Dehydron - Revision history

Cchem: 1 revision

2018-05-29T19:27:19Z

1 revision

OsvaldoMartin at 17:16, 3 May 2018

2018-05-03T17:16:28Z

Cchem: 1 revision

2017-06-26T04:31:22Z

1 revision

OsvaldoMartin: change license

2017-06-14T08:16:04Z

change license

Cchem: 1 revision

2016-05-31T05:42:45Z

1 revision

OsvaldoMartin: fix some typos

2016-05-26T20:31:48Z

fix some typos

Pyadmin: 22 revisions

2014-03-28T01:43:44Z

22 revisions

OsvaldoMartin: /* Usage */

2014-03-22T16:03:17Z

Usage

OsvaldoMartin: /* Methods */

2014-03-22T16:02:11Z

Methods

OsvaldoMartin: /* Change log */

2014-03-22T15:59:12Z

Change log

@@ Line 27: / Line 27: @@
 <source lang="python">
-dehydron [ selection [, angle_range [, max_distance [, desolv [, min_wrappers ]]]]]
+wrappy [ selection [, angle_range [, max_distance [, desolv [, min_wrappers ]]]]]
 </source>

@@ Line 3: / Line 3: @@
 |filename  = plugins/dehydron.py
 |author    = [[User:OsvaldoMartin|Osvaldo Martin]]
-|license   = GPL
+|license   = MIT
 }}
 =Introduction=

@@ Line 49: / Line 49: @@
 * Desolvatation sphere radius: this parameter controls the radius of the two spheres centred at the Cα 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). The default value (19) was taken from a statistical analysis of ~7400 high-quality proteins form the Protein Data Bank (see below).
-* Max wrappers: a hydrogen bond surrounded with more "wrappers" than "max_wrappers" is a dehydron. The default value (35) was taken from a statistical analysis of ~7400 high-quality proteins form the Protein Data Bank (see below).
+* Max wrappers: a hydrogen bond surrounded with more "wrappers" than "max_wrappers" is a buried hydrogen bond. The default value (35) was taken from a statistical analysis of ~7400 high-quality proteins form the Protein Data Bank (see below).
 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 plug-in count as wrappers any non-polar carbon from any protein chain, organic ligand or other type of molecule, if the atoms belong "selection" (see below). 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 plug-in does not count atoms from other objects
@@ Line 56: / Line 56: @@
 =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]]
+[[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 stimate 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-stimated 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 hydrongen 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).
+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.

@@ Line 49: / Line 49: @@
 * Desolvatation sphere radius: this parameter controls the radius of the two spheres centred at the Cα 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). The default value (19) was taken from a statistical analysis of ~7400 high-quality proteins form the Protein Data Bank (see below).
 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 plug-in count as wrappers any non-polar carbon from any protein chain, organic ligand or other type of molecule, if the atoms belong "selection" (see below). 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 plug-in does not count atoms from other objects
 * Selection: This parameter allows the user to select which part of system is used to calculate dehydrons. This parameter is useful, for example, to calculate dehydronds for different objects independently or to easily calculate dehydrons with and without an organic ligand. The default selection is "all". Compute dehydrons for an specific selection is equivalent to delete all but the selected atoms and then compute dehydrons.
 =Methods=

@@ Line 58: / Line 58: @@
 [[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 stimate 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-stimated 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 hydrongen bond with less than 19 wrappers is defined as a dehydron (27-8 = 19).
+An analysis of 7476 high quality X-ray proteins was performed in order to stimate 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-stimated 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 hydrongen 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.

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 *# 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.
 ==References==