biomodals

Bioinformatics tools running on modal.

install and set up modal

pip install modal
python3 -m modal setup

OmegaFold

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

minimap2 (short reads example)

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

AFDesign

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

DiffDock

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

pdb2png

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

ANARCI

A tool for annotating antibody sequences https://github.com/oxpig/ANARCI

modal run modal_anarci.py --input-fasta in/anarci/antibody.faa

MD_protein_ligand

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

BindCraft

Basic PDL1 binder (example from https://github.com/martinpacesa/BindCraft)

wget https://raw.githubusercontent.com/martinpacesa/BindCraft/refs/heads/main/example/PDL1.pdb
GPU=A100 modal run modal_bindcraft.py --input-pdb PDL1.pdb --number-of-final-designs 1

nextflow

Minimal hello world app, with conda and nextflow installed (not trivial!)

modal run modal_nextflow_example.py

Boltz-1

Boltz-1, an open source AlphaFold 3-like model.

echo ">A_PROTEIN_INSULIN\nMAWTPLLLLLLSHCTGSLSQPVLTQPTSLSASPGASARFTCTLRSGINVGTYRIYWYQQKPGSLPRYLLRYKSDSDKQGSGVPSRFSGSKDASTNAGLLLISGLQSEDEADYYCAIWYSSTS\n>B|RNA|\nACUGACUGGAAGUCCCCCGUAGUACCCGACG\n>C|smiles\nN[C@@H](Cc1ccc(O)cc1)C(=O)O" > test_boltz.faa
modal run modal_boltz.py --input-faa test_boltz.faa

Chai-1

Chai-1, another open source AlphaFold 3-like model.

echo ">protein|name=insulin\nMAWTPLLLLLLSHCTGSLSQPVLTQPTSLSASPGASARFTCTLRSGINVGTYRIYWYQQKPGSLPRYLLRYKSDSDKQGSGVPSRFSGSKDASTNAGLLLISGLQSEDEADYYCAIWYSSTS\n>RNA|name=rna\nACUGACUGGAAGUCCCCCGUAGUACCCGACG\n>ligand|name=caffeine\nN[C@@H](Cc1ccc(O)cc1)C(=O)O" > test_chai1.faa
modal run modal_chai1.py --input-faa test_chai1.faa

Other modal repos

• RNA Seq Pipeline by @tdsone