A new GROMOS force field for hexopyranose-based carbohydrates. - Roberto D. Lins; Philippe H. Hünenberger (J. Comput. Chem., 2005)

An improved nucleic acid parameter set for the GROMOS force field. - Thereza A. Soares; Philippe H. Hünenberger; Mika A. Kastenholz; Vincent Kräutler; Thomas Lenz; Roberto D. Lins; Chris Oostenbrink; Wilfred F. van Gunsteren (J. Comput. Chem., 2005)

Northwest Trajectory Analysis Capability: A Platform for Enhancing Biophysics Analysis. - Elena S. Peterson; Eric G. Stephan; Abbie Corrigan; Roberto D. Lins; Thereza A. Soares; Randy Scarberry; Stuart Rose; Leigh Williams; Canhai Lai; Terence Critchlow; Tjerk P. Straatsma (BIOCOMP, 2008)

Molecular Models to Emulate Confinement Effects on the Internal Dynamics of Organophosphorous Hydrolase. - Diego Enry Barreto Gomes; Roberto D. Lins; Pedro Geraldo Pascutti; Tjerk P. Straatsma; Thereza A. Soares (BSB, 2008)

Influence of Scaffold Stability and Electrostatics on Top7-Based Engineered Helical HIV-1 Epitopes. - Isabelle F. T. Viana; Rafael Dhalia; Marco A. Krieger; Ernesto T. A. Marques Jr.; Roberto D. Lins (BSB, 2013)

IMSPeptider: A computational peptide collision cross-section area calculator based on a novel molecular dynamics simulation protocol. - Ranieri V. de Carvalho; Daniel Lopez-Ferrer; Katia S. Guimarães; Roberto D. Lins (J. Comput. Chem., 2013)

Extension and validation of the GROMOS 53A6glyc parameter set for glycoproteins. - Laercio Pol-Fachin; Hugo Verli; Roberto D. Lins (J. Comput. Chem., 2014)

Polymyxin Binding to the Bacterial Outer Membrane Reveals Cation Displacement and Increasing Membrane Curvature in Susceptible but Not in Resistant Lipopolysaccharide Chemotypes. - Denys E. S. Santos; Laercio Pol-Fachin; Roberto D. Lins; Thereza A. Soares (J. Chem. Inf. Model., 2017)

Unraveling the Role of Nanobodies Tetrad on Their Folding and Stability Assisted by Machine and Deep Learning Algorithms. - Matheus Vitor Ferreira Ferraz; Wenny Camilla dos Santos Adan; Roberto D. Lins (BSB, 2020)

Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations. - Victor H. Rusu; Denys E. S. Santos; Marcelo Depólo Polêto; Marcelo Galheigo; Antônio Tadeu A. Gomes; Hugo Verli; Thereza A. Soares; Roberto D. Lins (J. Chem. Inf. Model., 2020)

SuAVE: A Tool for Analyzing Curvature-Dependent Properties in Chemical Interfaces. - Denys E. S. Santos; Frederico J. S. Pontes; Roberto D. Lins; Kaline Coutinho; Thereza A. Soares (J. Chem. Inf. Model., 2020)

Estimating Absolute Protein-Protein Binding Free Energies by a Super Learner Model. - Elton José Ferreira Chaves; João Sartori; Whendel M. Santos; Carlos H. B. Cruz; Emmanuel N. Mhrous; Manassés F. Nacimento-Filho; Matheus Vitor Ferreira Ferraz; Roberto D. Lins (J. Chem. Inf. Model., 2025)

Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning. - Matheus Vf Ferraz; W. Camilla S. Adan; Tayná E. Lima; Adriele J. C. Santos; Sérgio O. de Paula; Rafael Dhalia; Gabriel da Luz Wallau; Rebecca C. Wade; Isabelle F. T. Viana; Roberto D. Lins (PLoS Comput. Biol., 2025)