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vanddraabe
View on CRAN: Click
here
Download and install vanddraabe package within the R console
Install from CRAN:
install.packages("vanddraabe")
Install from Github:
library("remotes")
install_github("cran/vanddraabe")
Install by package version:
library("remotes")
install_version("vanddraabe", "1.1.1")
Attach the package and use:
library("vanddraabe")
Maintained by
Emilio Xavier Esposito
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
First Published: 2017-08-11
Latest Update: 2023-04-03
Description:
Identify and analyze conserved waters within crystallographic
protein structures and molecular dynamics simulation trajectories. Statistical
parameters for each water cluster, informative graphs, and a PyMOL session
file to visually explore the conserved waters and protein are returned.
Hydrophilicity is the propensity of waters to congregate near specific protein
atoms and is related to conserved waters. An informatics derived set of
hydrophilicity values are provided based on a large, high-quality X-ray
protein structure dataset.
How to cite:
Emilio Xavier Esposito (2017). vanddraabe: Identification and Statistical Analysis of Conserved Waters Near
Proteins. R package version 1.1.1, https://cran.r-project.org/web/packages/vanddraabe. Accessed 23 Apr. 2025.
Other packages that cited vanddraabe R package
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Other R packages that vanddraabe depends,
imports, suggests or enhances
Functions, R codes and Examples using
the vanddraabe R package
Some associated functions: AlignOverlap . BoundWaterEnvPlots . BoundWaterEnvSummaryPlot . BoundWaterEnvironment.interact . BoundWaterEnvironment . BoundWaterEnvironment.quality . BvalueBarplot . BvalueBarplot.summ . CalcAlignOverlap . CleanProteinStructures . ClusterSummaryPlots . ClusterWaters.MDS . ClusterWaters . ConservationPlot . ConservationSet . ConservedWaterStats . ConservedWaters.MDS . ConservedWaters . CreatePyMOLscript . DetermineChainsOfInterest . ExtractFileTimeStamp . ExtractPDBids . FileTimeStamp . FreeSASA.diff . FreeSASAcheck . HasXWaters . HydrophilicityEvaluation . HydrophilicityTable . MobNormBvalEvalPlots . Mobility . MobilityBarplot . MobilityBarplot.summ . Nearby . NormalizedBvalue . OccupancyBarplot . OccupancyBarplot.summ . PDB.1ecd . PDB.5rxn . ProtHetWatIndices . RemoveHydrogenAtoms . RemoveModeledAtoms . RemoveOoR.b . RemoveOoR.o . RescaleValues . RetainChainsOfInterest . RetainWatersWithinX . ReturnPDBfullPath . StandardizeAsparticAcidNames . StandardizeCysteineNames . StandardizeGlutamicAcidNames . StandardizeHistidineNames . StandardizeLysineNames . TimeSpan . UniqueAtomHashes . aaStandardizeNames . calcAtomClassHydrophilicity . calcAtomHydrationEstimate . calcBvalue . calcNearbyHydrationFraction . calcNumHydrogenBonds . check.cluster.method . colorPalettes . getAtomTypeCounts . getProtAtomsNearWater . getRCSBdata . getResTypeCounts . getResidueData . nBvalueBarplot . names.backbone.atoms . names.polar.atoms . names.res.AtomTypes . names.resATs.carb.sulf . names.resATs.nitro.neut . names.resATs.nitro.pos . names.resATs.oxy.neg . names.resATs.oxy.neut . names.residues . names.sidechain.atoms . names.waters . normBvalueBarplot.summ . openxlsxCellStyles . oxAlignOverlapSheet . oxClusterStatsSheet . oxClusterSummarySheet . oxInitWaterDataSheet . oxPDBcleanedSummarySheet . oxPlainDataSheet . oxRCSBinfoSheet . oxWaterOccurrenceSheet . res2xyz . resAtomType2AtomClass . thrombin.1hai . thrombin10.PDBs.align . vanddraabe . write.basic.pdb . write.conservedWaters.pdb .
Some associated R codes: AlignOverlap.R . BoundWaterEnvironments.R . ChainsOfInterest.R . CleanProteinStructures.R . ClusterWaters.R . ConservedWaters.R . Constants.R . CreatePyMOLscript.R . Dataset_documentation.R . FreeSASA.R . HydrophilicityEvaluation.R . HydrophilicityTable_documentation.R . getRCSBdata.R . openxlsxCommands.R . plots.R . utilities.R . vanddraabe.R . Full vanddraabe package functions and examples
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