structure: Sample structure data

In michalstolarczyk/BALCONY: Better ALignment CONsensus analYsis

Description

This sample structure data consists of the amino acids names forming tunnels and their numbers is analyzed protein. The data is a result of CAVER which is a software tool for analysis and visualization of tunnels and channels in protein structures.

Format

A structure object with three elements:

structure_matrix

A matrix of characters "S" and "N" marking on sequence the structural element; "S" - amino acid forms the analyzed structure, "N" - amino acid which does not form the structure. Number of rows of the matrix corresponds to the number of structures analyzed

structure_numbers

A vector containing the numbers of the amino acids in the sequence of interest (no gaps)

structure_probabilities

A matrix of numeric values: probabilities of corresponding to the structural information from first element of the output, which helps to reduce the effect of non-consistent structural amino acids on the conservativity analysis of the structure of interest

Details

The tunnel analysis with CAVER was performed on human epoxide hydrolase structure (PDB ID: 4JNC) 50ns MD simulation.

Value

A character vector of length of the aligned sequence containing consesus sequence based on the input alignment

Note

Please note that this function masks the seqinr package function consensus

References

CAVER: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002708
4JNC: http://www.sciencedirect.com/science/article/pii/S0960894X13004885

Examples

data("structure")
structure

michalstolarczyk/BALCONY documentation built on May 7, 2019, 6:08 a.m.