The generation module¶
With the generation module, you can generate a conformational ensemble for your protein of interest.
📝 Setting up your parameters file¶
Before generating an ensemble, you must create a parameters file either:
Using the provided .html form;
Directly, by editing the provided parameters file template.
Below you can find a description of the minimum required parameters.
| Parameter | Description | |
|---|---|---|
| Job Name | Name for generated files and folders. | |
| Input Structure/Sequence | Full-length structure available or Full IDP |
Path to structure/sequence in .pdb/.txt format. A UniProt accession code can also be provided, in which case the corresponding structure from the AlphaFold Protein Structure Database is retrieved. |
| Folded domains available, missing IDRs (Uses modelling module) |
Path to FASTA file(s) containing the sequences of all (folded + disordered) protein domains, from N- to C-terminal. Can be provided either in FASTA or Multi-FASTA format. |
|
| Path to PDB file(s) containing the structures of all folded protein domains, from N- to C-terminal. Can be provided as a single PDB file with multiple MODEL entries. |
||
| Size of Ensemble | Desired number of conformers in the generated ensemble. | |
| Database(s) | Mapping of database IDs to the path of their respective database files. Currently supported file formats include .pkl, .csv and .parquet. |
|
| Sampling Target(s) | Protein regions to be targeted for conformational sampling. You must assign for each desired sampling target a protein chain, a range of residue numbers, a database ID to sample from (matching one defined in Databases(s)) and a sampling mode ('Tripeptide', if neighbouring residue information is to be considered, or 'Single Residue' otherwise). |
|
| Output Path | Path to desired output directory. A directory named Job Name will be created here, with all generated files and folders. |
|
Generate a conformational ensemble¶
To generate an ensemble, simply provide Ensemblify with the path to your parameters file.
(ensemblify_env) $ ensemblify generation -p parameters_file.yml
from ensemblify.generation import generate_ensemble
generate_ensemble('parameters_file.yml')
Get suggestions for target sampling regions¶
In case you are unsure which regions of your protein you want to sample, you can provide Ensemblify with your protein’s UniProt accession.
This will trigger automatic queries of useful structure/disorder related databases (MobiDB, TED, AFDB), outputting informative reports about the protein’s domain annotations.
For example, if you were interested in modelling full-length Galectin-3 (UniProt accession P17931):
(ensemblify_env) $ ensemblify generation -st P17931
from ensemblify.generation import suggest_targets
suggest_targets('P17931')