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. - Yovani Marrero-Ponce; Juan A. Castillo-Garit; Ervelio Olazabal; Hector S. Serrano; Alcidez Morales; Nilo Castañedo; Froylán Ibarra-Velarde; Alma Huesca-Guillen; Elisa Jorge; Arletys del Valle; Francisco Torrens; Eduardo A. Castro (J. Comput. Aided Mol. Des., 2004)

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. - Yovani Marrero-Ponce (J. Chem. Inf. Model., 2004)

3D-chiral Atom, Atom-type, and Total Non-stochastic and Stochastic Molecular Linear Indices and their Applications to Central Chirality Codification. - Yovani Marrero-Ponce; Juan A. Castillo-Garit (J. Comput. Aided Mol. Des., 2005)

Ligand-Based Virtual Screening and in Silico Design of New Antimalarial Compounds Using Nonstochastic and Stochastic Total and Atom-Type Quadratic Maps. - Yovani Marrero-Ponce; Maité Iyarreta-Veitía; Alina Montero-Torres; Carlos Romero-Zaldivar; Carlos A. Brandt; Priscilla E. Ávila; Karin Kirchgatter; Yanetsy Machado (J. Chem. Inf. Model., 2005)

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. - Yovani Marrero-Ponce; Francisco Torrens; Ysaias José Alvarado; Richard Rotondo (J. Comput. Aided Mol. Des., 2006)

Bond-based 2D TOMOCOMD-CARDD approach for drug discovery: aiding decision-making in 'in silico' selection of new lead tyrosinase inhibitors. - Yovani Marrero-Ponce; Mahmud Tareq Hassan Khan; Gerardo M. Casañola-Martín; Arjumand Ather; Mukhlis N. Sultankhodzhaev; Ramón García-Domenech; Francisco Torrens; Richard Rotondo (J. Comput. Aided Mol. Des., 2007)

Bond-based linear indices in QSAR: computational discovery of novel anti-trichomonal compounds. - Yovani Marrero-Ponce; Alfredo Meneses-Marcel; Oscar Miguel Rivera-Borroto; Ramón García-Domenech; Jesús Vicente de Julián-Ortiz; Alina Montero-Torres; José Antonio Escario; Alicia Gómez Barrio; David Montero Pereira; Juan José Nogal; Ricardo Grau; Francisco Torrens; et al. (J. Comput. Aided Mol. Des., 2008)

Applying pattern recognition methods plus quantum and physico-chemical molecular descriptors to analyze the anabolic activity of structurally diverse steroids. - Yoanna María Alvarez-Ginarte; Yovani Marrero-Ponce; José Alberto Ruiz-García; Luis Alberto Montero-Cabrera; José Manuel García de la Vega; Pedro Noheda Marin; Rachel Crespo-Otero; Francisco Torrens Zaragoza; Ramón García-Domenech (J. Comput. Chem., 2008)

Bond-based 3D-chiral linear indices: Theory and QSAR applications to central chirality codification. - Juan A. Castillo-Garit; Yovani Marrero-Ponce; Francisco Torrens; Ramón García-Domenech; Vicente Romero-Zaldivar (J. Comput. Chem., 2008)

Comparison of Combinatorial Clustering Methods on Pharmacological Data Sets Represented by Machine Learning-Selected Real Molecular Descriptors. - Oscar Miguel Rivera-Borroto; Yovani Marrero-Ponce; José Manuel García de la Vega; Ricardo del Corazón Grau-Ábalo (J. Chem. Inf. Model., 2011)

Retrained Classification of Tyrosinase Inhibitors and "In Silico" Potency Estimation by Using Atom-Type Linear Indices: A Powerful Tool for Speed up the Discovery of Leads. - Gerardo M. Casañola-Martín; Mahmud Tareq Hassan Khan; Huong Le-Thi-Thu; Yovani Marrero-Ponce; Ramón García-Domenech; Francisco Torrens; Antonio Rescigno (Int. J. Chemoinformatics Chem. Eng., 2012)

Derivatives in discrete mathematics: a novel graph-theoretical invariant for generating new 2/3D molecular descriptors. I. Theory and QSPR application. - Yovani Marrero-Ponce; Oscar Martínez Santiago; Yoan Martínez López; Stephen J. Barigye; Francisco Torrens (J. Comput. Aided Mol. Des., 2012)

Relations frequency hypermatrices in mutual, conditional and joint entropy-based information indices. - Stephen J. Barigye; Yovani Marrero-Ponce; Yoan Martínez López; Francisco Torrens; Luis Manuel Artiles-Martínez; Ricardo W. Pino-Urias; Oscar Martínez Santiago (J. Comput. Chem., 2013)

QuBiLS-MIDAS: A parallel free-software for molecular descriptors computation based on multilinear algebraic maps. - César R. García-Jacas; Yovani Marrero-Ponce; Liesner Acevedo-Martínez; Stephen J. Barigye; José R. Valdés-Martiní; Ernesto Contreras-Torres (J. Comput. Chem., 2014)

