vanddraabe (version 1.1.1)

HydrophilicityEvaluation: Hydrophilicity Evaluation

Description

Calculate the hydrophilicity values for a set of protein structures.

Usage

HydrophilicityEvaluation(prefix = "alignTesting/",
  h2o.prot.dist.max = 6, bound.h2o.dist.max = 4, min.num.h2o = 20,
  probeRadius = 1.4, dataset = "top56")

Arguments

prefix

The directory containing the protein structures; e.g., "alignTesting/"

h2o.prot.dist.max

Maximum distance between the water oxygen atoms and the protein for consideration in the determination for hydrophilicity values; default: 6.0

bound.h2o.dist.max

Maximum distance between the water oxygen atoms and the protein for inclusion in the calculation of hydrophilicity values; default: 4.0

min.num.h2o

Minimum number of water oxygen atoms within a protein structure for it to be included in the calculation of hydrophilicity values; default: 20

probeRadius

Water molecule probe radius; default: 1.4

dataset

Name of the dataset to be used; e.g.,"top56"

Value

This function returns:

• PDB.info: a summary of the data for each protein structure analyzed

  • PDBid: PDB id

  • time: duration for hydrophilicity evaluation

  • num.res: number of protein residues

  • num.res.buried: number of protein residues with NO solvent exposure

  • num.res.SurExp: number of protein residues with solvent accessible surface area

  • pct.res.SurExp: percentage of protein residues with solvent

  • SASA.total: total protein solvent accessible surface area; Angstroms^2^

  • SASA.lost: total protein solvent accessible surface area lost due to bound waters; Angstroms^2^

  • pct.SASA.exposed: percentage protein solvent accessible surface area \((SASA.total - SASA.lost) / SASA.total\)

  • num.prot.atom: number of protein atoms

  • num.atom.buried: number of protein atoms with NO solvent exposure

  • num.atom.SurExp: number of protein atoms with solvent accessible surface area

  • pct.atom.SurExp: percentage protein atoms with solvent accessible surface area \((SASA.total - SASA.lost) / SASA.total\)

  • num.h2o: number of waters in the system

  • num.h2o.lte.prot.max: number of waters within h2o.prot.dist.max cutoff

  • num.SurBound.h2o: number of surface bound waters; water within bound.h2o.dist.max cutoff

  • num.bb.h2o.inter: number of backbone - water interactions

  • num.sc.h2o.inter: number of sidechain - water interactions

  • num.res.h2o.inter: number of interactions between residues and water

  • num.h2o.res.inter: number of interactions between water and residue (residues are a unit)

  • num.h2o.resAtom.inter: number of water-atom interactions

• SASA.results: data.frame of protein atoms within the h2o.prot.dist.max of each water oxygen atom

• df.AtomTypes.all: total number of AtomTypes for each structure

• df.AtomTypes.buried: number of buried AtomTypes for each structure

• df.AtomTypes.SurExp: number of surface exposed AtomTypes for each structure

• df.AtomTypes.h2o.nearby: number of surface exposed AtomTypes within h2o.prot.dist.max (default 6 Ang) of an individual water

• df.AtomTypes.h2o.bound: number of surface exposed AtomTypes within bound.h2o.dist.max (default 4 Ang) of an indvidual water

• df.AtomTypes.h2o.inter: number of surface exposed AtomTypes with the shortest distance to an individual water

• df.residue.hydro:

• HydrophilicityTable: hydrophilicity table based on provided protein structures

• AtomTypeClasses.hydratFract:

• no.h2o: proteins (PDB IDs) without the minimum number of user defined waters min.num.h2o

• call: parameters provided by the user

• duration: duration of complete HydrophilicityEvaluation() calculation

Details

The hydrophilicity values of individual atomtypes is determined using a collection of protein structures. For each water oxygen atom within at the most 4 Angstroms of a solvent accessible (exposed) protein atom, these occurrences are recorded. The number of solvent accessible atom types interacting with a water molecule are divided by the number of solvent accessible atom types. In general the more diverse data available, the better the informatics based hydrophilicity values should correlate with various experimental values.

NOTE: Hydrogen atoms are removed for instances when the protein structures have not be cleaned with CleanProteinStructures().

References

Leslie A Kuhn, Craig A Swanson, Michael E Pique, John A Tainer, and Elizabeth D Getzof. Atomic and Residue Hydrophilicity in the Context of Folded Protein Structures. PROTEINS: Structure, Function, and Genetics, 1995, 23 (4), pp 536-547. DOI: 10.1002/prot.340230408 PMID: 8749849

See Also

Other "Hydrophilicity Evaluation" "Bound Water Environment": calcAtomClassHydrophilicity, calcAtomHydrationEstimate, getProtAtomsNearWater, getResidueData

Examples

# NOT RUN {
 HydrophilicityEvaluation <- function(prefix = "alignTesting/",
                                      h2o.prot.dist.max = 6.0,
                                      bound.h2o.dist.max = 4.0,
                                      min.num.h2o = 20,
                                      probeRadius = 1.4,
                                      dataset = "top56")
# }
# NOT RUN {
# }