TrendBio

#31 · Structural bio & protein design

DFT reference data refines torsion parameters and hybrid ML/MM simulation setup

1 preprint · 2 published
Items per day, last 8 weekstoday: 3

The dominant thread is quantum-mechanical reference data supplying the fidelity of molecular energy models for biomolecular simulation. AFFDO, a GPU-accelerated platform, refits GAFF2 torsion parameters for drug-like ligands against DFT reference data, improving agreement with QM. CHARMM-GUI Hybrid ML/MM Builder automates preparation of protein-ligand systems and input files for hybrid neural network potential/molecular mechanics simulations. What is new is the coupling of GPU-accelerated DFT-level reference data with parameter refitting and hybrid ML/MM system construction. The DBFE preprint, an alchemy-free absolute binding free energy method in implicit solvent with publicly released code, addresses a separate problem and is not representative of this thread.

Published papers

Preprints

  • Binding Free Energies without Alchemy

    arXivMichael Brocidiacono et al.

    Proposes Direct Binding Free Energy (DBFE), an alchemy-free end-state absolute binding free energy method in implicit solvent, with code released publicly.

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