Added p53 scaffolding example

Author: Joseph Watson

examples/design_motifscaffolding_with_target.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+# Here, we're running one of the motif-scaffolding benchmark examples, in the presence of a target
+# Specifically, we're scaffolding the Mdm2-interacting peptide from p53
+# We specify the output path and input pdb (the p53-Mdm2 complex)
+# We specify the protein we want to build, with the contig input:
+#   - the Mdm2 target protein (residues A25-109), with a chain break.
+#   - 0-70 residues (randomly sampled)
+#   - residues 17-29 (inclusive) on the B chain of the input (the p53 helix)
+#   - 0-70 residues (randomly sampled)
+# We also constrain the total length of the diffused chain to be within 70 and 120 residues
+# We generate 10 designs
+# As in the paper (at least for some of the designs we tested), we use the complex-finetuned model
+
+python ../scripts/run_inference.py inference.output_prefix=example_outputs/design_motifscaffolding_with_target inference.input_pdb=input_pdbs/1YCR.pdb 'contigmap.contigs=[A25-109/0 0-70/B17-29/0-70]' contigmap.length=70-120 inference.num_designs=10 inference.ckpt_override_path=../models/Complex_base_ckpt.pt