Adolfo B. Poma

Structural modelling and biophysical analyses reveal a dimeric coiled-coil architecture in the FAZ10 central region of Trypanosoma brucei

This study determines the dimeric coiled-coil structure of the FAZ10 central region in Trypanosoma brucei using structural modeling and biophysical analysis.

An optimized contact map for GoMartini 3 enabling conformational changes in protein assemblies

The paper optimizes the contact map in GoMartini 3 by integrating dynamic contact information from AA-MD simulations, improving conformational sampling and representation in biomolecular assemblies.

Exploring Conformational Transitions of RNA Dimers via Machine Learning Potentials

This study uses machine learning potentials to explore RNA dimer conformations, showing improved accuracy over classical models.

A Comparative Nanomechanical Study of Antibody and Nanobody Binding to SARS-CoV-2 Variants

This study compares the mechanical stability of antibody and nanobody interactions with SARS-CoV-2 variants using nanomechanical simulations.

GoMartini 3: From large conformational changes in proteins to environmental bias corrections

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.

Benchmarking coarse-grained simulation methods for investigation of transport tunnels in enzymes

This study benchmarks coarse-grained simulation methods for analyzing enzyme transport tunnels, finding they efficiently capture tunnel geometry but vary in replicating all-atom dynamics.