Add LigandMPNN Nextflow pipeline for protein sequence design

2026-03-18 22:31:13 +01:00
commit e7261ba7ce
15 changed files with 6825 additions and 0 deletions
--- a/sc_examples.sh
+++ b/sc_examples.sh
@@ -0,0 +1,55 @@
+#1 design a new sequence and pack side chains (return 1 side chain packing sample - fast) 
+python run.py \
+        --model_type "ligand_mpnn" \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/sc_default_fast" \
+        --pack_side_chains 1 \
+        --number_of_packs_per_design 0 \
+        --pack_with_ligand_context 1
+
+#2 design a new sequence and pack side chains (return 4 side chain packing samples) 
+python run.py \
+        --model_type "ligand_mpnn" \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/sc_default" \
+        --pack_side_chains 1 \
+        --number_of_packs_per_design 4 \
+        --pack_with_ligand_context 1
+
+
+#3 fix specific residues for design and packing 
+python run.py \
+        --model_type "ligand_mpnn" \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/sc_fixed_residues" \
+        --pack_side_chains 1 \
+        --number_of_packs_per_design 4 \
+        --pack_with_ligand_context 1 \
+        --fixed_residues "C6 C7 C8 C9 C10 C11 C12 C13 C14 C15" \
+        --repack_everything 0
+
+#4 fix specific residues for sequence design but repack everything 
+python run.py \
+        --model_type "ligand_mpnn" \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/sc_fixed_residues_full_repack" \
+        --pack_side_chains 1 \
+        --number_of_packs_per_design 4 \
+        --pack_with_ligand_context 1 \
+        --fixed_residues "C6 C7 C8 C9 C10 C11 C12 C13 C14 C15" \
+        --repack_everything 1
+
+
+#5 design a new sequence using LigandMPNN but pack side chains without considering ligand/DNA etc atoms 
+python run.py \
+        --model_type "ligand_mpnn" \
+        --seed 111 \
+        --pdb_path "./inputs/1BC8.pdb" \
+        --out_folder "./outputs/sc_no_context" \
+        --pack_side_chains 1 \
+        --number_of_packs_per_design 4 \
+        --pack_with_ligand_context 0