new method
Posts tagged “new method”.
Automated lineage designation from viral genomic data
This study describes an automated framework for lineage designation from phylogenetic and genomic data, designed to scale to very large viral datasets while remaining consistent and interpretable.
RNA-protein complex refinement using AI modeling and docking
This article explains a workflow for refining protein-RNA complexes by combining AI-based structural models with flexible docking and enhanced sampling.
Bi-alignments for incongruent RNA sequence and structure evolution
This paper introduces bi-alignments, a formal framework for cases where RNA sequence homology and RNA structural homology cannot be captured by the same alignment.
Co-transcriptional riboswitch modeling with ViennaRNA
A landscape-based method for modeling how cotranscriptional folding and ligand binding interact in kinetically controlled riboswitches, illustrated with the 2'dG riboswitch from Mesoplasma florum.
In silico design of ligand-triggered RNA switches
A computational workflow for designing ligand-triggered RNA switches, with emphasis on sequence design, folding kinetics, and candidate prioritization.