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

Journal of cheminformatics

García-Jacas CR, Contreras-Torres E, Marrero-Ponce Y, Pupo-Meriño M, Barigye SJ, Cabrera-Leyva L.
PMID: 26925168
J Cheminform. 2016 Feb 25;8:10. doi: 10.1186/s13321-016-0122-x. eCollection 2016.

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 introduced. These descriptors codify chemical information for relations between two, three and four atoms by using several (dis-)similarity...

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García-Jacas CR, Contreras-Torres E, Marrero-Ponce Y, et al. Examining the predictive accuracy of the novel 3D N-linear algebraic molecular codifications on benchmark datasets. J Cheminform. 2016;8:10doi: 10.1186/s13321-016-0122-x.
García-Jacas, C. R., Contreras-Torres, E., Marrero-Ponce, Y., Pupo-Meriño, M., Barigye, S. J., & Cabrera-Leyva, L. (2016). Examining the predictive accuracy of the novel 3D N-linear algebraic molecular codifications on benchmark datasets. Journal of cheminformatics, 810. https://doi.org/10.1186/s13321-016-0122-x
García-Jacas, César R, et al. "Examining the predictive accuracy of the novel 3D N-linear algebraic molecular codifications on benchmark datasets." Journal of cheminformatics vol. 8 (2016): 10. doi: https://doi.org/10.1186/s13321-016-0122-x
García-Jacas CR, Contreras-Torres E, Marrero-Ponce Y, Pupo-Meriño M, Barigye SJ, Cabrera-Leyva L. Examining the predictive accuracy of the novel 3D N-linear algebraic molecular codifications on benchmark datasets. J Cheminform. 2016 Feb 25;8:10. doi: 10.1186/s13321-016-0122-x. eCollection 2016. PMID: 26925168; PMCID: PMC4768433.
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Distributed and multicore QuBiLS-MIDAS software v2.0: Computing chiral, fuzzy, weighted and truncated geometrical molecular descriptors based on tensor algebra.

Journal of computational chemistry

García-Jacas CR, Marrero-Ponce Y, Vivas-Reyes R, Suárez-Lezcano J, Martinez-Rios F, Terán JE, Aguilera-Mendoza L.
PMID: 32058625
J Comput Chem. 2020 May 05;41(12):1209-1227. doi: 10.1002/jcc.26167. Epub 2020 Feb 14.

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 QuBiLS-MIDAS software is the only one that computes atom-pair and alignment-free geometrical MDs (3D-MDs) from several distance...

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García-Jacas CR, Marrero-Ponce Y, Vivas-Reyes R, et al. Distributed and multicore QuBiLS-MIDAS software v2.0: Computing chiral, fuzzy, weighted and truncated geometrical molecular descriptors based on tensor algebra. J Comput Chem. 2020;41(12):1209-1227doi: 10.1002/jcc.26167.
García-Jacas, C. R., Marrero-Ponce, Y., Vivas-Reyes, R., Suárez-Lezcano, J., Martinez-Rios, F., Terán, J. E., & Aguilera-Mendoza, L. (2020). Distributed and multicore QuBiLS-MIDAS software v2.0: Computing chiral, fuzzy, weighted and truncated geometrical molecular descriptors based on tensor algebra. Journal of computational chemistry, 41(12), 1209-1227. https://doi.org/10.1002/jcc.26167
García-Jacas, César R, et al. "Distributed and multicore QuBiLS-MIDAS software v2.0: Computing chiral, fuzzy, weighted and truncated geometrical molecular descriptors based on tensor algebra." Journal of computational chemistry vol. 41,12 (2020): 1209-1227. doi: https://doi.org/10.1002/jcc.26167
García-Jacas CR, Marrero-Ponce Y, Vivas-Reyes R, Suárez-Lezcano J, Martinez-Rios F, Terán JE, Aguilera-Mendoza L. Distributed and multicore QuBiLS-MIDAS software v2.0: Computing chiral, fuzzy, weighted and truncated geometrical molecular descriptors based on tensor algebra. J Comput Chem. 2020 May 05;41(12):1209-1227. doi: 10.1002/jcc.26167. Epub 2020 Feb 14. PMID: 32058625.
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Smoothed Spherical Truncation based on Fuzzy Membership Functions: Application to the Molecular Encoding.

