Dehydron

Type	PyMOL Plugin
Download	plugins/dehydron.py
Author(s)	Osvaldo Martin
License	GPL
This code has been put under version control in the project Pymol-script-repo

Introduction

A dehydron calculator plugin for PyMOL. This plugin calculates dehydrons and display them onto the protein structure.

A dehydron is a main chain hydrogen bond incompletely shielded from water attack. For a brief introduction to the dehydron concept, please read http://en.wikipedia.org/wiki/Dehydron

Installation

Linux

This plugin is ready "out-of-box" for Linux users through the project Pymol-script-repo

Windows

This plugin is ready "out-of-box" for win users through the project Pymol-script-repo

Usage

Dehydrons calculated and displayed in PyMOL.

There are four parameters the user can change:

Two of them control the hydrogen bonds detection.

• Angle range: deviation in degrees from the optimal hydrogen bond angle (C=0 N-H).
  
• Max distance: maximum donor-aceptor distance.
  

And the other two control the dehydron detection

• Desolvatation sphere radius: this parameter controls the radius of the two spheres centered at the C^α carbon of the donor and acceptor residues. A dehydron is defined by the number of "wrappers" inside this two spheres.
  
• Cut-off wrappers: a hydrogen bond surrounded with less "wrappers" than "Cut-off wrappers" is a dehydron.
  

A wrapper is defined as a carbon atom not bonded directly to an oxygen or nitrogen atom, i.e. a non-polar carbon atom.

Acknowledgement

The H-bond detection code is based on the list_mc_hbonds.py script from Robert L. Campbell http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/

References

Citation for Dehydrons:
Fernández A. and Scott R.; "Adherence of packing defects in soluble proteins", Phys. Rev. Lett. 91, 018102 (2003).

Fernández A., Rogale K., Scott R. and Scheraga H.A.; "Inhibitor design by wrapping packing defects in HIV-1 proteins", PNAS, 101, 11640-45 (2004).

Fernández A. "Transformative Concepts for Drug Design: Target Wrapping" (ISBN 978-3642117916), Springer-Verlag, Berlin, Heidelberg (2010).