IsAb example for Antibodies D44.1 and Cemiplimab

This repository contains the intermediate and output data involved in the design process of antibodies D44.1 and cemiplimab by IsAb protocol.

1_original_data_[step1]

This directory contains structure files of lysozyme, and three PD1 obtained from protein data bank.

The sequence of antibodies D44.1 and cemiplimab were obtained from IMGT:

Cemiplimab
H: EVQLLESGGVLVQPGGSLRLSCAASGFTFSNFGMTWVRQAPGKGLEWVSGISGGGRDTYFADSVKGRFTISRDNSKNTLYLQMNSLKGEDTAVYYCVKWGNIYFDYWGQGTLVTVSS
L: DIQMTQSPSSLSASVGDSITITCRASLSINTFLNWYQQKPGKAPNLLIYAASSLHGGVPSRFSGSGSGTDFTLTIRTLQPEDFATYYCQQSSNTPFTFGPGTVVDFR

D44.1
H: QVQLQESGAEVMKPGASVKISCKATGYTFSTYWIEWVKQRPGHGLEWIGEILPGSGSTYYNEKFKGKATFTADTSSNTAYMQLSSLTSEDSAVYYCARGDGNYGYWGQGTTLTVSS
L: DIELTQSPATLSVTPGDSVSLSCRASQSISNNLHWYQQKSHESPRLLIKYVSQSSSGIPSRFSGSGSGTDFTLSINSVETEDFGMYFCQQSNSWPRTFGGGTKLEIK

2_modeling_3d_structure_[step2]

This directory contains 3D structrues of antibodies cemiplimab and D44.1 modelled from RosettaAntibody.

3_relaxed_structure_[step3]

This directory contains the structrues of lysozyme and three PD1 relaxed by RosettaRelax protocol. The script used to acquire this looks like

relax.static.linuxgccrelease \
-database rosetta_bin_linux_2020.08.61146_bundle/main/database \
-s PD1v2.pdb \
-in:file:fullatom \
-out:pdb \
-relax:thorough \
-relax:constrain_relax_to_start_coords \
-relax:ramp_constraints false \
-ex1 \
-use_input_sc -flip_HNQ \
-no_optH false \
-nstruct 10

4_global_docking_results_[step4]

This directory contains the global docking results of cemiplimab-PD1 and D44.1-lysozyme complexes from ClusPro.

5_local_docking_results_[step5]

This directory contains local docking results of cemiplimab-PD1 and D44.1-lysozyme complexes from SnugDock.

6_affinity_maturation_results_[step7]

This directory contains cemiplimab four point mutation and D44.1 double muations designed by affinity maturation protocol. The script of affinity maturation protocol. The script used to acquire this looks like

rosetta_scripts.static.linuxgccrelease \
-linmem_ig 100 \
-use_input_sc \
-ex1 \
-nstruct 10 \
-s proteins_0887.pdb \
-parser:protocol design.xml \
-out:suffix _design \
-scorefile proteins_0887.fasc