Journal of computational chemistry

García-Jacas CR, Marrero-Ponce Y, Brizuela CA, Suárez-Lezcano J, Martinez-Rios F.
PMID: 31647589
J Comput Chem. 2020 Jan 30;41(3):203-217. doi: 10.1002/jcc.26089. Epub 2019 Oct 24.

A novel spherical truncation method, based on fuzzy membership functions, is introduced to truncate interatomic (or interaminoacid) relations according to smoothing values computed from fuzzy membership degrees. In this method, the molecules are circumscribed into a sphere, so that...

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García-Jacas CR, Marrero-Ponce Y, Brizuela CA, et al. Smoothed Spherical Truncation based on Fuzzy Membership Functions: Application to the Molecular Encoding. J Comput Chem. 2019;41(3):203-217doi: 10.1002/jcc.26089.
García-Jacas, C. R., Marrero-Ponce, Y., Brizuela, C. A., Suárez-Lezcano, J., & Martinez-Rios, F. (2020). Smoothed Spherical Truncation based on Fuzzy Membership Functions: Application to the Molecular Encoding. Journal of computational chemistry, 41(3), 203-217. https://doi.org/10.1002/jcc.26089
García-Jacas, César R, et al. "Smoothed Spherical Truncation based on Fuzzy Membership Functions: Application to the Molecular Encoding." Journal of computational chemistry vol. 41,3 (2020): 203-217. doi: https://doi.org/10.1002/jcc.26089
García-Jacas CR, Marrero-Ponce Y, Brizuela CA, Suárez-Lezcano J, Martinez-Rios F. Smoothed Spherical Truncation based on Fuzzy Membership Functions: Application to the Molecular Encoding. J Comput Chem. 2020 Jan 30;41(3):203-217. doi: 10.1002/jcc.26089. Epub 2019 Oct 24. PMID: 31647589.
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QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations.

Journal of cheminformatics

Valdés-Martiní JR, Marrero-Ponce Y, García-Jacas CR, Martinez-Mayorga K, Barigye SJ, Vaz d'Almeida YS, Pham-The H, Pérez-Giménez F, Morell CA.
PMID: 29086120
J Cheminform. 2017 Jun 07;9(1):35. doi: 10.1186/s13321-017-0211-5.

BACKGROUND: In previous reports, Marrero-Ponce et al. proposed algebraic formalisms for characterizing topological (2D) and chiral (2.5D) molecular features through atom- and bond-based ToMoCoMD-CARDD (acronym for Topological Molecular Computational Design-Computer Aided Rational Drug Design) molecular descriptors. These MDs codify...

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Valdés-Martiní JR, Marrero-Ponce Y, García-Jacas CR, et al. QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations. J Cheminform. 2017;9(1):35doi: 10.1186/s13321-017-0211-5.
Valdés-Martiní, J. R., Marrero-Ponce, Y., García-Jacas, C. R., Martinez-Mayorga, K., Barigye, S. J., Vaz d'Almeida, Y. S., Pham-The, H., Pérez-Giménez, F., & Morell, C. A. (2017). QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations. Journal of cheminformatics, 9(1), 35. https://doi.org/10.1186/s13321-017-0211-5
Valdés-Martiní, José R, et al. "QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations." Journal of cheminformatics vol. 9,1 (2017): 35. doi: https://doi.org/10.1186/s13321-017-0211-5
Valdés-Martiní JR, Marrero-Ponce Y, García-Jacas CR, Martinez-Mayorga K, Barigye SJ, Vaz d'Almeida YS, Pham-The H, Pérez-Giménez F, Morell CA. QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations. J Cheminform. 2017 Jun 07;9(1):35. doi: 10.1186/s13321-017-0211-5. PMID: 29086120; PMCID: PMC5462671.
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Database fingerprint (DFP): an approach to represent molecular databases.

Journal of cheminformatics

Fernández-de Gortari E, García-Jacas CR, Martinez-Mayorga K, Medina-Franco JL.
PMID: 28224019
J Cheminform. 2017 Feb 06;9:9. doi: 10.1186/s13321-017-0195-1. eCollection 2017.

BACKGROUND: Molecular fingerprints are widely used in several areas of chemoinformatics including diversity analysis and similarity searching. The fingerprint-based analysis of chemical libraries, in particular of large collections, usually requires the molecular representation of each compound in the library...

