Pub. online:7 Nov 2023Type:Research ArticleOpen Access
Journal:Informatica
Volume 34, Issue 4 (2023), pp. 743–769
Abstract
Ligand-Based Virtual Screening accelerates and cheapens the design of new drugs. However, it needs efficient optimizers because of the size of compound databases. This work proposes a new method called Tangram CW. The proposal also encloses a knowledge-based filter of compounds. Tangram CW achieves comparable results to the state-of-the-art tools OptiPharm and 2L-GO-Pharm using about a tenth of their computational budget without filtering. Activating it discards more than two thirds of the database while keeping the desired compounds. Thus, it is possible to consider molecular flexibility despite increasing the options. The implemented software package is public.
Journal:Informatica
Volume 26, Issue 4 (2015), pp. 649–662
Abstract
A multitude of heuristic stochastic optimization algorithms have been described in literature to obtain good solutions of the box-constrained global optimization problem often with a limit on the number of used function evaluations. In the larger question of which algorithms behave well on which type of instances, our focus is here on the benchmarking of the behavior of algorithms by applying experiments on test instances. We argue that a good minimum performance benchmark is due to pure random search; i.e. algorithms should do better. We introduce the concept of the cumulative distribution function of the record value as a measure with the benchmark of pure random search and the idea of algorithms being dominated by others. The concepts are illustrated using frequently used algorithms.