Las Vegas algorithm in the prediction of intrinsic solubility of drug-like compounds

IF 2.7 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Journal of molecular graphics & modelling Pub Date : 2025-03-04 DOI:10.1016/j.jmgm.2025.109004
Aleksandar M. Veselinović , Alla P. Toropova , Andrey A. Toropov , Alessandra Roncaglioni , Emilio Benfenati
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Abstract

A randomized algorithm that always succeeds in producing a correct output, but whose running time depends on random events is known as a Las Vegas algorithm. In this study, the Las Vegas algorithm aimed to improve QSPR models of intrinsic solubility of drug-like compounds obtained by the Monte Carlo method. Corresponding computational experiments were carried out with the CORAL software. The developed QSPR models were rigorously validated using a battery of statistical parameters, demonstrating excellent predictive ability and robustness. It has been shown, that the Las Vegas algorithm is a suitable way to improve the predictive potential of models obtained with the Monte Carlo technique. Additionally, the study identified key molecular fragments derived from the SMILES notation descriptors that influence the intrinsic solubility (increase or decrease). Overall, this work underscores the efficacy of the Monte Carlo method optimization with applied Las Vegas algorithm in constructing conformation-independent QSPR models with strong predictive power for prediction of intrinsic solubility of drug-like compounds.

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来源期刊
Journal of molecular graphics & modelling
Journal of molecular graphics & modelling 生物-计算机:跨学科应用
CiteScore
5.50
自引率
6.90%
发文量
216
审稿时长
35 days
期刊介绍: The Journal of Molecular Graphics and Modelling is devoted to the publication of papers on the uses of computers in theoretical investigations of molecular structure, function, interaction, and design. The scope of the journal includes all aspects of molecular modeling and computational chemistry, including, for instance, the study of molecular shape and properties, molecular simulations, protein and polymer engineering, drug design, materials design, structure-activity and structure-property relationships, database mining, and compound library design. As a primary research journal, JMGM seeks to bring new knowledge to the attention of our readers. As such, submissions to the journal need to not only report results, but must draw conclusions and explore implications of the work presented. Authors are strongly encouraged to bear this in mind when preparing manuscripts. Routine applications of standard modelling approaches, providing only very limited new scientific insight, will not meet our criteria for publication. Reproducibility of reported calculations is an important issue. Wherever possible, we urge authors to enhance their papers with Supplementary Data, for example, in QSAR studies machine-readable versions of molecular datasets or in the development of new force-field parameters versions of the topology and force field parameter files. Routine applications of existing methods that do not lead to genuinely new insight will not be considered.
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