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Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps.
Dixit SB, Beveridge DL, Case DA, Cheatham TE 3rd, Giudice E, Lankas F, Lavery R, Maddocks JH, Osman R, Sklenar H, Thayer KM, Varnai P. Dixit SB, et al. Among authors: beveridge dl. Biophys J. 2005 Dec;89(6):3721-40. doi: 10.1529/biophysj.105.067397. Epub 2005 Sep 16. Biophys J. 2005. PMID: 16169978 Free PMC article.
Hidden Markov models from molecular dynamics simulations on DNA.
Thayer KM, Beveridge DL. Thayer KM, et al. Among authors: beveridge dl. Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):8642-7. doi: 10.1073/pnas.132148699. Epub 2002 Jun 18. Proc Natl Acad Sci U S A. 2002. PMID: 12072566 Free PMC article.
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps.
Beveridge DL, Barreiro G, Byun KS, Case DA, Cheatham TE 3rd, Dixit SB, Giudice E, Lankas F, Lavery R, Maddocks JH, Osman R, Seibert E, Sklenar H, Stoll G, Thayer KM, Varnai P, Young MA. Beveridge DL, et al. Biophys J. 2004 Dec;87(6):3799-813. doi: 10.1529/biophysj.104.045252. Epub 2004 Aug 23. Biophys J. 2004. PMID: 15326025 Free PMC article.
Ion motions in molecular dynamics simulations on DNA.
Ponomarev SY, Thayer KM, Beveridge DL. Ponomarev SY, et al. Among authors: beveridge dl. Proc Natl Acad Sci U S A. 2004 Oct 12;101(41):14771-5. doi: 10.1073/pnas.0406435101. Epub 2004 Oct 1. Proc Natl Acad Sci U S A. 2004. PMID: 15465909 Free PMC article.
Toward a Universal Structural and Energetic Model for Prokaryotic Promoters.
Mishra A, Siwach P, Misra P, Jayaram B, Bansal M, Olson WK, Thayer KM, Beveridge DL. Mishra A, et al. Among authors: beveridge dl. Biophys J. 2018 Oct 2;115(7):1180-1189. doi: 10.1016/j.bpj.2018.08.002. Epub 2018 Aug 8. Biophys J. 2018. PMID: 30172386 Free PMC article.
84 results