Methods in molecular biology (Clifton, N.J.)
Jan 1, 2025
Machine learning algorithms, and in particular deep learning approaches, have recently garnered attention in the field of molecular biology due to remarkable results. In this chapter, we describe machine learning approaches specifically developed for...
Bioinformatics (Oxford, England)
Nov 28, 2024
MOTIVATION: RNA is implicated in numerous aberrant cellular functions and disease progressions, highlighting the crucial importance of RNA-targeted drugs. To accelerate the discovery of such drugs, it is essential to develop an effective computationa...
Briefings in bioinformatics
Sep 23, 2024
RNA 2'-O-methylation (Nm) is a crucial post-transcriptional modification with significant biological implications. However, experimental identification of Nm sites is challenging and resource-intensive. While multiple computational tools have been de...
Nucleic acids research
Jul 22, 2024
Accurate RNA structure models are crucial for designing small molecule ligands that modulate their functions. This study assesses six standalone RNA 3D structure prediction methods-DeepFoldRNA, RhoFold, BRiQ, FARFAR2, SimRNA and Vfold2, excluding web...
Briefings in bioinformatics
May 23, 2024
Around 50 years ago, molecular biology opened the path to understand changes in forms, adaptations, complexity, or the basis of human diseases through myriads of reports on gene birth, gene duplication, gene expression regulation, and splicing regula...
Briefings in bioinformatics
May 23, 2024
MOTIVATION: Coding and noncoding RNA molecules participate in many important biological processes. Noncoding RNAs fold into well-defined secondary structures to exert their functions. However, the computational prediction of the secondary structure f...
The Journal of chemical physics
May 7, 2024
Several enhanced sampling techniques rely on the definition of collective variables to effectively explore free energy landscapes. The existing variables that describe the progression along a reactive pathway offer an elegant solution but face a numb...
Bioinformatics (Oxford, England)
Mar 29, 2024
MOTIVATION: The diverse structures and functions inherent in RNAs present a wealth of potential drug targets. Some small molecules are anticipated to serve as leading compounds, providing guidance for the development of novel RNA-targeted therapeutic...
Bioinformatics (Oxford, England)
Feb 1, 2024
MOTIVATION: Accurate prediction of RNA subcellular localization plays an important role in understanding cellular processes and functions. Although post-transcriptional processes are governed by trans-acting RNA binding proteins (RBPs) through intera...
Nucleic acids research
Jan 11, 2024
Compared with proteins, DNA and RNA are more difficult languages to interpret because four-letter coded DNA/RNA sequences have less information content than 20-letter coded protein sequences. While BERT (Bidirectional Encoder Representations from Tra...