RNA | CoBAI Lab

The distinct structural propensities of poly-C, A, and U single-stranded RNA

Mon, 03 Aug 2026 00:00:00 +0000

Protein crowders remodel RNA electrostatics, hydration, and dynamics: a challenge to steric crowding models

Sat, 01 Aug 2026 00:00:00 +0000

HB-CUFIX for GROMACS

Thu, 30 Jul 2026 00:00:00 +0000

Overview

HB-CUFIX is an RNA force-field refinement developed using small-angle X-ray scattering (SAXS) experiments. It extends the CUFIX corrections by improving hydrogen-bonding and base-stacking interactions, allowing molecular dynamics simulations to reproduce RNA structures and conformational dynamics more accurately.

The force field has been evaluated using helix-junction-helix RNA duplexes and single-stranded RNA systems, providing improved descriptions of both structured and flexible RNA molecules.

HB-CUFIX extends the CUFIX framework through refined hydrogen-bonding and base-stacking interactions for RNA simulations.

Key Features

Refined against experimental SAXS measurements
Extends the original CUFIX corrections for RNA
Improves hydrogen-bonding and base-stacking interactions
Benchmarked using helix-junction-helix RNA duplexes
Evaluated with flexible single-stranded RNA systems
Compatible with GROMACS molecular dynamics simulations
Designed to improve RNA structural and dynamic ensembles

Software and Force-Field Files

The HB-CUFIX force-field files are available from the following repository:

Installation

Copy the GROMACS-compatible force-field folder into your working directory:

cp -r HB_cufix_RNA.ff /path/to/your/working/directory/

Associated Publication

Weiwei He, Nawavi Naleem, Diego Kleiman, and Serdal Kirmizialtin.
“Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix-Junction-Helix RNA.”
The Journal of Physical Chemistry Letters 2022, 13, 3400–3408.

View Publication

From scattering curves to structure: interpretable machine learning maps SAXS/WAXS signals to RNA structural details

Tue, 14 Jul 2026 00:00:00 +0000

Sequence-dependent conformational preferences of disordered single-stranded RNA

Tue, 29 Oct 2024 00:00:00 +0000

Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics

Fri, 10 Nov 2023 00:00:00 +0000

Insights into the structural stability of major-groove RNA triplexes by WAXS-guided molecular dynamics simulations

Mon, 11 Jul 2022 00:00:00 +0000

Refining the RNA force field with small-angle X-ray scattering of helix-junction-helix RNA

Mon, 11 Apr 2022 00:00:00 +0000

Visualizing RNA structures by SAXS-driven molecular dynamics simulations

Fri, 18 Feb 2022 00:00:00 +0000