calcNearbyHydrationFraction: Calculate Nearby Atom Hydration Fraction
In vanddraabe: Identification and Statistical Analysis of Conserved Waters Near Proteins
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Description
Calculate the mobility values of waters for a structure.
Usage
1
calcNearbyHydrationFraction(names.res.nearby.atoms)
Arguments
names.res.nearby.atoms
string of residue-atom name for nearby atoms
Details
The summation, mean, and standard deviation of the hydrophilicity
fraction for the protein atoms within the user specified distance for the
BoundWaterEnvironment() function are calculated and returned.
Value
Hydrophilicity fraction sum, mean, and standard deviation.
Author(s)
Emilio Xavier Esposito emilio@exeResearch.com
References
Paul C Sanschagrin and Leslie A Kuhn. Cluster analysis of
consensus water sites in thrombin and trypsin shows conservation between
serine proteases and contributions to ligand specificity. Protein
Science, 1998, 7 (10), pp 2054-2064.
DOI: 10.1002/pro.5560071002
PMID: 9792092
WatCH webpage
See Also
Other "Bound Water Environment": BoundWaterEnvironment.interact,
BoundWaterEnvironment.quality,
BoundWaterEnvironment,
Mobility, NormalizedBvalue,
calcBvalue,
calcNumHydrogenBonds
vanddraabe documentation built on June 8, 2019, 1:03 a.m.
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Description Usage Arguments Details Value Author(s) References See Also
Description
Calculate the mobility values of waters for a structure.
Usage
1 | calcNearbyHydrationFraction(names.res.nearby.atoms)
|
Arguments
names.res.nearby.atoms |
string of residue-atom name for nearby atoms |
Details
The summation, mean, and standard deviation of the hydrophilicity
fraction for the protein atoms within the user specified distance for the
BoundWaterEnvironment() function are calculated and returned.
Value
Hydrophilicity fraction sum, mean, and standard deviation.
Author(s)
Emilio Xavier Esposito emilio@exeResearch.com
References
Paul C Sanschagrin and Leslie A Kuhn. Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity. Protein Science, 1998, 7 (10), pp 2054-2064. DOI: 10.1002/pro.5560071002 PMID: 9792092 WatCH webpage
See Also
Other "Bound Water Environment": BoundWaterEnvironment.interact,
BoundWaterEnvironment.quality,
BoundWaterEnvironment,
Mobility, NormalizedBvalue,
calcBvalue,
calcNumHydrogenBonds
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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