ADAPT
The ADAPT (Assisted Design of Antibody and Protein Therapeutics) platform guides the selection
of mutants that improve/modulate the affinity of antibodies. Predicted affinities are based on
a consensus z-score from three scoring functions (FoldX, Rosetta, SIE-SCWRL). Computational
predictions are interleaved with experimental validation, significantly enhancing the robustness
of the design and selection of mutants.
Click
here for download and installation instructions.
Usage
Wrapper script for a complete ADAPT run, including structure initialization, processing mutations
and analyzing scores, for one of the three scoring functions:
$ run_ADAPT.sh -runtype FoldX|Rosetta|SIE-SCWRL -pdb myfile.pdb -mutfile mutation_list -folder folder
The above wrapper script calls the following scripts, which can also be invoked independently:
Script for the wild-type structure initialization for a given scoring function. The script should be
run in the WT folder:
$ prep_structure.sh -runtype FoldX|Rosetta|SIE-SCWRL -pdb myfile.pdb
Script to process a list of mutations for a given scoring function. The script should be run from
the folder containing the WT subfolder. The mutation subfolders are automatically generated as
each mutation in the list is processed and will contain all files related to that mutation.
$ run_mutlist.sh -runtype FoldX|Rosetta|SIE-SCWRL -mutfile mutation_list
Scripts to process a particular mutation. These scripts should be run in the specific sub-folder
corresponding to a given Mutant.
$ run_foldx.sh -pdb StartingStructure.pdb -mutation_string mut
$ run_rosetta.sh -pdb StartingStructure.pdb -mutation_string mut
$ run_sie-scwrl.sh -pdb StartingStructure.pdb -mutation_string mut
Script to calculate the z-scores for all the mutants for a given scoring function. The script should
be run from the folder containing the WT subfolder. An optional MAD or MeanAD value can be specified
for double and higher order mutants.
$ calc_zscore.sh -runtype FoldX|Rosetta|SIE-SCWRL [-mad MAD_value] [-meanad MeanAD_value]
How to cite
If you use adapt in your work, please cite:
- Sulea, T., Deprez, C., Corbeil, C. R., Purisima, E. O. (2023). Optimizing Antibody-Antigen Binding Affinities with the ADAPT Platform. Methods in molecular biology (Clifton, N.J.), 2552, 361–374. [link]
References
- Sulea, T., Hussack, G., Ryan, S., Tanha, J., Purisima, E. O. (2018). Application of Assisted Design of Antibody and Protein Therapeutics (ADAPT) improves efficacy of a Clostridium difficile toxin A single-domain antibody. Scientific reports, 8(1), 2260. [link]
- Vivcharuk, V., Baardsnes, J., Deprez, C., Sulea, T., Jaramillo, M., Corbeil, C. R., Mullick, A., Magoon, J., Marcil, A., Durocher, Y., O'Connor-McCourt, M. D., Purisima, E. O. (2017). Assisted Design of Antibody and Protein Therapeutics (ADAPT). PloS one, 12(7), e0181490. [link]
How to contact us
Send feedback, suggestions or queries to mm-admin@nrc-cnrc.gc.ca.
