ILE {ClusTorus}R Documentation

ILE: Structure of the Isoleucine

Description

An isomer of leucine, essential branched-chain aliphatic amino acid found in many proteins.

Usage

ILE

Format

This list contains the following components:

tbl

a numeric matrix of psi, phi, and chi torsion angles.

Details

ILE data is generated with collection of different pdb files. To select adequate protein data, we use PISCES server. (the method is introduced in articles of references.) To select high-quality protein data, we use several benchmarks: resolution : 1.6A(angstrom) or better, R-factor : 0.22 or better, Sequence percentage identity: <= 25 Then, we select ILE only angular data for each protein data. To see the detail code, visit https://github.com/sungkyujung/ClusTorus

Source

This data is extracted from PISCES server http://dunbrack.fccc.edu/pisces/

References

Data description is from https://www.rcsb.org/ligand/ILE.

The data extracting method is from Harder, T., Boomsma, W., Paluszewski, M. et al.(2010) "Beyond rotamers: a generative, probabilistic model of side chains in proteins". BMC Bioinformatics 11, 306 doi: 10.1186/1471-2105-11-306 and

Kanti V. Mardia , John T. Kent , Zhengzheng Zhang , Charles C. Taylor & Thomas Hamelryck (2012) "Mixtures of concentrated multivariate sine distributions with applications to bioinformatics", Journal of Applied Statistics, 39:11, 2475-2492, DOI: 10.1080/02664763.2012.719221

See Also

Description of the angluar information is from the 'value' part of torsion.pdb in the package bio3d.


[Package ClusTorus version 0.1.3 Index]