bamboo.training: Training Dataset

In bamboo: Protein Secondary Structure Prediction Using the Bamboo Method

Description

This training dataset gives the names, the primary structure (amino acid sequences), and the secondary structure of 15,201 individual proteins from the ASTRAL SCOP 1.75 structure set filtered at 95% sequence identity as used in the paper cited below.

Usage

bamboo.training

Format

A data frame containing 15,201 observations on the following 3 variables.

1. name: protein name;

2. primary: protein primary structure (amino acid sequence) in 20 letters denoting the 20 amino acids;

3. hetc: secondary structure in 4 letters denoting the 4 structure types: helix (H), strand (E), turn (T) and coil (C).

Source

Chandonia JM, Hon G, Walker NS, Conte LL, Koehl P, et al. (2004) The astral compendium in 2004. Nucleic Acids Research 32: D189-D192

References

Q. Li, D. B. Dahl, M. Vannucci, H. Joo, J. W. Tsai (2014), Bayesian Model of Protein Primary Sequence for Secondary Structure Prediction, PLOS ONE, 9(10), e109832. <DOI:10.1371/journal.pone.0109832>

bamboo documentation built on April 14, 2020, 6:53 p.m.