Van der waals energy and desolvation energy interpretaion

HADDOCK
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The HADDOCK metrics include energy values for Van der Waals and Desolvation. How are these energy values generated by HADDOCK? Does the negative and positive values of these energies have special meaning or it follows the know literature information? Thank you

2

Hi there,

Yes, it follows the standard literature information, with negative values having a favorable impact on the interaction while positive ones would rather disrupt the interaction.

The reported values (for each metric) is the sum of the metric over all the inter-molecular interactions.

I hope this answer will help you.

Regards

3

Hi,
Thanks for the response. The last part of my question is okay. I want to repeat the first part in a more precise way, i.e.,

  1. Can you tell me which physical properties are “hiding” behind the terms VdW energies and desolvation energies?
  2. Which effects are limiting in either of the two properties?
  3. And how are they calculated when using HADDOCK?

Thank you

4

Evdw is the intermolecular van der Waals energy and Eelec is the intermolecular electrostatic energy calculated with the OPLS force field [1]. Edesol represents an empirical desolvation energy term adapted from previous studies [2], which estimates the energetic gain or penalty of burying specific side chains upon complex formation.

[1] Jorgensen, W. L. & Tirado-Rives, J. The OPLS optimized potentials for liquid simulations. J. Am. Chem. Soc. 110, 1657–1666 (1988).

[2] Fernández-Recio, J., Totrov, M. & Abagyan, R. Identification of protein–protein interaction sites from docking energy landscapes. J. Mol. Biol. 335, 843–865 (2004).

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Check also our online manual and the list of publications at HADDOCK – Bonvin Lab