Paulo C. T. Souza

The paper shows that human signal peptides are inefficiently cleaved by yeast SPCs due to differences in SPC-lipid interactions and membrane thinning profiles.

This paper develops a 3D-printed microfluidic chip with synchrotron SAXS for real-time monitoring of hexosome formation and identifies key parameters affecting their structure.

The paper improves a coarse-grained model for biomolecular condensates by enhancing dilute-state properties, showing better condensed-phase behavior but not full quantitative accuracy.

This study uses simulations to analyze LNP-mediated siRNA delivery, revealing pH-dependent structural changes and a mechanism for endosomal escape involving RNA-lipid interactions.

The paper introduces a web portal for the Martini Force Field Initiative to facilitate open collaboration and resource management in biomolecular simulations.

The paper updates the MAD web server with new tools and an enhanced database for building and simulating coarse-grained polymer models using the Martini force field.

The paper introduces Auto-MartiniM3, a tool for automating the coarse-graining of small molecules for Martini 3 simulations, validated on 81 molecules and complex cases like caffeine.

The paper introduces COBY, a coarse-grained system builder for creating complex membrane systems with improved accuracy using Martini molecule models.

This paper introduces an enhanced G[o]Martini model that improves protein dynamics simulation and addresses inaccuracies in the Martini protein model through diverse case studies.

This paper introduces Martini 3 protein modeling, comparing three structure bias methods for maintaining protein structures in simulations.

The paper evaluates AlphaFold's ability to predict PROTAC-mediated protein interfaces and finds it struggles with small interfaces, impacting PROTAC design.

This study shows that cholesterol depletion alters Nav1.7 structure and function, affecting its gating and drug response, with implications for pain management.

The paper presents a computational method to predict PROTAC-compatible protein-protein interfaces using docking and scoring techniques, achieving high accuracy in benchmark tests.