RNA and protein 3D structure modeling: similarities and differences

Abstract

In analogy to proteins, the function of RNA depends on its structure and dynamics, which are encoded in the linear sequence. While there are numerous methods for computational prediction of protein 3D structure from sequence, there have been very few such methods for RNA. This review discusses template-based and template-free approaches for macromolecular structure prediction, with special emphasis on comparison between the already tried-and-tested methods for protein structure modeling and the very recently developed “protein-like” modeling methods for RNA. We highlight analogies between many successful methods for modeling of these two types of biological macromolecules and argue that RNA 3D structure can be modeled using “protein-like” methodology. We also highlight the areas where the differences between RNA and proteins require the development of RNA-specific solutions.FigureApproaches for predicting RNA structure. Top: Template-free modeling. Bottom: Template-based modeling

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

“…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.…”

RNA Folding: Structure Prediction, Folding Kinetics and Ion Electrostatics

“…In the following, we will focus on the RNA tertiary structure prediction methods which can be classified into three types: knowledge-based structure modelling, physics-based structure modelling, and knowledge/physics-hybridized structure modelling; see Table 11.1 for a summary on the algorithms for RNA tertiary structure prediction . Other reviews are also available [74][75][76][77][78][79].…”

“…Homology-based modelling can be used to predict any RNA molecules no matter how large or small, as long as the user can find a template and an effective alignment between the template and the target [14,15,79]. So this method is also called template-based modelling.…”

“…Although the PDB/NDB database covers many important families, it may be difficult to find a proper template RNA for a particular target. In addition, creating an accurate and biologically relevant targettemplate sequence alignment is also a critical issue [79,80].…”

Modelling and Development of Electrical Aptasensors: A Short Review

“…For the current state of art, they have to be meant as useful complements to traditional X-ray and NMR methods since their predictive capability is not complete. However, the strong activity in this field gives reason to hope for increasingly efficient results [47][48][49].…”