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Fernández-de Gortari E, García-Jacas CR, Martinez-Mayorga K, et al. Database fingerprint (DFP): an approach to represent molecular databases. J Cheminform. 2017;9:9doi: 10.1186/s13321-017-0195-1.
Fernández-de Gortari, E., García-Jacas, C. R., Martinez-Mayorga, K., & Medina-Franco, J. L. (2017). Database fingerprint (DFP): an approach to represent molecular databases. Journal of cheminformatics, 99. https://doi.org/10.1186/s13321-017-0195-1
Fernández-de Gortari, Eli, et al. "Database fingerprint (DFP): an approach to represent molecular databases." Journal of cheminformatics vol. 9 (2017): 9. doi: https://doi.org/10.1186/s13321-017-0195-1
Fernández-de Gortari E, García-Jacas CR, Martinez-Mayorga K, Medina-Franco JL. Database fingerprint (DFP): an approach to represent molecular databases. J Cheminform. 2017 Feb 06;9:9. doi: 10.1186/s13321-017-0195-1. eCollection 2017. PMID: 28224019; PMCID: PMC5293704.
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Correction to Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set.

Journal of chemical information and modeling

Pinacho-Castellanos SA, García-Jacas CR, Gilson MK, Brizuela CA.
PMID: 34161087
J Chem Inf Model. 2021 Jul 26;61(7):3736. doi: 10.1021/acs.jcim.1c00656. Epub 2021 Jun 23.

No abstract available.

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Pinacho-Castellanos SA, García-Jacas CR, Gilson MK, et al. Correction to Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set. J Chem Inf Model. 2021;61(7):3736doi: 10.1021/acs.jcim.1c00656.
Pinacho-Castellanos, S. A., García-Jacas, C. R., Gilson, M. K., & Brizuela, C. A. (2021). Correction to Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set. Journal of chemical information and modeling, 61(7), 3736. https://doi.org/10.1021/acs.jcim.1c00656
Pinacho-Castellanos, Sergio A, et al. "Correction to Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set." Journal of chemical information and modeling vol. 61,7 (2021): 3736. doi: https://doi.org/10.1021/acs.jcim.1c00656
Pinacho-Castellanos SA, García-Jacas CR, Gilson MK, Brizuela CA. Correction to Alignment-Free Antimicrobial Peptide Predictors: Improving Performance by a Thorough Analysis of the Largest Available Data Set. J Chem Inf Model. 2021 Jul 26;61(7):3736. doi: 10.1021/acs.jcim.1c00656. Epub 2021 Jun 23. PMID: 34161087.
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GOWAWA Aggregation Operator-based Global Molecular Characterizations: Weighting Atom/bond Contributions (LOVIs/LOEIs) According to their Influence in the Molecular Encoding.

Molecular informatics

García-Jacas CR, Cabrera-Leyva L, Marrero-Ponce Y, Suárez-Lezcano J, Cortés-Guzmán F, García-González LA.
PMID: 30070434
Mol Inform. 2018 Dec;37(12):e1800039. doi: 10.1002/minf.201800039. Epub 2018 Aug 02.

A different perspective to compute global weighted definitions of molecular descriptors from the contributions of each atom (LOVIs) or covalent bond (LOEIs) within a molecule is presented, using the generalized ordered weighted averaging - weighted averaging (GOWAWA) aggregation operator....

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García-Jacas CR, Cabrera-Leyva L, Marrero-Ponce Y, et al. GOWAWA Aggregation Operator-based Global Molecular Characterizations: Weighting Atom/bond Contributions (LOVIs/LOEIs) According to their Influence in the Molecular Encoding. Mol Inform. 2018;37(12):e1800039doi: 10.1002/minf.201800039.
García-Jacas, C. R., Cabrera-Leyva, L., Marrero-Ponce, Y., Suárez-Lezcano, J., Cortés-Guzmán, F., & García-González, L. A. (2018). GOWAWA Aggregation Operator-based Global Molecular Characterizations: Weighting Atom/bond Contributions (LOVIs/LOEIs) According to their Influence in the Molecular Encoding. Molecular informatics, 37(12), e1800039. https://doi.org/10.1002/minf.201800039
García-Jacas, César R, et al. "GOWAWA Aggregation Operator-based Global Molecular Characterizations: Weighting Atom/bond Contributions (LOVIs/LOEIs) According to their Influence in the Molecular Encoding." Molecular informatics vol. 37,12 (2018): e1800039. doi: https://doi.org/10.1002/minf.201800039
García-Jacas CR, Cabrera-Leyva L, Marrero-Ponce Y, Suárez-Lezcano J, Cortés-Guzmán F, García-González LA. GOWAWA Aggregation Operator-based Global Molecular Characterizations: Weighting Atom/bond Contributions (LOVIs/LOEIs) According to their Influence in the Molecular Encoding. Mol Inform. 2018 Dec;37(12):e1800039. doi: 10.1002/minf.201800039. Epub 2018 Aug 02. PMID: 30070434.
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Predicting reactive sites with quantum chemical topology: carbonyl additions in multicomponent reactions.

