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CalzaAlessandro/README.md

Alessandro Calza

Molecular modelling: a protein binding pocket transitioning from a transparent network to a molecular surface, within a liquid bubble

Computational chemist at the University of Bologna, working on molecular recognition and simulations for medicine and the environment.

ORCID Google Scholar LinkedIn

I study protein–ligand and supramolecular host–guest interactions, membranes, and nanomaterial interfaces. My projects include candidate drug-delivery systems, protein adsorption, and contaminant binding to graphene oxide for water remediation.

I use atomistic and coarse-grained molecular dynamics, docking, and virtual screening. I develop force-field parameters and molecular libraries, analyze structures and simulation trajectories, and build simulation workflows in Python and Bash for high-performance computing (HPC) systems.

My interests include fragrance chemistry and formulations, molecular databases, AI/ML and agentic workflows for molecular research, and the transfer of modelling methods between biological and materials systems.

Models and structural data

Atomic structures and geometric models of eleven physiological regions in native human serum albumin, sampled in three independent 1 µs simulations. Includes protein and pocket representatives, cavity geometries and volume tables.

Methods and results

Coarse-grained models for linear perfluoroalkyl substances, with parameterization, validation and GROMACS simulation files.

Published in Journal of Chemical Theory and Computation (2026).
Article · Model library

Software in development

Build and functionalize graphene oxide sheets with explicit connectivity. Includes QM reference and force-field parameterization workflows.

Build progressively cationized proteins through electrostatics-guided carboxyl amidation, relax their structures and export parameters for Amber, OpenMM and GROMACS.

Both tools are in development. See their READMEs for validation status; new parameters, charges and topologies are preliminary.

Pinned Loading

  1. martini-linear-pfas martini-linear-pfas Public

    Martini 3 coarse-grained models and GROMACS simulation files for linear PFAS

    1

  2. hsa-native-pockets hsa-native-pockets Public

    Native HSA structures and geometric models of eleven physiological binding regions.

  3. cationize-protein cationize-protein Public

    Progressive electrostatic-guided protein cationization for Amber, OpenMM and GROMACS

    Python

  4. go-surface-workbench go-surface-workbench Public

    Graphene oxide generation, covalent functionalization and force-field parameterization.

    HTML