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.
Volume 32, Issue 3 (2021), pp. 477–498
This work compares different algorithms to replace the genetic optimizer used in a recent methodology for creating realistic and computationally efficient neuron models. That method focuses on single-neuron processing and has been applied to cerebellar granule cells. It relies on the adaptive-exponential integrate-and-fire (AdEx) model, which must be adjusted with experimental data. The alternatives considered are: i) a memetic extension of the original genetic method, ii) Differential Evolution, iii) Teaching-Learning-Based Optimization, and iv) a local optimizer within a multi-start procedure. All of them ultimately outperform the original method, and the last two do it in all the scenarios considered.
Volume 31, Issue 4 (2020), pp. 821–839
Ligand Based Virtual Screening methods are widely used in drug discovery as filters for subsequent in-vitro and in-vivo characterization. Since the databases processed are enormously large, this pre-selection process requires the use of fast and precise methodologies. In this work, the similarity between compounds is measured in terms of electrostatic potential. To do so, we propose a new and alternative methodology, called LBVS-Electrostatic. Accordingly to the obtained results, we are able to conclude that many of the compounds proposed with our novel approach could not be discovered with the classical one.
Pub. online:1 Jan 2018Type:Research ArticleOpen Access
Volume 29, Issue 1 (2018), pp. 21–39
The heliostat field of Solar Central Receiver Systems takes up to 50% of the initial investment and can cause up to 40% of energetic loss in operation. Hence, it must be carefully optimized. Design procedures usually rely on particular heliostat distribution models. In this work, optimization of the promising biomimetic distribution model is studied. Two stochastic population-based optimizers are applied to maximize the optical efficiency of fields: a genetic algorithm, micraGA, and a memetic one, UEGO. As far as the authors know, they have not been previously applied to this problem. However, they could be a good option according to their structure. Additionally, a Brute-Force Grid is used to estimate the global optimum and a Pure-Random Search is applied as a baseline reference. Our empirical results show that many different configurations of the distribution model lead to very similar solutions. Although micraGA exhibits poor performance, UEGO achieves the best results in a reduced time and seems appropriate for the problem at hand.