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BioBloom Documentation 📚

Full documentation for the BioBloom project repository.

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Project Overview

BioBloom explores microalgae proteomes as a source of bioactive compounds with pharmacological potential.
We focus on bioactive peptides (esp. ACE inhibitors for cardiovascular health) by:

1. Mining microalgal proteomes,
2. Querying the BIOPEP-UWM database,
3. Filtering peptide lists & removing duplicates,
4. Screening ADMET properties with AdmetLab 3.0,
5. Converting between FASTA ⇄ SMILES ⇄ PDB,
6. Generating peptide 3D structures,
7. Preparing receptor structures,
8. Producing input/output for pLM4ACE and docking pipelines.

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Repository Structure

biopep_uwm/

Automation of the BIOPEP-UWM batch processing:

• selenium_biopep_batch_processing.py – ACE inhibitory activity screening.
• selenium_batch_processing_scraper.py – enzyme action analysis.
• search_for_novel_peptides.py – compare BIOPEP results with known ACE inhibitors.
• unify_a_platensis_biopep_output.py – merge & deduplicate A. platensis BIOPEP peptide lists.

admet/

Filtering and unifying ADMET screening results:

• unify_admet_output_a_platensis.py – merge species-specific ADMET outputs.

molecular_docking/

Peptide/receptor structure preparation:

• generate_peptide_structures_pyrosetta.py – build PDBs from FASTA with PyRosetta.
• repack_receptor_pyrosetta.py – side-chain repacking of ACE receptor.
• place_pep_into_ace.py – peptide placement into ACE binding pocket.
• select_top_peptides_for_molecular_docking.py – rank/filter peptides by ADMET criteria.

pLM4ACE/

Formatting utilities for the pLM4ACE model:

• prepare_pLM4ACE_input.py – create input files.
• split_pLM4ACE_input.py – split input into batches.
• unify_pLM4ACE_output.py – merge model outputs.

smiles_conversion/

Cheminformatics utilities:

• smiles_converter.py – bidirectional FASTA ⇄ SMILES.
• create_fasta_input_for_smiles_conversion.py – prep FASTA for conversion.
• extract_smiles_without_names.py – clean SMILES files (remove labels, keep strings only).

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Requirements

• Python 3.9+
• PyRosetta (licensed, manual install)
• Chrome + Chromedriver (auto-installed with webdriver-manager)

Python dependencies

pip install biopython selenium tqdm openpyxl pandas numpy rdkit-pypi