Journal Article

RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures

Osowiecki, Maciej, Adamiak, Ryszard W., Popenda, Mariusz, Zok, Tomasz, Szachniuk, Marta, Antczak, Maciej

2018

Overview

Background Computational RNA 3D structure prediction and modeling are rising as complementary approaches to high-resolution experimental techniques for structure determination. They often apply to substitute or complement them. Recently, researchers’ interests have directed towards in silico methods to fit, remodel and refine RNA tertiary structure models. Their power lies in a problem-specific exploration of RNA conformational space and efficient optimization procedures. The aim is to improve the accuracy of models obtained either computationally or experimentally. Results Here, we present RNAfitme, a versatile webserver tool for remodeling of nucleobase- and nucleoside residue conformations in the fixed-backbone RNA 3D structures. Our approach makes use of dedicated libraries that define RNA conformational space. They have been built upon torsional angle characteristics of PDB-deposited RNA structures. RNAfitme can be applied to reconstruct full-atom model of RNA from its backbone; remodel user-selected nucleobase/nucleoside residues in a given RNA structure; predict RNA 3D structure based on the sequence and the template of a homologous molecule of the same size; refine RNA 3D model by reducing steric clashes indicated during structure quality assessment. RNAfitme is a publicly available tool with an intuitive interface. It is freely accessible at http://rnafitme.cs.put.poznan.pl/ Conclusions RNAfitme has been applied in various RNA 3D remodeling scenarios for several types of input data. Computational experiments proved its efficiency, accuracy, and usefulness in the processing of RNAs of any size. Fidelity of RNAfitme predictions has been thoroughly tested for RNA 3D structures determined experimentally and modeled in silico.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: 3D structure refinement / Acids / Algorithms / Automation / Backbone / Base Sequence / Bioinformatics / Biomedical and Life Sciences / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Computer applications / Conformation / Glutamine - chemistry / Homology / Internet / Libraries / Life Sciences / Mathematical models / Methods / Microarrays / Model accuracy / Models, Molecular / Molecular modeling / Nucleic Acid Conformation / Nucleoside modeling / Nucleosides / Nucleosides - genetics / Nucleotide Motifs / Nucleotide sequence / Phosphates / Protein structure / Quality assessment / Quality control / Ribonucleic acid / RNA / RNA - chemistry / RNA - genetics / RNA 3D structure / RNA, Transfer - chemistry / RNA, Transfer - genetics / Sequence Analysis, RNA / Software / Structural analysis / Tertiary structure / Three dimensional models / Transfer RNA / Web applications