auto dock uses Lamarckian algorithm.........

Autodock 4.2 has implemented 4 different search algorithms: Lamarkian, Simulated Annealing, Genetic Algorithm and Local Search. When I need a detailed search, and I'm not bothered about time I use lamarkian, but if you need a bit of speed you can use the local search, wich is not the beast search algorithm but the computation is quite fast.

I second Javier Klett. however if you have ample amount of computational power then you dont have worry about time consumption and in that case LGA is one of the best algorithms.

The most common explanation would be: The genetic algorithm follows Darwin's theory of evolution i.e. survival of the fittest. In Lamarkian, one is allowed to adopt during ones lifetime. I agree with Javier's reasoning on the preference for Lamarkian. Only use local search if you expect minute or no conformation changes.

In the GA and Lamarkian GA, the number of energy evaluations and the number of generations affect how long a docking will run. Lamarkian GA, children are allowed to inherit the local search adaptations of their parents. If you really want to find the difference then follow the autodock protocol and check how the result vary. well I prefer LGA .

There are number of factors affecting quality of results you might obtain using GA and LGA. I would advise changing following parameters in docking run. Due to limited space I would be as brief as possible...First and foremost... Both the GA and LGA begin with a population of random ligand conformations in random orientations and at random translations. You must decide the number of individuals in the population, you can do this using " ga_pop_size ": Typically, 50 is found to be a good value. AutoDock counts the number of energy evaluations and the number of generations as the docking run proceeds: the run terminates if either limit is reached (" ga_num_evals " and " ga_num_generations " respectively). You should critically set the number of the best individuals in the current population that automatically survive into the next generation, using " ga_elitism ": typically this is 1. You should also specify a proper value for the rate of gene mutation using " ga_mutation_rate " and the rate of gene crossover " ga_crossover_rate "; typically these are 0.02 and 0.80 respectively, although setting " ga_crossover_rate " to 0.00 reduces the genetic algortihm (GA) to an evolutionary programming (EP) method. If the EP approach is used, you should also use an increased mutation rate to ensure a good exploration of the search space. The number of generations for picking the worst individual is set by " ga_window_size " and is usually 10. Hope this helps...

Cheers and AutoDock ROCKZZZ

If you are doing Virtual screening go with AutoDock vina, If you identified the ligand and wants to know in depth about Protein-Ligand interaction choose AutoDock 4.2. If you choose remote in PyRX and LGA, time will not be a constraint. It works fast. Just give 50 runs for the LGA, you will get the optimized results...

Genetic algorithm performs global search only but LGA algorithm is a hybrid algorithm (both genetic and local search). Hence, it is more efficient and has enhanced performance relative to genetic algorithm alone. In LGA each generation is followed by local search on a user defined proportion of the population. Please read this article for detailed understanding:

GARRETT M. MORRIS,DAVID S. GOODSELL, ROBERT S. HALLIDAY,RUTH HUEY,WILLIAM E. HART, RICHARD K. BELEW, ARTHUR J. OLSON. Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function. Journal of Computational Chemistry, Vol. 19, No. 14, 1639-1662 (1998).

I agree with the quotes made by above persons, i recommend LGA personally, but if you want to differentiate between false positives and true negatives from the clusters, you need more pose (conformers), in that case GA is better.

autodock vina uses LGA algorithms?

Monte Carlo Simulated Annealing (SA) is old one, But now a Genetic Algorithm (GA); & Lamarckian Genetic Algorithm (LGA) is best for autodock