List of Publications

RESEARCH PAPERS

[Only published, in print and accepted papers are listed]

PUBLICATIONS

Published Papers

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.

Marrero-Ponce, Y.; Cabrera, M., A.; Romero, V.; Ofori, E.; Montero, L. A. Total and Local Quadratic Indices of the “Molecular Pseudograph’s Atom Adjacency Matrix”. Application to Prediction of Caco-2 Permeability of Drugs. Int. J. Mol. Sci. 2003, 4, 512-536.

González-Díaz, H; Marrero-Ponce, Y.; Hernández, I; Bastida, I;  Tenorio, E; Nasco, O; Uriarte, U; Castañedo, N.; Cabrera, M.A.; Aguila, E.; Marrero, O.; Morales, A.; Pérez, M. 3D-MEDNEs: An Alternative “In Silico” Technique for Chemical Research in Toxicology. 1. Prediction of Chemically Induced Agranulocytosis. Chem. Res. Toxicol. 2003, 16, 1318-1327.

Marrero-Ponce, Y.; Cabrera, M. A.; Romero, V.; González, D. H.; Torrens, F. A New Topological Descriptors Based Model for Predicting Intestinal Epithelial Transport of Drugs in Caco-2 Cell Culture. J. Pharm. Pharm. Sci. 2004, 7, 186-199.

Marrero-Ponce, Y.; González-Díaz, H.;  Romero-Zaldivar, V.; Torrens, F.; Castro, E. A. 3D-Chiral Quadratic Indices of the “Molecular Pseudograph’s Atom Adjacency Matrix” and their Application to Central Chirality Codification: Classification of ACE Inhibitors and Prediction of s-Receptor Antagonist Activities. Bioorg. Med. Chem. 2004,  12, 5331-5342.

*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.

*This paper has recently been recognised in the "Top-50 most cited articles" as published in Bioorganic & Medicinal Chemistry 2003-2006 [Citaton Source: Scopus (www.scopus.com)]

Marrero-Ponce, Y.; Nodarse, D.; González-Díaz, H.;  Ramos de Armas, R.; Romero-Zaldivar, V.; Torrens, F.; Castro, E. Nucleic Acid Quadratic Indices of the “Macromolecular Graph’s Nucleotides Adjacency Matrix”.  Modeling of Footprints after the Interaction of Paromomycin with the HIV-1 Y-RNA Packaging Region. Int. J. Mol. Sci. 2004, 5, 276-293 (see also CPS: physchem/0401004.)

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.

Marrero-Ponce, Y.; Castillo-Garit, J. A.; Torrens, F.; Romero-Zaldivar, V.; Castro, E. Atom, Atom-Type and Total Linear Indices of the “Molecular Pseudograph’s Atom Adjacency Matrix”: Application to QSPR/QSAR Studies of Organic Compounds. Molecules. 2004, 9, 1100-1123.

Marrero-Ponce, Y.; Medina, R.; Castro, E. A.; de Armas, R.; González, H.; Romero, V.; Torrens, F. Protein Quadratic Indices of the “Macromolecular Pseudograph’s a-Carbon Atom Adjacency Matrix”. 1. Prediction of Arc Repressor Alanine-mutant’s Stability. Molecules. 2004, 9, 1124–1147.

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, 615-633.

Marrero-Ponce, Y.; Montero-Torres, A.; Romero-Zaldivar, C.; Iyarreta-Veitía, I.; Mayón Peréz, M.; García Sánchez, R. Non-Stochastic and Stochastic Linear Indices of the “Molecular Pseudograph’s Atom Adjacency Matrix”: Application to “in silico” Studies for the Rational Discovery of New Antimalarial Compounds. Bioorg. Med. Chem. 2005, 13, 1293-1304.

Marrero-Ponce, Y.; Castillo-Garit, J.A.; Olazabal, E.; Serrano, H. S.; Morales, A.; Castañedo, N.; Ibarra-Velarde, F.; Huesca-Guillen, A.; Jorge, E.; Sánchez, A. M.; Torrens, F.; Castro, E. A. Atom, Atom-Type and Total Molecular Linear Indices as a Promising Approach for Bioorganic & Medicinal Chemistry: Theoretical and Experimental Assessment of a Novel Method for Virtual Screening and Rational Design of New Lead Anthelmintic. Bioorg. Med. Chem. 2005, 13, 1005-1020.

