ModeRNA: a tool for comparative modeling of RNA 3D structure

Rother, Magdalena B.; Rother, Kristian; Puton, Tomasz; Bujnicki, Janusz M.

doi:10.1093/nar/gkq1320

Cited by 252 publications

(217 citation statements)

References 69 publications

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“…If the target sequence exhibited detectable similarity to an RNA with known experimentally determined structure (as happened in the case of Puzzles 4 and 8), the Bujnicki group generated models of the whole molecule or its parts using a template-based (comparative) modeling method ModeRNA (Rother et al 2011b) or its server version (Rother et al 2011a). Remodeling of uncertain regions and modeling of RNA molecules that lacked suitable templates relied mostly on template-free folding using the coarse-grained method SimRNA ).…”

Section: Bujnicki Groupmentioning

confidence: 99%

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Miao

Adamiak

Antczak

et al. 2017

RNA

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185

209

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RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5 ′ -triphosphate, glutamine) and proteins (YbxF), and one set describes large conformational changes between ligand-free and ligand-bound states. The Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homologyderived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal a notable need for an algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.ustrasbg.fr/rnapuzzles/.

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Section: Bujnicki Groupmentioning

confidence: 99%

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Miao

Adamiak

Antczak

et al. 2017

RNA

Self Cite

185

209

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“…As a consequence, exciting developments in the field of de novo structure prediction have occurred in the last few years: computer-assisted modeling tools (Martinez et al 2008;Jossinet et al 2010); conformational space search (Parisien and Major 2008); discrete molecular dynamics (Ding et al 2008a); knowledge-based, coarse-grained refinement (Jonikas et al 2009); template-based Rother et al 2011b); and force-field-based approaches (Das et al 2010) inspired by proven proteinfolding techniques adapted to the RNA field (for review, see Rother et al 2011a). All these new approaches are pushing the limits of automatic RNA structure prediction from short sequences of a few nucleotides to medium-sized molecules with several dozens.…”

Section: Introductionmentioning

confidence: 99%

RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

Cruz¹,

Blanchet²,

Boniecki³

et al. 2012

RNA

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274

301

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We report the results of a first, collective, blind experiment in RNA three-dimensional (3D) structure prediction, encompassing three prediction puzzles. The goals are to assess the leading edge of RNA structure prediction techniques; compare existing methods and tools; and evaluate their relative strengths, weaknesses, and limitations in terms of sequence length and structural complexity. The results should give potential users insight into the suitability of available methods for different applications and facilitate efforts in the RNA structure prediction community in ongoing efforts to improve prediction tools. We also report the creation of an automated evaluation pipeline to facilitate the analysis of future RNA structure prediction exercises.

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“…Recently, several models have been developed for the prediction for RNA structures (Michel and Westhof 1990;Tan et al 2006;Das and Baker 2007;Shapiro et al 2007;Ding et al 2008;Parisien and Major 2008;Rother et al 2011;Westhof et al 2011). These models are good at predicting some structures at high-accuracy resolution.…”

Section: Structures Of the Dimersmentioning

confidence: 99%

Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal

Cao¹,

Chen²

2011

RNA

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We develop a statistical mechanical model to predict the structure and folding stability of the RNA/RNA kissing-loop complex. One of the key ingredients of the theory is the conformational entropy for the RNA/RNA kissing complex. We employ the recently developed virtual bond-based RNA folding model (Vfold model) to evaluate the entropy parameters for the different types of kissing loops. A benchmark test against experiments suggests that the entropy calculation is reliable. As an application of the model, we apply the model to investigate the structure and folding thermodynamics for the kissing complex of the HIV-1 dimerization initiation signal. With the physics-based energetic parameters, we compute the free energy landscape for the HIV-1 dimer. From the energy landscape, we identify two minimal free energy structures, which correspond to the kissing-loop dimer and the extended-duplex dimer, respectively. The results support the two-step dimerization process for the HIV-1 replication cycle. Furthermore, based on the Vfold model and energy minimization, the theory can predict the native structure as well as the local minima in the free energy landscape. The root-mean-square deviations (RMSDs) for the predicted kissing-loop dimer and extended-duplex dimer are~3.0 Å . The method developed here provides a new method to study the RNA/RNA kissing complex.

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ModeRNA: a tool for comparative modeling of RNA 3D structure

Cited by 252 publications

References 69 publications

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal

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