DSSP API

The DSSP API runs a secondary structure annotation protocol on input PDB structures using the Dictionary of Secondary Structure in Proteins (DSSP) originally designed by Wolfgang Kabsch and Chris Sander to standardize secondary structure assignment based on atomic coordinates.

Command Line Interface

Examples

Annotate secondary structure composition of the pdb input.pdb:

lev engine submit dssp input.pdb

Annotate chain A from multiple pdb files:

lev engine submit dssp *.pdb --chain A

Flags

  • --pdb-file (str) (Required)
    • Input PDB file(s) to annotate
  • --chain (str) (Optional)
    • Return results for a specific chain, default = all chains
  • --batch-size (int) (Optional)
    • Number of files to process in parallel, default = 1

Python Interface

Examples

from engine import EngineClient

client = EngineClient()
client.authorize()

# Annotate secondary structure composition of input.pdb
result = submit_dssp(
    pdb_path="input.pdb"
)

Outputs

The DSSP API returns a CSV file with the secondary structure composition of each input PDB structure.

The CSV file contains the following schema (see DSSP documentation for more details):

Model - PDB structure 
Chain - Chain ID
SS - overall secondary structure (helices, beta strands)
Alpha_Helix - percentage of alpha helices
Beta_Bridge - percentage of beta bridges
Strand - percentage of beta strands
Helix_3 - percentage of 310 helices
Helix_5 - percentage of pi-helices 
Turn - percentage of turns
Bend - percentage of bends
Unstructured - percentage of unstructured regions

Updated: