Project Overview

This repository is a work in progress and will be updated as I progress through the challenge.

Files and Directories

• pred_test.ipynb – The main file where I experiment with the data and model.

• reference_structures/ – Contains reference complex PDB files for aligning test data.
  All training data is limited to the first 100 data points.

• train_complex_truth/ – Contains complexes PDB of the training data provided by the challenge.

• train_complex_predicted/ – Contains complexes PDB of the training data predicted by Boltz-1

• train_ligand_output/ – Extracted Predicted ligand in SDFs from train_complex_predicted.

• train_ligand_bond_fixed/ – Contains Boltz-1 predicted ligands with bond order fixed using MolReBond.

• Its missing the 0th molecule, so 99 molecules effectively. The first molecule has some issues.

Test Outputs

• test_ligand_outputs/ - Test ligand predictions extracted from the Boltz-1 test complexes. Contains 195 MOL2 files, ligand_0.mol2 through ligand_194.mol2.
• test_ligand_outputs_bond_fixed/ - MolReBond bond-order-corrected test ligand predictions. Contains 183 SDF files. The 12 missing ligands are 19, 34, 51, 62, 64, 92, 111, 115, 123, 125, 183, and 184; MolReBond/RDKit failed on these because the MOL2/reference chemistry triggered aromaticity/kekulization errors while assigning bond orders.
• input_folders/test_fasta/ - FASTA inputs for the 195 test cases.
• input_folders/yaml_test/ - YAML inputs for the 195 test cases.
• boltz_results_test_fasta/ - Raw Boltz-1 test prediction directory. This includes the 195 model CIF files used to extract the test ligands plus confidence and pLDDT files.

Each predicted complex is stored as boltz_results_test_fasta/predictions/seq_<index>/seq_<index>_model_0.cif. These CIF files contain the predicted protein chains and ligand together. To get the predicted protein complex without the ligand, load the CIF in PyMOL and save the polymer selection, for example:

import pymol

index = 0
pymol.cmd.load(f"boltz_results_test_fasta/predictions/seq_{index}/seq_{index}_model_0.cif", "predicted")
pymol.cmd.save(f"test_complex_proteins/seq_{index}_protein.pdb", "predicted and polymer")