Physical chemistry chemical physics : PCCP

Ramírez-Palma DI, García-Jacas CR, Carpio-Martínez P, Cortés-Guzmán F.
PMID: 32307508
Phys Chem Chem Phys. 2020 May 07;22(17):9283-9289. doi: 10.1039/d0cp00300j. Epub 2020 Apr 20.

Quantum Chemical Topology (QCT) is a well established structural theoretical approach, but the development of its reactivity component is still a challenge. The hypothesis of this work is that the reactivity of an atom within a molecule is a...

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Ramírez-Palma DI, García-Jacas CR, Carpio-Martínez P, et al. Predicting reactive sites with quantum chemical topology: carbonyl additions in multicomponent reactions. Phys Chem Chem Phys. 2020;22(17):9283-9289doi: 10.1039/d0cp00300j.
Ramírez-Palma, D. I., García-Jacas, C. R., Carpio-Martínez, P., & Cortés-Guzmán, F. (2020). Predicting reactive sites with quantum chemical topology: carbonyl additions in multicomponent reactions. Physical chemistry chemical physics : PCCP, 22(17), 9283-9289. https://doi.org/10.1039/d0cp00300j
Ramírez-Palma, David I, et al. "Predicting reactive sites with quantum chemical topology: carbonyl additions in multicomponent reactions." Physical chemistry chemical physics : PCCP vol. 22,17 (2020): 9283-9289. doi: https://doi.org/10.1039/d0cp00300j
Ramírez-Palma DI, García-Jacas CR, Carpio-Martínez P, Cortés-Guzmán F. Predicting reactive sites with quantum chemical topology: carbonyl additions in multicomponent reactions. Phys Chem Chem Phys. 2020 May 07;22(17):9283-9289. doi: 10.1039/d0cp00300j. Epub 2020 Apr 20. PMID: 32307508.
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Multi-Server Approach for High-Throughput Molecular Descriptors Calculation based on Multi-Linear Algebraic Maps.

Molecular informatics

García-Jacas CR, Aguilera-Mendoza L, González-Pérez R, Marrero-Ponce Y, Acevedo-Martínez L, Barigye SJ, Avdeenko T.
PMID: 27490863
Mol Inform. 2015 Jan;34(1):60-9. doi: 10.1002/minf.201400086. Epub 2014 Nov 28.

The present report introduces a novel module of the QuBiLS-MIDAS software for the distributed computation of the 3D Multi-Linear algebraic molecular indices. The main motivation for developing this module is to deal with the computational complexity experienced during the...

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García-Jacas CR, Aguilera-Mendoza L, González-Pérez R, et al. Multi-Server Approach for High-Throughput Molecular Descriptors Calculation based on Multi-Linear Algebraic Maps. Mol Inform. 2014;34(1):60-9doi: 10.1002/minf.201400086.
García-Jacas, C. R., Aguilera-Mendoza, L., González-Pérez, R., Marrero-Ponce, Y., Acevedo-Martínez, L., Barigye, S. J., & Avdeenko, T. (2015). Multi-Server Approach for High-Throughput Molecular Descriptors Calculation based on Multi-Linear Algebraic Maps. Molecular informatics, 34(1), 60-9. https://doi.org/10.1002/minf.201400086
García-Jacas, César R, et al. "Multi-Server Approach for High-Throughput Molecular Descriptors Calculation based on Multi-Linear Algebraic Maps." Molecular informatics vol. 34,1 (2015): 60-9. doi: https://doi.org/10.1002/minf.201400086
García-Jacas CR, Aguilera-Mendoza L, González-Pérez R, Marrero-Ponce Y, Acevedo-Martínez L, Barigye SJ, Avdeenko T. Multi-Server Approach for High-Throughput Molecular Descriptors Calculation based on Multi-Linear Algebraic Maps. Mol Inform. 2015 Jan;34(1):60-9. doi: 10.1002/minf.201400086. Epub 2014 Nov 28. PMID: 27490863.
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N-linear algebraic maps for chemical structure codification: a suitable generalization for atom-pair approaches?.

