QuBiLs-MAS Publications

QuBiLS-MAS Theory

Atom-based 0D-2,5-Chiral Algebraic descriptors

  1. Marrero-Ponce, Y. Total and Local Quadratic Indices of the Molecular Pseudograph’s Atom Adjacency Matrix: Applications to the Prediction of Physical Properties of Organic Compounds. Molecules. 2003, 8, 687-726. DOI: 10.3390/80900687
  2. Marrero-Ponce, Y. Total and Local (Atom and Atom-Type) Molecular Quadratic Indices: Significance-Interpretation, Comparison to Other Molecular Descriptors and QSPR/QSAR Applications. Bioorg. Med. Chem. 2004, 12, 6351-6369. DOI: 10.1016/j.bmc.2004.09.034
  3. Marrero-Ponce, Y.; Castillo-Garit, J. A. 3D-Chiral Atom, Atom-type, and Total Non-Stochastic and Stochastic Molecular Linear Indices and their Application to Central Chirality Codification. J. Comput. Aided.-Mol. Des. 2005, 19, 369–383. DOI: 10.1007/s10822-005-7575-8
  4. Marrero-Ponce, Y. Linear Indices of the “Molecular Pseudograph’s Atom Adjacency Matrix”: Definition, Significance-Interpretation and Application to QSAR Analysis of Flavone Derivatives as HIV-1 Integrase Inhibitors. J. Chem. Inf. Comput. Sci. 2004, 44, 2010-2026. DOI: 10.1021/ci049950k
  5. Castillo-Garit, J. A.; Marrero-Ponce, Y.; Torrens, F.; Rotondo, R. Atom-based Stochastic and non-Stochastic 3D-Chiral Bilinear Indices and their Applications to Central Chirality Codification. J. Mol. Graph. Model. 2007, 26, 32-47. DOI: 10.1016/j.jmgm.2006.09.007

Bond-based 0D-2,5-Chiral Algebraic descriptors

  1. Marrero-Ponce, Y.; Torrens, F.; Alvarado, Y. J: Rotondo, R. Bond-Based Global and Local (Bond, Group and Bond-Type) Quadratic Indices and Their Applications to Computer-Aided Molecular Design. 1. QSPR Studies of Diverse Sets of Organic Chemicals. J. Comput. Aided Mol. Des. 2006, 20, 685-701. DOI: 10.1007/s10822-006-9089-4
  2. Castillo-Garit, J. A.; Marrero-Ponce, Y.; Torrens, F., García-Domenech, R.; Romero-Zaldivar, V. Bond-Based 3D-Chiral Linear Indices: Theory and QSAR Applications to Central Chirality Codification. J. Comput. Chem. 2008, 29, 2500–2512. DOI: 10.1002/jcc.20964
  3. Marrero-Ponce, Y.; Martinez-E. R.; Casañola-Martín. G. M.; Pérez-Giménez, F.; Echevería-Días, Y.; Rodriguez-Borges, J. E. Bond-Extended non-Stochastic and Stochastic Bilinear Indices. 1. QSPR/QSAR Applications to the Description of Properties/activities of Small-Medium Size Organic Compounds. Int. J. Quant. Chem. 2011, 111, 8–34. DOI: 10.1002/qua.22392
  4. Marrero-Ponce, Y.; Martínez, R. E.; Casañola-Martín. G. M.; Castillo-Garit, J., A.; Echevería-Díaz, Y.; Romero Zaldivar, V.; Tygat, J.; Rodriguez Borges J. E.; García-Domenech, R.; Torrens, F.; Pérez-Giménez, F. Bond-based Linear Indices of the non-Stochastic and Stochastic Edge Adjacency Matrix. 1. Theory and Modeling of CHEMPHYS Properties of Organic Molecules. Mol. Divers. 2010. 14,731–753. DOI: 10.1007/s11030-009-9201-5

QuBiLS-MAS Software

  1. Valdés-Martiní, J. R.; Marrero-Ponce, Y.; García-Jacas, C. R.; Martinez-Mayorga, K.; Barigye, S. J.; Vaz d‘Almeida, Y. S.; Pham-The, Hai.; Pérez-Giménez, F.; Morell, C. A. 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. 2017, 9 (35), 1-26. DOI: 10.1186/s13321-017-0211-5

