3D
Posts tagged “3D”.
Sequence editability of the theophylline RNA aptamer
Molecular dynamics of five theophylline aptamer variants whose binding site is left unchanged: which edits in the surrounding helices keep ligand recognition intact, and which weaken it from the outside.
From structure to function in Musashi-RNA complexes
This review article surveys how computational modeling, molecular dynamics, and AI-derived structures help explain Musashi-RNA recognition in both cellular regulation and viral pathogenesis.
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.
RNA–RNA interaction analysis of Japanese encephalitis virus
This study combines computational and biophysical analysis to characterize a long-range RNA-RNA interaction in Japanese encephalitis virus and to test the role of the conserved cyclization sequence.
How Musashi-1 recognizes RNA: molecular dynamics of RBD1 and RBD2 binding
Molecular dynamics and binding-energy calculations are used here to compare how Musashi-1 recognizes different RNA motifs and to identify determinants of binding specificity.