Deciphering the sequence-dependent unfolding pathways of an RNA pseudoknot with steered molecular dynamics

Giedroc DP, Cornish PV (2009) Virus Res 139:193–208

Article  PubMed  CAS  Google Scholar 

Staple DW, Butcher SE (2005) PLoS Biol 3:e213

Article  PubMed  PubMed Central  Google Scholar 

Dam ET, Pleij K, Draper D (1992) Biochemistry 31:11666–11676

Google Scholar 

Devi G, Zhou Y, Zhong Z, Toh DF, Chen G (2015) Wiley Interdiscip Rev RNA 6:111–128

Article  PubMed  CAS  Google Scholar 

Cao S, Giedroc DP, Chen SJ (2010) RNA 16:538–552

Article  PubMed  PubMed Central  CAS  Google Scholar 

Chen G, Chang KY, Chou MY, Bustamante C, Tinoco I Jr (2009) Proc Natl Acad Sci USA 106:12706–12711

Article  PubMed  PubMed Central  CAS  Google Scholar 

Yang L, Kaixin DF, Manchugondanahalli T, Krishna S, Zhong Z, Liu Y, Wang S, Gong Y, Chen G (2020) Biochemistry 59:4429–4438

Article  PubMed  CAS  Google Scholar 

Zhong Z, Yang L, Zhang H, Shi J, Vandana JJ, Lam DTUH, Olsthoorn RCL, Lu L, Chen G (2016) Sci Rep 6:39549

Article  PubMed  PubMed Central  CAS  Google Scholar 

Hansen TM, Reihani SN, Oddershede LB, Sørensen MA (2007) Proc Natl Acad Sci USA 104:5830–5835

Article  PubMed  PubMed Central  CAS  Google Scholar 

Chou MY, Chang KY (2010) Nucleic Acids Res 38:1676–1685

Article  PubMed  CAS  Google Scholar 

Yu CH, Noteborn MH, Pleij CW, Olsthoorn RC (2011) Nucleic Acids Res 39:8952–8959

Article  PubMed  PubMed Central  CAS  Google Scholar 

Olsthoorn RC, Reumerman R, Hilbers CW, Pleij CW, Heus HA (2010) Nucleic Acids Res 38:7665–7672

Article  PubMed  PubMed Central  CAS  Google Scholar 

Liphardt J, Napthine S, Kontos H, Brierley I (1999) J Mol Biol 288:321–335

Article  PubMed  PubMed Central  CAS  Google Scholar 

Sung D, Kang H (1998) Nucleic Acids Res 26:1369–1372

Article  PubMed  PubMed Central  CAS  Google Scholar 

Dam TEB, Verlaan PW, Pleij CW (1995) RNA 1:146–154

PubMed  PubMed Central  Google Scholar 

Lu H, Isralewitz B, Krammer A, Vogel V, Schulten K (1998) Biophys J 75:662–671

Article  PubMed  PubMed Central  CAS  Google Scholar 

Gao M, Wilmanns M, Schulten K (2002) Biophys J 83:3435–3445

Article  PubMed  PubMed Central  CAS  Google Scholar 

Lu H, Schulten K (1999) Chem Phys 247:141–153

Article  CAS  Google Scholar 

G. Hummer and A. Szabo. Proc. Natl. Acad. Sci. U S A. 2001, 98, 3658–3661.

Park S, Schulten K (2004) J Chem Phys 120:5946

Article  PubMed  CAS  Google Scholar 

Michiels PJ, Versleijen AA, Verlaan PW, Pleij CW, Hilbers CW, Heus HA (2001) J Mol Biol 310:1109–1123

Article  PubMed  CAS  Google Scholar 

Dam T, Brierley EI, Inglis S, Pleij C (1994) Nucleic Acids Res 22:2304–2310

Article  PubMed  PubMed Central  Google Scholar 

Lu XJ, Olson WK (2008) Nat Protoc 3:1213–1227

Article  PubMed  PubMed Central  CAS  Google Scholar 

Abraham MJ, Murtola T, Schulz R, Páll S, Smith JC, Hess B, Lindahl E (2015) SoftwareX 1–2:19–25

Article  Google Scholar 

Zgarbová M, Otyepka M, Šponer J, Mládek A, Banáš P, Cheatham TE III, Jurečka P (2011) J Chem Theory Comput 7:2886–2902

Article  PubMed  PubMed Central  Google Scholar 

Pérez A, Marchán I, Svozil D, Sponer J, Cheatham TE, Laughton CA, Orozco M (2007) Biophys J 92:3817–3829

Article  PubMed  PubMed Central  Google Scholar 

Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) J Comput Chem 18:1463–1472

Article  CAS  Google Scholar 

Essmann U, Perera L, Berkowitz MLT, Lee H, Pedersen LG (1995) J Chem Phys 103:8577–8593

Article  CAS  Google Scholar 

Berendsen HJC, Postma JPM, Gunsteren WFV, Dinola A, Haak JR (1984) J Chem Phys 81:3684–4369

Article  CAS  Google Scholar 

Bussi G, Donadio D, Parrinello M (2007) J Chem Phys 126:014101

Article  PubMed  Google Scholar 

Parrinello M, Rahman A (1981) J Appl Phys 52:7182–7190

Article  CAS  Google Scholar 

Bottaro S, Palma FD, Bussi G (2014) Nucleic Acids Res 42:21

Article  Google Scholar 

Gupta A, Bansal M (2016) Phys Chem Chem Phys 18:28767

Article  PubMed  CAS  Google Scholar 

Motta S, Pandini A, Fornili A, Bonati L (2021) J Chem Theory Comput 17:2080–2089

Article  PubMed  PubMed Central  CAS  Google Scholar 

Ritchie DB, Foster DA, Woodside MT (2012) Proc Natl Acad Sci USA 109:16167–16172

Article  PubMed  PubMed Central  CAS  Google Scholar 

Jarzynski C (1997) Phys Rev Lett 78:2690

Article  CAS 

Comments (0)

No login
gif