Protein Secondary Structure Casp12 Cb513 Ts115

Introduction

Protein secondary structure can be calculated based on its atoms' 3D coordinates once the protein's 3D structure is solved using X-ray crystallography or NMR. The benchmark dataset casp13 , cb513 and ts115 is used in here . Every character in the secondary protein sequence is amino acid and described in below :

1. C: Loops and irregular elements
2. E: β-strand
3. H: α-helix
4. B: β-bridge
5. G: 3-helix
6. I: π-helix
7. T: Turn
8. S: Bend

However, X-ray or NMR is expensive. Ideally, we would like to predict the secondary structure of a protein based on its primary sequence directly, which has had a long history.

Dataset

The main dataset lists peptide sequences and their corresponding secondary structures.
Description of columns:
2. seq: the sequence of the peptide
3. sst3: the three-state (Q3) secondary structure
4. sst8: the eight-state (Q8) secondary structure

This is a secondary structure datasets with Eight states (H,B,E,G,I,T,S,C). There are 8679 Non-Redundant chains (25%) in training data set . Three state :[H=(G,H,I); E=(B,E); C=(T,S,C)]
The link of dataset - Protein Secondary Structure