Marrero-Ponce, Y.; Huesca-Guillen, A.; Ibarra-Velarde, F. Quadratic Indices of the “Molecular Pseudograph’s Atom Adjacency Matrix” and Their Stochastic Forms: A Novel Approach for Virtual Screening and in silico Discovery of New Lead Paramphistomicide Drugs-like Compounds. J. Theor. Chem. (THEOCHEM). 2005, 717, 67-79.

Alvares-Ginarte, Y., M.; Crespo, R.; Montero-Cabrera, L., A.; Ruiz-Garcia, J., A.; Marrero-Ponce, Y.; Santana, R.; Pardillo-Fontdevilla, E.; Alonso-Becerra, E. A Novel in-silico Approach for QSAR Studies of Anabolic and Androgenic Activities in the 17β-hydroxy-5a-androstane Steroid Family. QSAR Comb. Sci. 2005, 24, 218-226.

Marrero-Ponce, Y.; Cabrera, M. A.;  Romero-Zaldivar, V.; Bermejo, M.; Siverio, D.; Torrens, F. Prediction of Intestinal Epithelial Transport of Drug in (Caco-2) Cell Culture from Molecular Structure using ‘in silico’ Approaches During Early Drug Discovery. Internet Electronic J. Mol. Des. 2005, 4, 124-150.

Marrero-Ponce, Y.; Medina-Marrero, R.; Castillo-Garit, J.A.; Romero-Zaldivar, V.; Torrens, F.; Castro, E. A. Protein Linear Indices of the “Macromolecular Pseudograph’s a-Carbon Atom Adjacency Matrix” in Bioinformatics. Part 1. Prediction of Protein Stability Effects of a Complete Set of Alanine Substitutions in Arc Repressor. Bioorg. Med. Chem. 2005, 13, 3003-3015.

**Marrero-Ponce, Y.; Medina-Marrero, R.; Torrens, F.; Martinez, Y.; Romero-Zaldivar, V.; Castro, E. A. Atom, Atom-type, and Total Non-Stochastic and Stochastic Quadratic Fingerprints: A promising approach for modeling of antibacterial activity. Bioorg. Med. Chem. 2005, 13, 2881-2899.

**World’s 7th most requested article in 3rd quarter of 2005 according to the American Chemical Society (http://www.cas.org/spotlight/rlist3q05j/rlist3q05j.html).

Marrero-Ponce, Y.; Castillo-Garit, J.A.; Nodarse, D. Linear Indices of the “Macromolecular Graph’s Nucleotides Adjacency Matrix” as a Promising Approach for Bioinformatics Studies. 1. Prediction of Paromomycin’s Affinity Constant with HIV-1 Y-RNA Packaging Region. Bioorg. Med. Chem. 2005, 13, 3397-3404.

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.

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.

Meneses-Marcel, A.; Marrero-Ponce, Y.; Machado-Tugores, Y.; Montero-Torres, A.; Montero Pereira, D.; Escario, J. A.; Nogal-Ruiz, J. J.; Ochoa, C.; Arán, V. J.; Martínez-Fernández, A. R., García Sánchez, R. N. A Linear Discrimination Analysis Based Virtual Screening of Trichomonacidal Lead-Like Compounds. Outcomes of in silico Studies Supported by Experimental Results. Bioorg. Med. Chem Lett. 2005, 17, 3838-3843.

Montero-Torres, A.; Celeste Vega, A.; Marrero-Ponce, Y.; Rolón, M.; Gómez-Barrio, A.; Escario, J. A.; Arán, V. J.; Martínez-Fernández, A. R.; Meneses-Marcel, A. A Novel Non-Stochastic Quadratic Fingerprints-based Approach for the “in silico” Discovery of New Antitrypanosomal Compounds. Bioorg. Med. Chem. 2005, 13, 6264-6275.

Casañola-Martin, G. M.; Khan, M. T. H.; Marrero-Ponce, Y.; Ather, A.; Sultankhodzhaev, M. N.; Torrens, F. New Tyrosinase Inhibitors Selected by Atomic Linear Indices-Based Classification Models. Bioorg. Med. Chem. Letter. 2006, 16, 324-330.

Marrero-Ponce, Y.; Meneses-Marcel, A.; Machado-Tugores, Y.; Montero Pereira, D.; Escario, J. A.; Nogal-Ruiz, J. J.; Ochoa, C.; Arán, V. J.; Martínez-Fernández, A. R., García Sánchez, R. N.; Montero-Torres, A.; Francisco Torrens. A Computer-Based Approach to the Rational Discovery of New Antitrichomonas Drugs by Atom-Type Linear Indices. Current Drug Discovery Technologies. 2005, 2, 245-265.

