Peptide Design Genetic Algorithm (PDGA)
python run_PDGA.py population-size mutation-rate generation-gap query similarity-threshold topology
run_PDGA.py 50 1 0.8 Ala-Leu-Cys1-His-Gaba-Cys1-Ile 300 cyclic
- each generation will have
(0.80)of the individuals will be replaced, and 100%
(1)of the new ones will be mutated
- PDGA will try to reach the MXFP value of the query
- compounds with CBD smaller than
Ala-Leu-Cys1-His-Gaba-Cys1-Ilewill be annotated in a results file
- the generated sequences will have cyclic topology.
topology can be
Sequences building blocks:
- the 20 natural amino acids as three-letters code (e.g.
Dap2,3-diaminopropionic acid as branching unit
Dab2,4-diaminobutyric acid as branching unit
BOrnOrnithine as branching unit
BLysLysine as branching unit
cyHead-to-tail cyclization. It is always placed at the beginning (left, N terminus) of the sequence.
Cys1First pair of cyclizes cysteines. Always in pair, never next to each other.
Cys2Second pair of cyclizes cysteines. They are always present in pair, never next to each other, present only if Cys1 is already part of the sequence.
Cys3Third pair of cyclizes cysteines. They are always present in pair, never next to each other, present only if Cys1 and Cys2 are already part of the sequence.
AcN-terminus acetylation. It is always placed at the beginning (N-terminus, left) of the sequence
NH2C-terminus amide. It is always placed at the end (C-terminus, right) of the sequence
By default, all building blocks are used. Using the method
exclude_buildingblock(bb) is possible to exclude all building blocks with the exception of the head to tail cyclization (cy) and the cyclized cysteines (Cys1, Cys2, Cys3), to exclude cyclization use “topology = linear”.
By default, PDGA stops after CBD = 0 from the query MXFP value is found 10 times. Using the method
ga.set_time_limit('hh:mm:ss') is possible to stop PDGA after a chosen time.
run_PDGA.py uses class PDGA in
To run the genetic algorithm with MXFP as fitness function, a valid Chemaxon licence is required and the specified libraries needs to be downloaded.