ConservedWaters.MDS: Conserved Molecular Dynamics Simulation Waters

In vanddraabe: Identification and Statistical Analysis of Conserved Waters Near Proteins

Description

Identifies conserved molecular dynamics simulation (MDS) waters from a collection of PDBs.

Usage

ConservedWaters.MDS(prefix = "", cluster = 2.4, chain = "all",
  prot.h2o.dist.min = 5.1, cluster.method = "complete",
  filename = "ProteinSystem")

Arguments

prefix	Directory of aligned structures; string.
cluster	Oxygen atoms within 2.4 Angstroms or less of each other are considered a cluster; numeric. Default value is 2.4 Angstroms.
chain	The chain to examine. The user can define "first" and the first chain alphabetically will be selected; this is the default. Defining "all" will result in all chains being explored. Alternatively the user can define individual the chains to include in the analysis; for example, c("A", "B", "C"). When defining chains, the chain designation must be characters.
prot.h2o.dist.min	The minimum distance (in Angstroms) between the protein and waters to be considered for the conserved water clusters. Water oxygen atoms greater than this distance are removed from the analysis. Default value is 5.10 Angstroms.
cluster.method	Method of clustering the waters; default is "complete". Any other method accepted by the stats::hclust() or fastcluster::hclust() functions are appropriate. The original method used by Sanschagrin and Kuhn is the complete linkage clustering method and is the default. Other options include "ward.D" (equivilant to the only Ward option in R versions 3.0.3 and earlier), "ward.D2" (implements Ward's 1963 criteria; see Murtagh and Legendre 2014), or "single" (related to the minimal spanning tree method and adopts a "friend of friends" clustering method). Please see fastcluster::hclust() for additional and complete information regarding clustering explanations.
filename	The filename prefix for the returned results. Default is "ProteinSystem"

Details

Only atoms within (less than or equal to) 5.10 Angstroms of the protein structures are included.

Value

This function returns:

• h2o.cluster.all: Clusters constructed from all waters present in the aligned PDB structures.

• h2o.cluster.passed: Clusters constructed from waters that passed the Mobility() and NormalizedBvalue() evaluations.

• h2o.cluster.summary: Summary of water clusters

• Excel workbook: containing the Cluster Statistics, Cluster Summaries for all and passed waters, Occurrence Summaries for all and passed waters, and the Initial Water Data data as individual tabs

• call: The user provided parameters for the function

Author(s)

Emilio Xavier Esposito [e-mail]

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

Hitesh Patel, Bjorn A. Gruning, Stefan Gunther, and Irmgard Merfort. PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering. Bioinformatics, 2014, 30 (20), pp 2978-2980. DOI: 10.1093/bioinformatics/btu424 PMID: 24990608 PyWATER on GitHub

vanddraabe documentation built on June 8, 2019, 1:03 a.m.