Marrero-Ponce, Y.; Medina-Marrero, R.; Martinez, Y.; Torrens, F.; Romero-Zaldivar, V.; Castro, E. A. Non-Stochastic and Stochastic Linear Indices of the Molecular Pseudograph’s Atom Adjacency Matrix: A Novel Approach for Computational –in silico- Screening and “Rational” Selection of New Lead Antibacterial Agents. J. Mol. Mod. 2006, 12, 255–271.

Castillo-Garit, J. A.; Marrero-Ponce, Y.; Torrens, F. Atom-based 3D-Chiral Quadratic Indices: 2. Prediction of the Corticosteroid-Binding Globulin Binding Affinity of the Thirty-one Benchmark Steroids data set. Bioorg. Med. Chem. 2006, 14, 2398-2408.

Celeste-Vega, M.; Montero-Torres, A.; Marrero-Ponce, Y.; Rolón, M.; Gómez-Barrio, A.; Escario, J. A.; Arán, V. J.; Martínez-Fernández, A. R., Meneses-Marcel, A. New Ligand-Based Approach for the Discovery of Antitrypanosomal Compounds. Bioorg. Med. Chem. Letter. 2006, 16, 1898–1904.

Montero-Torres, A.; García, R. N.; Marrero-Ponce, Y.; Machado-Tugores, Y.; Nogal, J. J.; Martínez, A. R.; Arán, V. J.; Ochoa, C.; Meneses-Marcel, A.; Torrens, F. Non-stochastic Quadratic Fingerprints and LDA-Based QSAR Models in Hit and Lead Generation Through Virtual Screening: Theoretical and Experimental Assessment of a Promising Method for the Discovery of New Antimalarial Compounds. Eur. J. Med. Chem. 2006, 41, 483-493.

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.

Alvarez-Ginarte, Y.; Crespo-Otero, R.; Marrero-Ponce, Y.; Padrón-García, A.; Montero-Cabrera, L. A.;  Ruiz-García, J. A.; Torrens, F. Quantitative Structure-Activity Relationship and Diversity Analysis of the 4,5a-dihydrotestosterone Steroid Family: Computational Molecular Models To Test The Anabolic/Androgenic Receptor. QSAR Comb. Sci. 2006, 25, 881–894.

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. DOI:10.1016/j.jmgm.2006.09.007

Accepted Papers

Marrero-Ponce, Y.; Torrens, F. Bond-Based Global and Local (Bond and Bond-Type) Quadratic Indices and Their Applications to Computer-Aided Molecular Design. 1. QSPR Studies of Octane Isomers. J. Comput. Aided Mol. Des. Accepted for publication.

Marrero-Ponce, Y.; Khan, M. T. H.; Casañola-Martin, G. M.; Ather, A.; Sultankhodzhaev, M. N.; Torrens, F. Atom-Based 2D Quadratic Indices in Drug Discovery of Novel Tyrosinase Inhibitors. Results of in silico Studies Supported by Experimental Results. QSAR Comb. Sci. Accepted for publication.

Marrero-Ponce, Y.; Khan, M. T. H.; Casañola-Martin, G. M.; Ather, A.; Khan, K.; M.; Sultankhodzhaev, M. N.; Torrens, F.; Rotondo, R. Bond-Based 2D TOMOCOMD-CARDD Approach for Drug Discovery: Aiding Decision-Making in ‘in silico’ Selection of New Lead Tyrosinase Inhibitors. J. Comput. Aided Mol. Des. Accepted for publication.

Edited Journals and Honorarium
Reviewer For:

·               Journal for Computer-Aided Molecular Design

·               Molecular Diversity

·               The Journal of Medicinal Chemistry

·               Chemical Research in Toxicology

·               Journal of Chemical Information and Modelling

·               Journal of Computational Chemistry

·               Pharmaceutical Research

·               Biopolymers

·               Journal of Polymer Science

·               Journal of Physical Chemistry

·               Computational and Theoretical Polymer Science

·               Journal of Drug Targeting

·               Polymer

·               QSAR & Combinatorial Science

·               Biochemistry

·               Bioorganic and Medicinal Chemistry Letters

·               Bioorganic Medicinal Chemistry

·               Int. J. Mol. Sci.

·               Molecules

·               Combinatorial Chemistry & High Throughput Screening

·               Journal of Biomolecular Screening

·               International Journal of Pharmaceutics

·               Journal of Pharmaceutical Science

·               Journal Molecular Modelling

·               Water Research