Dehydron

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Revision as of 18:54, 28 February 2012 by OsvaldoMartin (Talk | contribs)
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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

Contents

Introduction

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

A dehydron is a protein main chain hydrogen bond incompletely shielded from water attack. Dehydrons are sticky, since they promote the removal of surrounding water through protein associations or ligand binding. Dehydrons are less conserved than other structural motifs, hence identification of dehydrons could help to increase specificity during the rational drug design process.

For a brief introduction to the dehydron concept, please read wikipedia.

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 Windows users through the project Pymol-script-repo

Mac OsX

This plugin have not been tested on a Mac OsX machine, but it should work.

Usage

The plugin can be accessed using the following command:

dehydron [ object_selection [, angle_range [, max_distance [, desolv [, min_wrappers ]]]]]
Dehydrons calculated and displayed in PyMOL.


Or using a graphical environment (see accompanying figure)


There are five parameters the user can change:

Two of them control the hydrogen bonds detection.

Another two control the dehydron detection.

A wrapper is defined as a carbon atom not bonded directly to an oxygen or nitrogen atom, i.e. a non-polar carbon atom. The plugin count as wrappers any non-polar carbon from any protein chain, organic ligand or other type of molecule (if the atoms belong to the same object). This means that if you have, for example, a dimeric protein you will probably get different results for the dimer and for the isolated monomers. Instead, if you upload two (or more) different files the results will be independent because the plugin does not count atoms from other objects


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/

Changelog

All features in this version and most of the code was provided by Thomas Holder, thanks Thomas! :-)


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).

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