HiRE-RNA

[…] scientific data. it is possible to build a set of rules providing a guideline to create or improve serious games. we present arguments gathered from our own experience (phylo, docmolecules, the hire-rna contest and pangu) as well as examples from the growing literature on scientific serious games., science has an enormous impact on society; therefore, understanding and participating […]

[…] 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, […]

[…] 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 […]

[…] 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 […]

[…] in fig. .fig. 5, the 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 […]

[…] qualitatively effects such as experimentally observed narrowing of the minor groove due to cations, but the increased detail rendered it roughly 30% slower than the implicit model., 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, […]