Valentina Sora

MAVISp: A Modular Structure-Based Framework for Protein Variant Effects

MAVISp provides a modular structural framework for analyzing protein variant effects, offering over eight million variants across 1000 proteins with curated data and a web server for accessibility.

N-of-one differential gene expression without control samples using a deep generative model

This paper introduces a deep generative model to perform differential gene expression analysis on single cancer samples without control samples, outperforming DESeq2 in detecting differentially expressed genes.

PyInteraph2 and PyInKnife2 to analyze networks in protein structural ensembles

The paper introduces two open-source tools for analyzing protein structural ensembles using network theory, focusing on reproducibility and parameter stability.

RosettaDDGPrediction for high-throughput mutational scans: from stability to binding

RosettaDDGPrediction enables high-throughput calculation of free energy changes from amino acid substitutions using Rosetta, with tools for data aggregation and visualization.

psntools - a Python package for protein structure network analysis

psntools is a Python package for analyzing Protein Structure Networks, providing PSN-agnostic tools for studying protein dynamics and interactions.

Bcl-xL dynamics and cancer-associated mutations under the lens of protein structure networks and biomolecular simulations

The paper investigates Bcl-xL's allosteric communication between binding sites and evaluates how cancer mutations affect this mechanism using molecular dynamics and protein structure networks.