Dehydron

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A dehydron calculator plugin for PyMOL. This plugin calculates dehydrons and display them onto the protein structure.
 
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
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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 [http://en.wikipedia.org/wiki/Dehydron/ wikipedia].
  
 
== Installation ==
 
== Installation ==
Line 15: Line 17:
  
 
=== Windows ===
 
=== Windows ===
This plugin is ready "out-of-box" for win users through the project [[git_intro | Pymol-script-repo]]
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This plugin is ready "out-of-box" for Windows users through the project [[git_intro | Pymol-script-repo]]
 +
 
 +
=== Mac OsX ===
 +
This plugin have not been tested on a Mac OsX machine, but it should work.
  
 
== Usage ==
 
== Usage ==
[[Image:Dehydrons.png|400px|thumb|Dehydrons calculated and displayed in PyMOL.]]
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The plugin can be accessed using the following command:
There are four parameters the user can change:<br>
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<br>
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<source lang="python">
Two of them control the hydrogen bonds detection.<br>
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dehydron [ object_selection [, angle_range [, max_distance [, desolv [, min_wrappers ]]]]]
* Angle range: deviation in degrees from the optimal hydrogen bond angle (C=0 N-H).<br>
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</source>
* Max distance: maximum donor-aceptor distance.<br>
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<br>
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[[Image:Dehydrons.png|580px|thumb|Dehydrons calculated and displayed in PyMOL.]]
And the other two control the dehydron detection<br>
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* Desolvatation sphere radius: this parameter controls the radius of the two spheres centered at the ca carbon of the donor and acceptor residues. A dehydron is defined by the number of "wrappers" inside this two spheres.<br>
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* Cut-off wrappers: a hydrogen bond surrounded with less "wrappers" than "Cut-off wrappers" is a dehydron.<br>
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Or using a graphical environment (see accompanying figure)
 +
 
 +
 
 +
There are five 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-acceptor distance.
 +
 
 +
Another two control the dehydron detection.
 +
 
 +
* Desolvatation sphere radius: this parameter controls the radius of the two spheres centered at the carbon of the donor and acceptor residues. A dehydron is defined by the number of "wrappers" inside this two spheres.<br>
 +
* Min wrappers: a hydrogen bond surrounded with less "wrappers" than "min_wrappers" is a dehydron. Setting this parameter to a "high" value, something like 100, will return all main chain hydrogen bonds (according to the angle range and max distance parameters).
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 +
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
 +
 
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* Object selection: This parameter allows the user to calculate dehydrons ​​for different objects separately. The default behaviour is to calculate dehydrons for all objects.
  
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 ==
 
== 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/
 
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/
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 +
== Changelog ==
 +
 +
* 2012-01-28 (Version 1.0)
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*# First public version was released and put under version control. In the project, [http://www.pymolwiki.org/index.php/Git_intro Pymol-script-repo].
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*2012-01-14 (Version 1.1)
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*# Minor changes in the code most of them not visible for the end-user.
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*2012-02-28 (Version 1.5)
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*# The code was cleaned (e.g. remove global variables and other ugly stuff)
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*# The code was made available as a PyMOL command
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*# Better support for multiple objects
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All features in this version and most of the code was provided by [[User:Speleo3|Thomas Holder]], thanks Thomas! :-)
 +
  
 
== References ==
 
== References ==

Revision as of 18:54, 28 February 2012

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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