"11"^^ . . "9" . . "Otyepka, Michal" . "Computer Folding of RNA Tetraloops? Are We There Yet?"@en . "1"^^ . "4" . . "RIV/00216224:14740/13:00068733!RIV14-MSM-14740___" . . . "10.1021/ct301086z" . . "MOLECULAR-DYNAMICS SIMULATIONS; SARCIN RICIN LOOP; FORCE-FIELD; RIBOSOMAL-RNA; ANGSTROM RESOLUTION; CRYSTAL-STRUCTURE; ENERGY LANDSCAPE; NUCLEIC-ACIDS; DNA HAIRPIN; TERTIARY INTERACTIONS"@en . . . "Best, Robert B." . "Ban\u00E1\u0161, Pavel" . . . "Journal of Chemical Theory and Computation" . . "US - Spojen\u00E9 st\u00E1ty americk\u00E9" . "14740" . . . . "Kuhrova, Petra" . "Computer Folding of RNA Tetraloops? Are We There Yet?" . . . . . "1549-9618" . . . "Computer Folding of RNA Tetraloops? Are We There Yet?"@en . "000317438100025" . "[25C3A2F6755E]" . . . "RNA hairpin loops represent important RNA motifs with indispensable biological functions in RNA folding and tertiary interactions, with the 5'-UNCG-3' and 5'-GNRA-3' families being the most abundant. Molecular dynamics simulations represent a powerful method to investigate the structure, folding, and function of these tetraloops (TLs), but previous AMBER force fields were unable to maintain even the native structure of small TL RNAs. Here, we have used Replica Exchange Molecular Dynamics (REMD) with our recent reparameterization of AMBER RNA force field to study the folding of RNA hairpins containing representatives UNCG and GNRA TLs. We find that in each case, we are able to reach conformations within 2 A of the native structure, in contrast to results with earlier force fields." . "\u0160poner, Ji\u0159\u00ED" . . . "I, P(ED1.1.00/02.0068), P(ED2.1.00/03.0058), P(EE2.3.20.0017), P(EE2.3.20.0058), P(GAP208/12/1878), P(GBP208/12/G016), P(GBP305/12/G034), P(GPP301/11/P558)" . . "66583" . . . . "5"^^ . "RNA hairpin loops represent important RNA motifs with indispensable biological functions in RNA folding and tertiary interactions, with the 5'-UNCG-3' and 5'-GNRA-3' families being the most abundant. Molecular dynamics simulations represent a powerful method to investigate the structure, folding, and function of these tetraloops (TLs), but previous AMBER force fields were unable to maintain even the native structure of small TL RNAs. Here, we have used Replica Exchange Molecular Dynamics (REMD) with our recent reparameterization of AMBER RNA force field to study the folding of RNA hairpins containing representatives UNCG and GNRA TLs. We find that in each case, we are able to reach conformations within 2 A of the native structure, in contrast to results with earlier force fields."@en . . . "Computer Folding of RNA Tetraloops? Are We There Yet?" . . "http://pubs.acs.org/doi/pdf/10.1021/ct301086z" . "RIV/00216224:14740/13:00068733" .