Structural Effects of pH and Deacylation on Surfactant Protein C in an Organic Solvent Mixture: A Constant-pH MD Study. - Catarina A. Carvalheda; Sara R. R. Campos; Miguel Machuqueiro; António M. Baptista (J. Chem. Inf. Model., 2013)

A Simulated Intermediate State for Folding and Aggregation Provides Insights into ΔN6 β2-Microglobulin Amyloidogenic Behavior. - Sílvia G. Estácio; Heinrich Krobath; Diogo Vila-Viçosa; Miguel Machuqueiro; Eugene I. Shakhnovich; Patrícia F. N. Faísca (PLoS Comput. Biol., 2014)

Correction to "Structural Effects of pH and Deacylation on Surfactant Protein C in an Organic Solvent Mixture: A Constant-pH MD Study". - Catarina A. Carvalheda; Sara R. R. Campos; Miguel Machuqueiro; António M. Baptista (J. Chem. Inf. Model., 2015)

PypKa: A Flexible Python Module for Poisson-Boltzmann-Based pKa Calculations. - Pedro B. P. S. Reis; Diogo Vila-Viçosa; Walter Rocchia; Miguel Machuqueiro (J. Chem. Inf. Model., 2020)

pKPDB: a protein data bank extension database of pKa and pI theoretical values. - Pedro B. P. S. Reis; Djork-Arné Clevert; Miguel Machuqueiro (Bioinform., 2021)

Optimization of an in Silico Protocol Using Probe Permeabilities to Identify Membrane Pan-Assay Interference Compounds. - Pedro R. Magalhães; Pedro B. P. S. Reis; Diogo Vila-Viçosa; Miguel Machuqueiro; Bruno L. Victor (J. Chem. Inf. Model., 2022)

Novel US-CpHMD Protocol to Study the Protonation-Dependent Mechanism of the ATP/ADP Carrier. - Nuno F. B. Oliveira; Miguel Machuqueiro (J. Chem. Inf. Model., 2022)

Interfacial Dynamics and Growth Modes of β2-Microglobulin Dimers. - Nuno F. B. Oliveira; Filipe E. P. Rodrigues; João N. M. Vitorino; Patrícia F. N. Faísca; Miguel Machuqueiro (J. Chem. Inf. Model., 2023)

Arginine Residues Modulate the Membrane Interactions of pHLIP Peptides. - Tomás F. D. Silva; Hannah Visca; Craig Klumpp; Oleg A. Andreev; Yana K. Reshetnyak; Miguel Machuqueiro (J. Chem. Inf. Model., 2023)

pKa Calculations of GPCRs: Understanding Protonation States in Receptor Activation. - Carlos A. V. Barreto; João N. M. Vitorino; Pedro B. P. S. Reis; Miguel Machuqueiro; Irina S. Moreira (J. Chem. Inf. Model., 2024)

Is There a Functional Role for the Knotted Topology in Protein UCH-L1? - Sara G. F. Ferreira; Manoj K. Sriramoju; Shang-Te Danny Hsu; Patrícia F. N. Faísca; Miguel Machuqueiro (J. Chem. Inf. Model., 2024)

High Charge Density in Peptide Dendrimers is Required to Destabilize Membranes: Insights into Endosome Evasion. - Filipe E. P. Rodrigues; Tamis Darbre; Miguel Machuqueiro (J. Chem. Inf. Model., 2024)