HiRE-RNA

[…] nd hydrogen-bond interactions between bases. In addition, there is an explicit correction for the entropy of loop formation because it was found to be underestimated by this type of CG representation.HiRe-RNA− is a high-resolution CG model in which nucleotides containing purines and pyrimidines are modeled using seven and six beads, respectively: two corresponding to the phosphate group, three to […]

[…] al. derives its parameters from nearest neighbor energies and experimentally determined structures. TOPRNA captures effects of secondary structure constraints on loop conformations and free energies. HiRE-RNA depicts six-seven pseudoatoms per nucleotide with five pseudoatoms along the backbone. SimRNA, Bernauer et al., as well as the previous generation and current RACER model studied, all represe […]

[…] rams have been developed to assist RNA 3D structure prediction, including YAMMP [], NAB [], ERNA-3D [], MANIP [], S2S [], FARNA [], MC-Fold/MC-Sym [], RNA2D3D [], iFoldRNA [, ], NAST [], Assemble [], HiRE-RNA [], FARFAR [], RNABuilder [], ModeRNA [], OxRNA [], 3dRNA [], a coarse-grained model that includes salt effect [], our pk3D [], etc. However, this is not a complete list due to the rapid deve […]

[…] C3′, respectively. iFoldRNA (Sharma et al. ) and Vfold (Cao and Chen ; Shi et al. ) represent RNA by three pseudo-atoms per residue. Ren (Xia et al. , ) uses 5-bead to represent each nucleotide, and HiRE-RNA (Pasquali and Derreumaux ) uses six or seven pseudo-atoms for purine and pyrimidine residues, respectively. Coarse-grained systems are usually modeled with knowledge-based potentials that are […]

[…] own in Fig. .Fig. 5The coarse-grained DNA model from the Ouldridge group, which uses Morse-like potentials to reproduce base pairing and stacking with base-pair-type specific parameters [, ], and the HiRe-RNA model from the Derreumaux group [, , ], which uses Gaussian-type multibody terms to account for base pairing, can also fold nucleic acid molecules. However, both of these contain more interac […]

[…] The recent HiRE-RNA model by Pasquali and Derreumaux is a physics-based model for RNA folding, similar to the OPEP model for proteins. The model uses one bead for the phosphate, four beads for the sugar, and one […]