TY - JOUR

T1 - QuBiLS-MIDAS

T2 - A parallel free-software for molecular descriptors computation based on multilinear algebraic maps

AU - García-Jacas, César R.

AU - Marrero-Ponce, Yovani

AU - Acevedo-Martínez, Liesner

AU - Barigye, Stephen J.

AU - Valdés-Martiní, José R.

AU - Contreras-Torres, Ernesto

PY - 2014/7/5

Y1 - 2014/7/5

N2 - The present report introduces the QuBiLS-MIDAS software belonging to the ToMoCoMD-CARDD suite for the calculation of three-dimensional molecular descriptors (MDs) based on the two-linear (bilinear), three-linear, and four-linear (multilinear or N-linear) algebraic forms. Thus, it is unique software that computes these tensor-based indices. These descriptors, establish relations for two, three, and four atoms by using several (dis-)similarity metrics or multimetrics, matrix transformations, cutoffs, local calculations and aggregation operators. The theoretical background of these N-linear indices is also presented. The QuBiLS-MIDAS software was developed in the Java programming language and employs the Chemical Development Kit library for the manipulation of the chemical structures and the calculation of the atomic properties. This software is composed by a desktop user-friendly interface and an Abstract Programming Interface library. The former was created to simplify the configuration of the different options of the MDs, whereas the library was designed to allow its easy integration to other software for chemoinformatics applications. This program provides functionalities for data cleaning tasks and for batch processing of the molecular indices. In addition, it offers parallel calculation of the MDs through the use of all available processors in current computers. The studies of complexity of the main algorithms demonstrate that these were efficiently implemented with respect to their trivial implementation. Lastly, the performance tests reveal that this software has a suitable behavior when the amount of processors is increased. Therefore, the QuBiLS-MIDAS software constitutes a useful application for the computation of the molecular indices based on N-linear algebraic maps and it can be used freely to perform chemoinformatics studies.

AB - The present report introduces the QuBiLS-MIDAS software belonging to the ToMoCoMD-CARDD suite for the calculation of three-dimensional molecular descriptors (MDs) based on the two-linear (bilinear), three-linear, and four-linear (multilinear or N-linear) algebraic forms. Thus, it is unique software that computes these tensor-based indices. These descriptors, establish relations for two, three, and four atoms by using several (dis-)similarity metrics or multimetrics, matrix transformations, cutoffs, local calculations and aggregation operators. The theoretical background of these N-linear indices is also presented. The QuBiLS-MIDAS software was developed in the Java programming language and employs the Chemical Development Kit library for the manipulation of the chemical structures and the calculation of the atomic properties. This software is composed by a desktop user-friendly interface and an Abstract Programming Interface library. The former was created to simplify the configuration of the different options of the MDs, whereas the library was designed to allow its easy integration to other software for chemoinformatics applications. This program provides functionalities for data cleaning tasks and for batch processing of the molecular indices. In addition, it offers parallel calculation of the MDs through the use of all available processors in current computers. The studies of complexity of the main algorithms demonstrate that these were efficiently implemented with respect to their trivial implementation. Lastly, the performance tests reveal that this software has a suitable behavior when the amount of processors is increased. Therefore, the QuBiLS-MIDAS software constitutes a useful application for the computation of the molecular indices based on N-linear algebraic maps and it can be used freely to perform chemoinformatics studies.

KW - 3D N-linear indices

KW - Java language

KW - N-tuple simple stochastic

KW - N-tuple spatial-(dis)similarity matrix

KW - QuBiLS-MIDAS

KW - TOMOCOMD-CARDD

KW - chemical development kit

KW - double stochastic and mutual probability matrices

KW - scalability

KW - speed up

UR - http://www.scopus.com/inward/record.url?scp=84902072776&partnerID=8YFLogxK

U2 - 10.1002/jcc.23640

DO - 10.1002/jcc.23640

M3 - Artículo

C2 - 24889018

AN - SCOPUS:84902072776

SN - 0192-8651

VL - 35

SP - 1395

EP - 1409

JO - Journal of Computational Chemistry

JF - Journal of Computational Chemistry

IS - 18

ER -