Current drug metabolism

Garcia-Jacas CR, Marrero-Ponce Y, Barigye SJ, Valdes-Martini JR, Rivera-Borroto OM, Olivero-Verbel J.
PMID: 24909423
Curr Drug Metab. 2014;15(4):441-69. doi: 10.2174/1389200215666140605124506.

The present manuscript introduces, for the first time, a novel 3D-QSAR alignment free method (QuBiLS-MIDAS) based on tensor concepts through the use of the three-linear and four-linear algebraic forms as specific cases of n-linear maps. To this end, the...

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Garcia-Jacas CR, Marrero-Ponce Y, Barigye SJ, et al. N-linear algebraic maps for chemical structure codification: a suitable generalization for atom-pair approaches?. Curr Drug Metab. 2014;15(4):441-69doi: 10.2174/1389200215666140605124506.
Garcia-Jacas, C. R., Marrero-Ponce, Y., Barigye, S. J., Valdes-Martini, J. R., Rivera-Borroto, O. M., & Olivero-Verbel, J. (2014). N-linear algebraic maps for chemical structure codification: a suitable generalization for atom-pair approaches?. Current drug metabolism, 15(4), 441-69. https://doi.org/10.2174/1389200215666140605124506
Garcia-Jacas, Cesar R, et al. "N-linear algebraic maps for chemical structure codification: a suitable generalization for atom-pair approaches?." Current drug metabolism vol. 15,4 (2014): 441-69. doi: https://doi.org/10.2174/1389200215666140605124506
Garcia-Jacas CR, Marrero-Ponce Y, Barigye SJ, Valdes-Martini JR, Rivera-Borroto OM, Olivero-Verbel J. N-linear algebraic maps for chemical structure codification: a suitable generalization for atom-pair approaches?. Curr Drug Metab. 2014;15(4):441-69. doi: 10.2174/1389200215666140605124506. PMID: 24909423.
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Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs).

Journal of cheminformatics

García-Jacas CR, Cabrera-Leyva L, Marrero-Ponce Y, Suárez-Lezcano J, Cortés-Guzmán F, Pupo-Meriño M, Vivas-Reyes R.
PMID: 30362050
J Cheminform. 2018 Oct 25;10(1):51. doi: 10.1186/s13321-018-0306-7.

BACKGROUND: Several topological (2D) and geometric (3D) molecular descriptors (MDs) are calculated from local vertex/edge invariants (LOVIs/LOEIs) by performing an aggregation process. To this end, norm-, mean- and statistic-based (non-fuzzy) operators are used, under the assumption that LOVIs/LOEIs are...

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García-Jacas CR, Cabrera-Leyva L, Marrero-Ponce Y, et al. Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs). J Cheminform. 2018;10(1):51doi: 10.1186/s13321-018-0306-7.
García-Jacas, C. R., Cabrera-Leyva, L., Marrero-Ponce, Y., Suárez-Lezcano, J., Cortés-Guzmán, F., Pupo-Meriño, M., & Vivas-Reyes, R. (2018). Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs). Journal of cheminformatics, 10(1), 51. https://doi.org/10.1186/s13321-018-0306-7
García-Jacas, César R, et al. "Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs)." Journal of cheminformatics vol. 10,1 (2018): 51. doi: https://doi.org/10.1186/s13321-018-0306-7
García-Jacas CR, Cabrera-Leyva L, Marrero-Ponce Y, Suárez-Lezcano J, Cortés-Guzmán F, Pupo-Meriño M, Vivas-Reyes R. Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs). J Cheminform. 2018 Oct 25;10(1):51. doi: 10.1186/s13321-018-0306-7. PMID: 30362050; PMCID: PMC6755596.
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