Editing Dehydron (section)

=Methods=
[[Image:Wrappers_histogram.png|350px|thumb|<b>Figure 1</b>:Histogram of the number of wrappers per hydrogen bond (blue bars), the distribution of wrappers approximate a Gaussian distribution (red line). Parameters for the Gaussian fit (mean and standard deviation)are show in the grey box]]

An analysis of 7476 high quality X-ray proteins was performed in order to estimate the number of wrappers that should be used as a cut-off to determine whether to call an hydrogen bond a dehydron (i.e. the ''min wrappers''  parameter). Although this value have been already estimated in the literature; differences in the algorithms used before and the ones used by wrappy could lead to differences in the exact value of the cut-off and hence this parameter was re-estimated in order to obtain reliable calculation of the dehydrons. To compute the numbers of wrappers the following parameters were used  ''angle range''  = 40°, ''Max distance''  = 3.5 Å and ''desolvatation sphere''  = 6.5 Å. A non-redundant set of 7476 proteins were obtained from the Protein Data Bank. Each protein in this set conforms with the following criteria: Resolution < 2.0 Å,  R-factors <= 0.25, not containing DNA and/or RNA molecules. Additionally, proteins with a sequence identity of 30% were removed. The frequency of wrappers in this set of proteins approximate a Gaussian distribution (see figure 1) with a mean of ~27 and a standard deviation of ~8, hence an hydrogen bond with less than 19 wrappers is defined as a dehydron (27-8 = 19). In the same fashion and over-wrapped hydrogen bond is and hydrogen bond with more than 35 wrappers (27+8).

Using the same set of 7476 proteins it was obtained that on average a high quality and globular protein should have 0.62 hydrogen bonds per residue (with a standard deviation of 0.06) and 17 wrappers per residue (with a standard deviation of 2). Hydrogen bonds per residue and wrappers per residue could be used as indicators of the global protein structure quality. Wrappy reports such indicators as z-score, i.e. the number of standard deviations an observation is above or below the expected mean value.


== 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/


== Change log ==

* 2012-01-14 (Version 1.0)
*# First public version was released and put under version control. In the project, [http://www.pymolwiki.org/index.php/Git_intro Pymol-script-repo].

*2012-01-28 (Version 1.1) 
*# Minor changes in the code most of them not visible for the end-user.

*2012-02-28 (Version 1.5) 
*# The code was cleaned (e.g. remove global variables and other ugly stuff)
*# The code was made available as a PyMOL command
*# Better support for multiple objects
All features in this version and most of the code was provided by [[User:Speleo3|Thomas Holder]], thanks Thomas! :-)

*2012-03-14 (Version 1.6)
*# Representation is not changed to "cartoon" after each calculation
*# Total control over the selection from which dehydrons are calculated

*2013-03-26 (Version 1.7)
*# Wrappers were not correctly counted for structures with hydrogen atoms. 
Thanks Shafqat Rasool for reporting the bug.

*2013-07-19 (Version 2.0)
*# The plug-in was renamed to wrappy.
*# Wrappy reports, now, the hydrogen bonds per residue and the wrappers per residue as z-scores. The values of the mean and standard deviation, necessary to compute zscores, where taken from the analysis of ~7400 high quality X-ray proteins from the PDB.

*2014-03-22 (Version 2.1)
*# Wrappy reports all the hydrogens bonds. Dehydrons are displayed using red dashes, average wrapped hydrogens bonds are yellow, and over-wrapped hydrogens bonds are green.

==References==
Citation for Dehydrons:<br>
De Simone, A., Dodson, G. G., Verma, C. S., Zagari, A., and Fraternali, F. (2005). Prion and water: tight and dynamical hydration sites have a key role in structural stability. Proceedings of the National Academy of Sciences of the United States of America, 102(21), 75357540.

Fernández, A. and Berry, R. S. (2003). Proteins with h-bond packing defects are highly interactive with lipid bilayers: Implications for amyloidogenesis. Proceedings of the National Academy of Sciences, 100(5), 2391–2396.

Fernández, A. and Crespo, A. (2008). Protein wrapping: a molecular marker for association, aggregation and drug design. Chemical Society Reviews, 37(11), 2373.

Fernández, A. and Lynch, M. (2011). Non-adaptive origins of interactome complexity. Nature, 474(7352), 502–505.

Fernández, A., Rogale, K., Scott, R., and Scheraga, H. A. (2004a). Inhibitor design by wrapping packing defects in HIV-1 proteins. Proceedings of the National Academy of Sciences of the United States of America, 101(32), 1164011645.

Fernández, A., Scott, R., and Berry, R. S. (2004b). The nonconserved wrapping of conserved protein folds reveals a trend toward increasing connectivity in proteomic networks. Proceedings of the National Academy of Sciences of the United States of America, 101(9), 28232827.

Kabsch, W. and Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22(12),
2577–2637. PMID: 6667333.

Liang, H., Plazonic, K. R., Chen, J., Li, W.-H., and Fernández, A. (2008). Protein under-wrapping causes dosage sensitivity and decreases gene duplicability. PLoS Genetics, 4(1), e11.



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