Three-dimensional structures of RNA obtained by means of knowledge-based interaction potentials

Pliego-Pastrana, Patricia; Carbajal-Tinoco, Mauricio D.

doi:10.1103/physreve.81.041914

Cited by 8 publications

(6 citation statements)

References 19 publications

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“…For instance, one could use different nucleotide representations to generate potentials based on known physical interactions like nucleic acid base-pairing and stacking (compare refs. [10-12,25-27]), or from inter-atomic distances [24] or torsional angles [28], or a combination of the above [29]. Recently a coarse-grained potential was developed for RNA using parameterized bonded and non-bonded terms like those in traditional physics-based potentials [14].…”

Section: Potential Energy Functionmentioning

confidence: 99%

Modeling nucleic acids

Sim

Mináry

Levitt

2012

Current Opinion in Structural Biology

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Section: Potential Energy Functionmentioning

confidence: 99%

Modeling nucleic acids

Sim

Mináry

Levitt

2012

Current Opinion in Structural Biology

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“…Beyond the one-bead models [17][18][19][20], a number of coarse-grained models with higher resolution have been developed, such as three-bead [21,24], five-bead [27] and six to seven-bead model [28].…”

Section: Three-bead Coarse-grained Modelmentioning

confidence: 99%

RNA Folding: Structure Prediction, Folding Kinetics and Ion Electrostatics

Tan

Zhang

Shi

et al. 2014

Advances in Experimental Medicine and Biology

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Beyond the "traditional" functions such as gene storage, transport and protein synthesis, recent discoveries reveal that RNAs have important "new" biological functions including the RNA silence and gene regulation of riboswitch. Such functions of noncoding RNAs are strongly coupled to the RNA structures and proper structure change, which naturally leads to the RNA folding problem including structure prediction and folding kinetics. Due to the polyanionic nature of RNAs, RNA folding structure, stability and kinetics are strongly coupled to the ion condition of solution. The main focus of this chapter is to review the recent progress in the three major aspects in RNA folding problem: structure prediction, folding kinetics and ion electrostatics. This chapter will introduce both the recent experimental and theoretical progress, while emphasize the theoretical modelling on the three aspects in RNA folding.

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“…Again inclusion of secondary structure data and some tertiary contacts is required to achieve reasonable prediction accuracy. 25 Several other coarse-grained models of RNA have been developed [26][27][28] and have been combined with MD search techniques to model the 3D structure of large RNA molecules.…”

Section: Computational Approaches For Structure Prediction Of Rnamentioning

confidence: 99%

Theoretical studies of nucleic acids folding

Kara

Zacharias²

2013

WIREs Comput Mol Sci

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The mechanism of how RNA and DNA molecules fold into defined threedimensional (3D) structures is still not well understood. Molecular simulation approaches are increasingly being used to study structure formation processes of nucleic acids and to understand the driving forces for folding. It is possible to use molecular dynamics (MD) simulations based on a classical force field to follow the dynamics of nucleic acids at atomic resolution and high time resolution and including surrounding solvent molecules and ions explicitly. Recent studies indicate that it is possible to investigate folding of small motifs such as hairpin structures using MD simulations. However, this approach is still limited by the currently accessible time scales and force field accuracy. Advanced sampling methods such as the replica-exchange MD (REMD) approach allow significant enhancement of conformational sampling of nucleic acids and could help to systematically study structure formation processes and to refine force fields. In case of large RNAs or RNA containing macromolecular structures, coarse-grained representations can help to overcome current computational limitations. In combination with experimentally derived constraints and predicted secondary structure, several approaches have been developed to fold RNA molecules into possible 3D structures. Such structural model can often be helpful to plan experiments or to interpret experimental results. C 2013 John Wiley & Sons, Ltd.

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Three-dimensional structures of RNA obtained by means of knowledge-based interaction potentials

Cited by 8 publications

References 19 publications

Modeling nucleic acids

Modeling nucleic acids

RNA Folding: Structure Prediction, Folding Kinetics and Ion Electrostatics

Theoretical studies of nucleic acids folding

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