Weiwei He (何伟渭) | CoBAI Lab

CoBAI Lab is Hiring

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

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Preferential hydration, rather than ion correlation, drives ethanol-induced DNA condensation in monovalent salt

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

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

DES-AMBER for GROMACS

Fri, 31 Jul 2026 00:00:00 +0000

Overview

This resource provides a GROMACS-compatible conversion of the DES-AMBER RNA force field introduced by Tan and co-workers. The original force-field parameters have been organized into a GROMACS .ff directory so that DES-AMBER can be selected and used through standard GROMACS workflows. The converted files are intended to make the original DES-AMBER parameters more accessible to researchers performing RNA molecular dynamics simulations with GROMACS.

Force-Field Files

Installation

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

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

Usage

Prepare the RNA system using gmx pdb2gmx:

gmx pdb2gmx -f RNA_structure.pdb

When prompted to select a force field, choose the DES-AMBER entry from the current working directory

Compatibility and Validation

Users are encouraged to inspect the generated topology and validate representative systems before beginning production simulations.

Please report any conversion-related issues or inconsistencies so that the resource can be further evaluated and improved.

Original Reference

Dazhi Tan, Stefano Piana, Robert M. Dirks, and David E. Shaw.

“RNA Force Field with Accuracy Comparable to State-of-the-Art Protein Force Fields.”

Proceedings of the National Academy of Sciences 2018, 115(7), E1346–E1355.

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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.

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2026 International Workshop on Biophysics, Protein Engineering and Computational Biology

Tue, 21 Jul 2026 09:00:00 +0800

Weiwei He presented his research at the 2026 International Workshop on Biophysics, Protein Engineering and Computational Biology, held at NYU Shanghai on July 21–23, 2026. The workshop, orgnized by Profs. Fei Xia, John Zhang, and Mark Tuckerman, brought together researchers working across biophysics, protein engineering, computational biology, artificial intelligence, and molecular simulation.

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

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

Introduction to Molecular Simulation

Mon, 13 Jul 2026 00:00:00 +0000

Materials Overview

Introduction to molecular simulation methods and their applications to biomolecular systems.

Course materials available here.

Topics

Molecular simulation fundamentals
Force fields and molecular interactions
Structural analysis and visualization

Accurate prediction of mechanical properties of organic crystals using molecular dynamics-based nanoindentation simulations

Fri, 03 Oct 2025 00:00:00 +0000

Designing reversible photoswitching azobenzene-modified nucleotide for controlling biological function

Fri, 13 Jun 2025 00:00:00 +0000

Sequence-dependent conformational preferences of disordered single-stranded RNA

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

Mechanism of cationic lipid-induced DNA condensation: lipid-DNA coordination and divalent-cation charge fluctuations

Tue, 16 Jul 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

Sequence-dependent orientational coupling and electrostatic attraction in cation-mediated DNA-DNA interactions

Wed, 20 Sep 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

The structural plasticity of nucleic acid duplexes revealed by WAXS and molecular dynamics

Fri, 23 Apr 2021 00:00:00 +0000

Exploring cation-mediated DNA interactions using computer simulations

Sat, 30 May 2020 00:00:00 +0000

Catalytic asymmetric radical aminoperfluoroalkylation and aminodifluoromethylation of alkenes with fluoroalkylsulfonyl chlorides: a versatile platform for enantioenriched β-fluoroalkyl amines

Thu, 23 Mar 2017 00:00:00 +0000

Asymmetric construction of spirooxindoles via organocatalytic multicomponent reactions of diazooxindoles

Thu, 02 Jul 2015 00:00:00 +0000