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Updated: Mar 10, 2026

Dissipative Microgravimetry to Study the Binding Dynamics of the Phospholipid Binding Protein Annexin A2 to Solid-supported Lipid Bilayers Using a Quartz Resonator

Dissipative Microgravimetry to Study the Binding Dynamics of the Phospholipid Binding Protein Annexin A2 to Solid-supported Lipid Bilayers Using a Quartz Resonator

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On-the-Fly QM/MM Docking with Attracting Cavities.

Prasad Chaskar¹, Vincent Zoete¹, Ute F Röhrig¹

¹SIB Swiss Institute of Bioinformatics , Molecular Modeling Group, CH-1015 Lausanne, Switzerland.

Journal of Chemical Information and Modeling

|December 17, 2016

Summary

We created a new hybrid quantum mechanical/molecular mechanical (QM/MM) docking method. This advanced algorithm improves accuracy for metalloproteins and maintains performance for common drug targets.

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Production and Targeting of Monovalent Quantum Dots

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Published on: October 23, 2014

Area of Science:

Computational chemistry
Biochemistry
Drug discovery

Background:

Accurate molecular docking is crucial for drug discovery.
Treating polarization and metal interactions remains a challenge for classical methods.
Existing algorithms struggle with metalloproteins and covalent interactions.

Purpose of the Study:

To develop an on-the-fly hybrid quantum mechanical/molecular mechanical (QM/MM) docking algorithm.
To accurately model polarization and metal-ligand interactions in docking.
To improve upon classical docking methods for metalloproteins.

Main Methods:

Developed a hybrid QM/MM on-the-fly docking algorithm.
Integrated semiempirical self-consistent charge density functional tight-binding (SCC-DFTB) with the CHARMM force field.
Benchmarked against classical methods (Attracting Cavities, AutoDock, Vina, GOLD) on diverse datasets.

Main Results:

The QM/MM algorithm maintained accuracy on standard noncovalent complexes (Astex Diverse set).
Significant improvements were observed for zinc and heme metalloprotein datasets.
The method achieved these gains at a moderate computational cost.

Conclusions:

The hybrid QM/MM approach effectively addresses polarization and metal interactions in docking.
This method offers enhanced accuracy for metalloprotein-ligand binding.
It represents a valuable advancement for computational drug discovery.