Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking. - José Mario Martínez; Leandro Martínez (J. Comput. Chem., 2003)

Convergent algorithms for protein structural alignment. - Leandro Martínez; Roberto Andreani; José Mario Martínez (BMC Bioinform., 2007)

Continuous optimization methods for structure alignments. - Roberto Andreani; José Mario Martínez; Leandro Martínez; Flávio S. Yano (Math. Program., 2008)

PACKMOL: A package for building initial configurations for molecular dynamics simulations. - Leandro Martínez; Ricardo Andrade; Ernesto G. Birgin; José Mario Martínez (J. Comput. Chem., 2009)

Low Order-Value Optimization and applications. - Roberto Andreani; José Mario Martínez; Leandro Martínez; Flávio S. Yano (J. Glob. Optim., 2009)

Inexact restoration method for minimization problems arising in electronic structure calculations. - Juliano B. Francisco; José Mario Martínez; Leandro Martínez; Feodor Pisnitchenko (Comput. Optim. Appl., 2011)

A network model predicts the intensity of residue-protein thermal coupling. - Luciano Censoni; Heloisa dos Santos Muniz; Leandro Martínez (Bioinform., 2017)

Prediction of kinetics of protein folding with non-redundant contact information. - Luciano Censoni; Leandro Martínez (Bioinform., 2018)

Enhancing protein fold determination by exploring the complementary information of chemical cross-linking and coevolutionary signals. - Ricardo N. dos Santos; Allan J. R. Ferrari; Hugo C. R. de Jesus; Fábio C. Gozzo; Faruck Morcos; Leandro Martínez (Bioinform., 2018)

Parametric models to compute tryptophan fluorescence wavelengths from classical protein simulations. - Alvaro J. Lopez; Leandro Martínez (J. Comput. Chem., 2018)

TopoLink: evaluation of structural models using chemical crosslinking distance constraints. - Allan J. R. Ferrari; Milan A. Clasen; Louise U. Kurt; Paulo C. Carvalho; Fábio C. Gozzo; Leandro Martínez (Bioinform., 2019)

Statistical force-field for structural modeling using chemical cross-linking/mass spectrometry distance constraints. - Allan J. R. Ferrari; Fábio C. Gozzo; Leandro Martínez (Bioinform., 2019)

On the Interpretation of subtilisin Carlsberg Time-Resolved Fluorescence Anisotropy Decays: Modeling with Classical Simulations. - Alvaro J. Lopez; Emília P. Barros; Leandro Martínez (J. Chem. Inf. Model., 2020)

Structural discrimination analysis for constraint selection in protein modeling. - Guilherme F. Bottino; Allan J. R. Ferrari; Fábio C. Gozzo; Leandro Martínez (Bioinform., 2021)

Wrapping Up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus. - Martín Soñora; Leandro Martínez; Sergio Pantano; Matías R. Machado (J. Chem. Inf. Model., 2021)

CellListMap.jl: Efficient and customizable cell list implementation for calculation of pairwise particle properties within a cutoff. - Leandro Martínez (Comput. Phys. Commun., 2022)

Helical Content Correlations and Hydration Structures of the Folding Ensemble of the B Domain of Protein A. - Ander Francisco Pereira; Leandro Martínez (J. Chem. Inf. Model., 2024)

Moltiverse: Molecular Conformer Generation Using Enhanced Sampling Methods. - Mauricio Bedoya; Francisco Adasme-Carreño; Paula Andrea Peña-Martínez; Camila Muñoz-Gutiérrez; Luciano Peña-Tejo; José C. E. Márquez Montesinos; Erix Wiliam Hernández-Rodríguez; Wendy González; Leandro Martínez; Jans H. Alzate-Morales (J. Chem. Inf. Model., 2025)