The Multiscale Ernwin/SPQR RNA Structure Prediction Pipeline.
Methods Mol Biol
; 2726: 377-399, 2024.
Article
en En
| MEDLINE
| ID: mdl-38780739
ABSTRACT
Aside from the well-known role in protein synthesis, RNA can perform catalytic, regulatory, and other essential biological functions which are determined by its three-dimensional structure. In this regard, a great effort has been made during the past decade to develop computational tools for the prediction of the structure of RNAs from the knowledge of their sequence, incorporating experimental data to refine or guide the modeling process. Nevertheless, this task can become exceptionally challenging when dealing with long noncoding RNAs, constituted by more than 200 nucleotides, due to their large size and the specific interactions involved. In this chapter, we describe a multiscale approach to predict such structures, incorporating SAXS experimental data into a hierarchical procedure which couples two coarse-grained representations Ernwin, a helix-based approach, which deals with the global arrangement of secondary structure elements, and SPQR, a nucleotide-centered coarse-grained model, which corrects and refines the structures predicted at the coarser level.We describe the methodology through its application on the Braveheart long noncoding RNA, starting from the SAXS and secondary structure data to propose a refined, all-atom structure.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Difracción de Rayos X
/
Dispersión del Ángulo Pequeño
/
ARN Largo no Codificante
/
Conformación de Ácido Nucleico
Idioma:
En
Revista:
Methods Mol Biol
Asunto de la revista:
BIOLOGIA MOLECULAR
Año:
2024
Tipo del documento:
Article
País de afiliación:
Austria
Pais de publicación:
Estados Unidos