ADL: What are the parameters of the Autodock vina genetic algorithm?

Diogo Martins diogo.stmart at gmail.com
Thu May 14 10:10:45 PDT 2020


Hi Levy,

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:

"ga_run"
The number of independent runs ("ga_run" in Autodock4) is controlled by the
"--exhaustiveness" parameter in Vina.

"ga_pop_size"
There's no concept of population in Vina, but we can think of it as a
population with 1 individual.

"ga_num_evals"
The number of evaluations is not capped in Vina.

"ga_num_generations"
The equivalent could be the number of Monte Carlo steps. It is determined
at the beginning of the docking and increases with ligand complexity.

"ga_mutation_rate"
This would be 100% as the Monte Carlo step is always applied.

"sw_max_its"
The number of local search steps (Vina uses BFGS) is determined at the
beginning of the docking and increases with ligand complexity.

"ga_elitism"
There's nothing similar in Vina. Instead, an MC step is either rejected or
accepted.

"ga_crossover_rate"
There's nothing similar in Vina.

Hope this helps.

On Mon, 11 May 2020 at 16:39, Levy Bueno Alves <levybuenoalves at usp.br>
wrote:

> Hi,
> 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:
>
>
> *ga_pop_size*
>
> *ga_num_evals*
>
> *ga_num_generations*
>
> *ga_elitism*
>
>
> *ga_mutation_ratega_crossover_rate*
> *sw_max_its*
>
> Thanks
> At.te
>
>
> --
> *Levy Bueno Alves*
> *Postgraduate student*
> *Bioinformatics Group*
> *Department of Genetics, Ribeirão Preto Medical School, University of São
> Paulo - USP*
> ________________________________________________
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