QuBiLS-MAS Applications

  1. Marrero-Ponce, Y.; Castillo-Garit, J.A.; Olazabal, E.; Serrano, H. S.; Morales, A.; Castañedo, N.; Ibarra-Velarde, F.; Huesca-Guillen, A.; Jorge, E.; del Valle, A.; Torrens, F.; Castro, E. A. TOMOCOMD-CARDD, a Novel Approach for Computer-Aided “Rational” Drug Design: I. Theoretical and Experimental Assessment of a Promising Method for Computational Screening and in silico Design of New Anthelmintic Compounds. J. Comput. Aided Mol. Des. 2004, 18, 615-634. DOI: 10.1007/s10822-004-5171-y
  2. Marrero-Ponce, Y.; Iyarreta, M.; Montero, A.; Romero, C.; Brandt, C. A.; Ávila, P. E.; Kirchgatter, K. A.; Machado, Y. Ligand-Based Virtual Screening and in silico Design of New Antimalarial Compounds Using Non-Stochastic and Stochastic Total and Atom-type Quadratic Maps. J. Chem. Inf. Comput. Sci. 2005, 45, 1082-1100. DOI: 10.1021/ci050085t
  3. Marrero-Ponce, Y.; Meneses-Marcel, A.; Machado-Tugores, Y.; Escario, J. A.; Gómez-Barrio, A; Montero Pereira, D.; Nogal-Ruiz, J. J.; Arán, V. J.; Martínez-Fernández, A. R.; Torrens, F.; Rotondo, R. Predicting Antitrichomonal Activity: A Computational Screening Using Atom-Based Bilinear Indices and Experimental Proofs. Bioorg. Med. Chem. 2006, 14, 6502–6524. DOI: 10.1016/j.bmc.2006.06.016
  4. 4. Marrero-Ponce, Y.; Khan, M. T. H.; Casañola-Martin, G. M.; Ather, A.; Sultankhodzhaev, M. N.; Torrens, F.; Rotondo, R. Prediction of Tyrosinase Inhibition Spectra for Chemicals Using Novel Atom-Based Bilinear Indices. ChemMedChem. 2007, 2, 449-478. DOI: 10.1002/cmdc.200600186
  5. 5. Castillo-Garit, J. A.; Marrero-Ponce, Y.; Torrens, F.; García-Domenech, R. Estimation of ADME Properties in Drug Discovery: Predicting Caco-2 Cell Permeability Using Atom-Based Stochastic and Non-Stochastic Linear Indices. J. Pharm. Sci. 2008, 97, 1946-1976. DOI: 10.1002/jps.21122
  6. 6. Le-Thi-Thu, H.; Casas Cardoso, G.; Casañola-Martín, G. M.; Marrero-Ponce, Y.; Puris, A.; Torrens, A.; Rescigno, A.; Abad, C. QSAR Models for Tyrosinase Inhibitory Activity Description Applying Modern Statistical Classification Techniques: A Comparative Study. Chemom. Intell. Lab. Systems. 2010, 104, 249–259. DOI: 10.1016/j.chemolab.2010.08.016
  7. 7. Marrero-Ponce, Y.; Siverio Mota, D.; Galvez-Llompart, M.; Recio, M. C.; Giner, R. M.; García-Domenech,.; Torrens, F.; Arán, J.; Crawford, A. C.; de Witte, P. A. M. Discovering Novel Anti-Inflammatory Drug-Like Compounds by Aligning in silico and in vivo Screening: The Nitro-Indazolinone Chemotype. Eur. J. Med. Chem. 2011, 46, 5736-5753. DOI: 10.1016/j.ejmech.2011.07.053
  8. 8. Martins Alho, M. A.; Marrero-Ponce, Y.; Meneses-Marcel, A. M.; Machado Tugores, Y.; Montero-Torres, A.; Pérez-Giménez, F.; Gómez-Barrio, A.; Nogal, J. J.; García- Sánchez, R. R.; Celeste Vega, M.; Rolón, M.; Martínez-Fernández, A. R.; Escario, J. A.; Rivera, N.; Mondragón, M.; Mondragón, R.; Chicharro, R.; Arán, V. J. Antiprotozoan Lead Discovery by Aligning Dry and Wet Screening: Prediction, Synthesis, and Biological Assay of Novel Quinoxalinones. Biorg. Med. Chem.2014, 22, 1568–1585. DOI: 10.1016/j.bmc.2014.01.036
  9. 9. Marrero-Ponce, Y.; Yeniel González Castañeda, Ricardo Vivas-Reyes, Fredy Máximo Vergara, Vicente J. Arán, Juan A. Castillo-Garit, Facundo Pérez-Giménez, Francisco Torrens, Huong Le-Thi-Thu, Hai Pham-The, Yolanda Vera Montenegro; Froylán Ibarra-Velarde. Dry selection and wet evaluation for the rational discovery of new anthelmintics. Molecular Physics, 2017, 115, 2300-2313. DOI: 10.1080/00268976.2017.1296194
  10. Medina Marrero R.; Marrero-Ponce Y.; Barigye S. J.; Echeverría Díaz Y.; Acevedo-Barrios R.; Casañola-Martín G. M.; García Bernal M.; Torrens F.; Pérez-Giménez F. QuBiLs-MAS method in early drug discovery and rational drug identification of antifungal agents. SAR and QSAR in Environmental Research. 2015. 26 (11), 943-58. DOI: 10.1080/1062936X.2015.1104517
  11. García-Jacas C. R.; Marrero-Ponce Y.; Cortés-Guzmán F.; Suárez-Lezcano J.; Martinez-Rios F.; García-González L. A.; Pupo-Meriño M.; Martinez-Mayorga K. Enhancing Acute Oral Toxicity Predictions by using Consensus Modeling and Algebraic Form-Based 0D-to-2D Molecular Encodes. Chemical Research in Toxicology. 2019. 32 (6), 1178-1192. DOI: 10.1021/acs.chemrestox.9b00011