Overlap and diversity in antimicrobial peptide databases: compiling a non-redundant set of sequences. - Longendri Aguilera-Mendoza; Yovani Marrero-Ponce; Roberto Tellez-Ibarra; Monica T. Llorente-Quesada; Jesús Salgado; Stephen J. Barigye; Jun Liu (Bioinform., 2015)

ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins. - Yasser B. Ruiz-Blanco; Waldo Paz; James Green 001; Yovani Marrero-Ponce (BMC Bioinform., 2015)

Examining the predictive accuracy of the novel 3D N-linear algebraic molecular codifications on benchmark datasets. - César R. García-Jacas; Ernesto Contreras-Torres; Yovani Marrero-Ponce; Mario Pupo-Meriño; Stephen J. Barigye; Lisset Cabrera-Leyva (J. Cheminformatics, 2016)

Relational Agreement Measures for Similarity Searching of Cheminformatic Data Sets. - Oscar Miguel Rivera-Borroto; José Manuel García de la Vega; Yovani Marrero-Ponce; Ricardo Grau (IEEE ACM Trans. Comput. Biol. Bioinform., 2016)

QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations. - José R. Valdés-Martiní; Yovani Marrero-Ponce; César R. García-Jacas; Karina Martínez-Mayorga; Stephen J. Barigye; Yasser Silveira Vaz d'Almeida; Hai Pham-The; Facundo Pérez-Giménez; Carlos A. Morell (J. Cheminformatics, 2017)

Choquet integral-based fuzzy molecular characterizations: when global definitions are computed from the dependency among atom/bond contributions (LOVIs/LOEIs). - César R. García-Jacas; Lisset Cabrera-Leyva; Yovani Marrero-Ponce; José Suárez-Lezcano; Fernando Cortés-Guzmán; Mario Pupo-Meriño; Ricardo Vivas-Reyes (J. Cheminformatics, 2018)

Graph-based data integration from bioactive peptide databases of pharmaceutical interest: toward an organized collection enabling visual network analysis. - Longendri Aguilera-Mendoza; Yovani Marrero-Ponce; Jesus A. Beltran; Roberto Tellez-Ibarra; Hugo A. Guillen-Ramirez; Carlos A. Brizuela (Bioinform., 2019)

Smoothed Spherical Truncation based on Fuzzy Membership Functions: Application to the Molecular Encoding. - César R. García-Jacas; Yovani Marrero-Ponce; Carlos A. Brizuela; José Suárez-Lezcano; Felix Martinez-Rios (J. Comput. Chem., 2020)

Distributed and multicore QuBiLS-MIDAS software v2.0: Computing chiral, fuzzy, weighted and truncated geometrical molecular descriptors based on tensor algebra. - César R. García-Jacas; Yovani Marrero-Ponce; Ricardo Vivas-Reyes; José Suárez-Lezcano; Felix Martinez-Rios; Julio E. Terán; Longendri Aguilera-Mendoza (J. Comput. Chem., 2020)

MuLiMs-MCoMPAs: A Novel Multiplatform Framework to Compute Tensor Algebra-Based Three-Dimensional Protein Descriptors. - Ernesto Contreras-Torres; Yovani Marrero-Ponce; Julio E. Terán; César R. García-Jacas; Carlos A. Brizuela; Juan Carlos Sánchez-Rodríguez (J. Chem. Inf. Model., 2020)

From a coenzyme-like mechanism to homochirality. - Osmel Martín; Yoelsy Leyva; José Suárez-Lezcano; Yunierkis Pérez-Castillo; Yovani Marrero-Ponce (Biosyst., 2023)

StarPep Toolbox: an open-source software to assist chemical space analysis of bioactive peptides and their functions using complex networks. - Longendri Aguilera-Mendoza; Sebastián Ayala-Ruano; Felix Martinez-Rios; Edgar Chávez; César R. García-Jacas; Carlos A. Brizuela; Yovani Marrero-Ponce (Bioinform., 2023)

MD-LAIs Software: Computing Whole-Sequence and Amino Acid-Level "Embeddings" for Peptides and Proteins. - Ernesto Contreras-Torres; Yovani Marrero-Ponce (J. Chem. Inf. Model., 2024)

Rethinking the applicability domain analysis in QSAR models. - José Ramón Mora; Edgar Márquez; Noel Pérez-Pérez; Ernesto Contreras-Torres; Yunierkis Pérez-Castillo; Guillermín Agüero-Chapín; Felix Martinez-Rios; Yovani Marrero-Ponce; Stephen J. Barigye (J. Comput. Aided Mol. Des., 2024)

Optimal Descriptor Subset Search via Chemical Information and Target Activity-Guided Algorithm for Antimicrobial Peptide Prediction. - Luis A. García-González; Yovani Marrero-Ponce; César R. García-Jacas; Sergio A. Aguila Puentes (J. Chem. Inf. Model., 2025)