PyMOL wizard for performing ML-based antibody evolution through brianhie/efficient-evolution. Utilizes haddocking/prodigy for measuring the binding affinity of the loaded antibody-antigen complex and assessing the impact of mutations.
The wizard can be installed with the Wizard Installer tool.
The wizard can be accessed in one of two ways:
- by writing
wizard evolutionin the PyMOL console; - by going to
Wizard->Antibody Evolutionin the external GUI (or the internal one, if in VR mode);
After selecting the molecule from the drop-down menu, specify the chain you want to obtain mutations for and click Generate Suggestions to acquire them. You can then select the desired mutation from the list, where each mutation is accompanied by the consensus score, and apply it. The Select Best Mutation button automatically selects the mutation which brings the greatest reduction in binding free energy.
Evaluating the binding affinity requires you to select the participating chains in the appropriate drop-down menus. Doing so will reveal the Evaluate Affinity button: click it to obtain the binding free energy of the complex in kcal/mol.
Each applied mutation adds a state to the selected object, creating a timeline of applied mutations. Each individual frame can be annotated with its binding affinity to track its changes through each round of evolution. Through the Undo button it is possible to revert the last mutation performed.