Difference between revisions of "Dehydron"

From PyMOLWiki
Jump to: navigation, search
Line 2: Line 2:
 
|type      = plugin
 
|type      = plugin
 
|filename  = plugins/dehydron.py
 
|filename  = plugins/dehydron.py
|author    = Osvaldo Martin
+
|author    = [[User:aloctavodia|Osvaldo Martin]]
 
|license  = GPL
 
|license  = GPL
 
}}
 
}}
 
== Introduction ==
 
== Introduction ==
A dehydron calculator plugin for PyMOL <br>
+
A dehydron calculator plugin for PyMOL. This plugin calculates dehydrons and display them onto the protein structure.
Author: Osvaldo Martin. e-mail: aloctavodia (at.) gmail.com
+
 
 +
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 [[git_intro | Pymol-script-repo]]
 +
 
 +
=== Windows ===
 +
This plugin is ready "out-of-box" for win users through the project [[git_intro | Pymol-script-repo]]
 +
 
 +
== Usage ==
 +
[[Image:Dehydrons.png|400px|thumb|Dehydrons calculated and displayed in PyMOL.]]
 +
There are four parameters the user can change:<br>
 +
<br>
 +
Two of them control the hydrogen bonds detection.<br>
 +
* Angle range: deviation in degrees from the optimal hydrogen bond angle (C=0 N-H).<br>
 +
* Max distance: maximum donor-aceptor distance.<br>
 +
<br>
 +
And the other two control the dehydron detection<br>
 +
* 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>
 +
* Cut-off wrappers: a hydrogen bond surrounded with less "wrappers" than "Cut-off wrappers" is a dehydron.<br>
 +
 
 +
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:<br>
 +
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).
  
Acknowledgement: The H-bond detection code is based on the list_mc_hbonds.py <br>
 
script from Robert L. Campbell http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
 
  
 
[[Category:Plugins]]
 
[[Category:Plugins]]
 
[[Category:Pymol-script-repo]]
 
[[Category:Pymol-script-repo]]

Revision as of 09:46, 18 January 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

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 ca 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).