The modelling module

With the modelling module, you can create a full-length structure of your protein of interest, by fusing together the structures of folded domains with disordered tails/inter-domain linkers. This structure can then be used as an input starting structure for conformational ensemble generation.

Create your full-length protein structure

To fuse disordered sequences with PDB structures into a full-length PDB structure, provide Ensemblify with:

CLI Parameter	Description
FASTA(s) (--fastas, -f)	FASTA file(s) with the sequences of all (folded + disordered) protein domains, from N- to C-terminal.
PDB(s) (--pdbs, -p)	PDB file(s) with the structures of all folded protein domains, from N- to C-terminal.
Trajectory ID (--id, -i)	Name for the created full-length fused PDB structure (without .pdb extension).

CLIPython

(ensemblify_env) $ ensemblify modelling \
    -f protein_name_all.fa \
    -p protein_name_all.pdb \
    -i protein_name