ILE {ClusTorus}

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:

phi

main chain torsion angle for atoms C,N,CA,C.

psi

main chain torsion angle for atoms N,CA,C,N.

chi1

side chain torsion angle for atoms N,CA,CB,*G.

chi2

side chain torsion angle for atoms CA,CB,*G,*D.

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., Frellsen, J., Johansson, K. E., & Hamelryck, T. (2010). Beyond rotamers: a generative, probabilistic model of side chains in proteins. BMC bioinformatics, 11(1), 1-13.

Mardia, K. V., Kent, J. T., Zhang, Z., Taylor, C. C., & Hamelryck, T. (2012). Mixtures of concentrated multivariate sine distributions with applications to bioinformatics. Journal of Applied Statistics, 39(11), 2475-2492.

See Also

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