QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations

JR Valdés-Martiní, Y Marrero-Ponce… - Journal of …, 2017 - Springer
Abstract Background In previous reports, Marrero-Ponce et al. proposed algebraic
formalisms for characterizing topological (2D) and chiral (2.5 D) molecular features through …

Smoothed spherical truncation based on fuzzy membership functions: application to the molecular encoding

CR García‐Jacas, Y Marrero‐Ponce… - Journal of …, 2020 - Wiley Online Library
A novel spherical truncation method, based on fuzzy membership functions, is introduced to
truncate interatomic (or interaminoacid) relations according to smoothing values computed …

Enhancing acute oral toxicity predictions by using consensus modeling and algebraic form-based 0D-to-2D molecular encodes

CR García-Jacas, Y Marrero-Ponce… - Chemical Research …, 2019 - ACS Publications
Quantitative structure–activity relationships (QSAR) are introduced to predict acute oral
toxicity (AOT), by using the QuBiLS-MAS (acronym for quadratic, bilinear and N-Linear maps …

QuBiLs-MAS method in early drug discovery and rational drug identification of antifungal agents

R Medina Marrero, Y Marrero-Ponce… - SAR and QSAR in …, 2015 - Taylor & Francis
The QuBiLs-MAS approach is used for the in silico modelling of the antifungal activity of
organic molecules. To this effect, non-stochastic (NS) and simple-stochastic (SS) atom …

Overproduce and select, or determine optimal molecular descriptor subset via configuration space optimization? Application to the prediction of ecotoxicological …

LA García‐González, Y Marrero‐Ponce… - Molecular …, 2023 - Wiley Online Library
Predicting the likely biological activity (or property) of compounds is a fundamental and
challenging task in the drug discovery process. Current computational methodologies aim to …

Conformation-dependent QSAR approach for the prediction of inhibitory activity of bromodomain modulators

CR García-Jacas, K Martinez-Mayorga… - SAR and QSAR in …, 2017 - Taylor & Francis
Epigenetic drug discovery is a promising research field with growing interest in the scientific
community, as evidenced by the number of publications and the large amount of structure …

Examining the predictive accuracy of the novel 3D N-linear algebraic molecular codifications on benchmark datasets

CR García-Jacas, E Contreras-Torres… - Journal of …, 2016 - Springer
Background Recently, novel 3D alignment-free molecular descriptors (also known as
QuBiLS-MIDAS) based on two-linear, three-linear and four-linear algebraic forms have been …

Distributed and multicore QuBiLS‐MIDAS software v2. 0: Computing chiral, fuzzy, weighted and truncated geometrical molecular descriptors based on tensor algebra

CR García‐Jacas, Y Marrero‐Ponce… - Journal of …, 2020 - Wiley Online Library
Advances to the distributed, multi‐core and fully cross‐platform QuBiLS‐MIDAS software v2.
0 (http://tomocomd. com/qubils-midas) are reported in this article since the v1. 0 release. The …

Novel 3D bio-macromolecular bilinear descriptors for protein science: Predicting protein structural classes

Y Marrero-Ponce, E Contreras-Torres… - Journal of theoretical …, 2015 - Elsevier
In the present study, we introduce novel 3D protein descriptors based on the bilinear
algebraic form in the ℝ n space on the coulombic matrix. For the calculation of these …

Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs)

CR García-Jacas, L Cabrera-Leyva… - Journal of …, 2018 - Springer
Background Several topological (2D) and geometric (3D) molecular descriptors (MDs) are
calculated from local vertex/edge invariants (LOVIs/LOEIs) by performing an aggregation …