ADL: What are the parameters of the Autodock vina genetic algorithm?
diogo.stmart at gmail.com
Thu May 14 10:10:45 PDT 2020
The search algorithm in Vina is iterated local search, which is basically a
sequence of Monte Carlo (MC) steps, in which each MC step is immediately
followed by local search minimization. Autodock4 uses a genetic algorithm.
Nevertheless, it is possible to find analogies for some of the parameters:
The number of independent runs ("ga_run" in Autodock4) is controlled by the
"--exhaustiveness" parameter in Vina.
There's no concept of population in Vina, but we can think of it as a
population with 1 individual.
The number of evaluations is not capped in Vina.
The equivalent could be the number of Monte Carlo steps. It is determined
at the beginning of the docking and increases with ligand complexity.
This would be 100% as the Monte Carlo step is always applied.
The number of local search steps (Vina uses BFGS) is determined at the
beginning of the docking and increases with ligand complexity.
There's nothing similar in Vina. Instead, an MC step is either rejected or
There's nothing similar in Vina.
Hope this helps.
On Mon, 11 May 2020 at 16:39, Levy Bueno Alves <levybuenoalves at usp.br>
> My name is Levy and I'm postgraduate student of Genetics in University of
> São Paulo. I would like to know what parameters are used in the Autodock
> Vina genetic algorithm. If possible, could you tell to me what are the
> values of the parameters? I would like to know the values that are used in
> the following parameters analogous to Autodock4:
> *Levy Bueno Alves*
> *Postgraduate student*
> *Bioinformatics Group*
> *Department of Genetics, Ribeirão Preto Medical School, University of São
> Paulo - USP*
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