modelling - Protein Modelling¶

High-level functionality for protein modelling. The goal is to model a given target sequence (or list of sequences for oligomers) given some template data. Commonly, the template does not cover the full target. This module offers capabilities to extract useful template data for the target and to fill the remaining structural data to create a full model of the target. In its simplest form, you can use a target-template alignment and a template structure to create a model fully automatically as follows:

from ost import io
from promod3 import modelling

# get raw model
tpl = io.LoadPDB('data/1crn_cut.pdb')
aln = io.LoadAlignment('data/1crn.fasta')
aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)

# build final model
final_model = modelling.BuildFromRawModel(mhandle)
io.SavePDB(final_model, 'model.pdb')

The various steps involved in protein modelling are described here: