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vanddraabe  

Identification and Statistical Analysis of Conserved Waters Near Proteins
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]
All associated links for this package
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 28 Mar. 2025.
Previous versions and publish date:
1.0.0 (2017-08-11 18:15), 1.1.1 (2019-06-08 00:02)
Other packages that cited vanddraabe R package
View vanddraabe citation profile
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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