016. PMID: 27911493
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding.
Walter AE, Turner DH, Kim J, Lyttle MH, Müller P, Mathews DH, Zuker M. Walter AE, et al. Among authors: mathews dh. Proc Natl Acad Sci U S A. 1994 Sep 27;91(20):9218-22. doi: 10.1073/pnas.91.20.9218. Proc Natl Acad Sci U S A. 1994. PMID: 7524072 Free PMC article.
Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element.
Mathews DH, Banerjee AR, Luan DD, Eickbush TH, Turner DH. Mathews DH, et al. RNA. 1997 Jan;3(1):1-16. RNA. 1997. PMID: 8990394 Free PMC article.
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.
Mathews DH, Sabina J, Zuker M, Turner DH. Mathews DH, et al. J Mol Biol. 1999 May 21;288(5):911-40. doi: 10.1006/jmbi.1999.2700. J Mol Biol. 1999. PMID: 10329189
Predicting oligonucleotide affinity to nucleic acid targets.
Mathews DH, Burkard ME, Freier SM, Wyatt JR, Turner DH. Mathews DH, et al. RNA. 1999 Nov;5(11):1458-69. doi: 10.1017/s1355838299991148. RNA. 1999. PMID: 10580474 Free PMC article.
Thermodynamics of three-way multibranch loops in RNA.
Diamond JM, Turner DH, Mathews DH. Diamond JM, et al. Among authors: mathews dh. Biochemistry. 2001 Jun 12;40(23):6971-81. doi: 10.1021/bi0029548. Biochemistry. 2001. PMID: 11389613
Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops.
Mathews DH, Turner DH. Mathews DH, et al. Biochemistry. 2002 Jan 22;41(3):869-80. doi: 10.1021/bi011441d. Biochemistry. 2002. PMID: 11790109
Dynalign: an algorithm for finding the secondary structure common to two RNA sequences.
Mathews DH, Turner DH. Mathews DH, et al. J Mol Biol. 2002 Mar 22;317(2):191-203. doi: 10.1006/jmbi.2001.5351. J Mol Biol. 2002. PMID: 11902836
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. Among authors: mathews dh. RNA. 2004 Jun;10(6):978-87. doi: 10.1261/rna.5216204. RNA. 2004. PMID: 15146081 Free PMC article.
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