structure: A sample structure data

Description Format Details See Also Examples

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.

See Also

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

Examples

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data("structure")
structure

BALCONY documentation built on May 1, 2019, 10:31 p.m.