Bioinformatics tools running on modal.
pip install modal
python3 -m modal setup
Runs omegafold --model 2 <fasta>
This can run out of memory, and may need an 80GB A100.
modal run modal_omegafold.py --input-fasta in/omegafold/insulin.faa
Runs minimap2 -ax sr <fasta> <reads>
Just a simple example of running a binary on a powerful box.
modal run modal_minimap2.py --input-fasta in/minimap2/mito.fasta --input-reads in/minimap2/reads.fastq
Create a cyclic peptide against a pdb file (using pdb-redo data by default)
modal run modal_afdesign.py --pdb 4MZK --target-chain A
Set the first and last amino acid of the (cyclic) peptide to cysteine.
Here using a small number of iterations for speed reasons...
Use --soft-iters 30 --hard-iters 6 or more for better results.
modal run modal_afdesign.py --pdb 1A00 --target-chain A --soft-iters 2 --hard-iters 2 --binder-len 6 --set-fixed-aas C....C
Create a linear peptide against a local PDB file that has been manually edited. This is unfortunately sometimes necessary when e.g. a chain is too long or there are too many chains.
modal run modal_afdesign.py --pdb in/afdesign/1igy_cropped.fixed.pdb --target-chain B
Dock a .mol2 file against a local pdb file. DiffDock may require an 80GB A100 to run for larger proteins.
modal run modal_diffdock.py --pdb in/diffdock/1igy.pdb --mol2 in/diffdock/1igy.mol2
A simple pymol-based script to convert PDBs to PNGs for easy output viewing.
modal run modal_pdb2png.py --input-pdb in/pdb2png/1igy.pdb --protein-zoom 0.8 --protein-color 240,200,190
A tool for annotating antibody sequences https://github.com/oxpig/ANARCI
modal run modal_anarci.py --input-fasta in/anarci/antibody.faa
Basic MD
modal run modal_MD_protein_ligand.py --pdb-id in/md_protein_ligand/1A1O_reordered.pdb
Basic MD protein + ligand
modal run modal_md_protein_ligand.py --pdb-id 4O75 --ligand-id 2RC --ligand-chain A