Publications de Andrea Cavalli

A tale of two codes: CUDA vs OpenACC for mass-zero constrained dynamics

Speed and efficiency of codes for atomistic simulations can be improved through refactoring and tailoring for GPU architectures. This activity, however, comes with associated, often overlooked, costs, namely a reduced readability and flexibility upon optim ...

SAGE PUBLICATIONS LTD2025

Binding Free Energy Calculations Based on the Path Collective Variable along a String Pathway

Andrea Cavalli

American Chemical Society (ACS)2025

Dynamical features of smooth muscle actin pathological mutants: The arginine-257(258)-Cysteine cases

Andrea Cavalli

The R257(8)C mutation in smooth muscle actins, ACTG2 and ACTA2, is the most frequent cause of severe genetic diseases: namely, visceral myopathy, and familial thoracic aortic aneurysms and dissections, which respectively, stem from impairment of the viscer ...

ELSEVIER2025

IsoBayes: a Bayesian approach for single-isoform proteomics inference

Andrea Cavalli

Motivation Studying protein isoforms is an essential step in biomedical research; at present, the main approach for analyzing proteins is via bottom-up mass spectrometry proteomics, which return peptide identifications, that are indirectly used to infer th ...

Oxford University Press (OUP)2025

NanoShaperWeb: Molecular Surface and Pocket Detection Made Visual

Andrea Cavalli

Analyzing molecular surfaces to predict functional sites and identify protein cavities for small molecule binding is essential in structural biology and drug discovery, particularly when targeting allosteric sites or designing PROTACs. Moreover, measuring ...

American Chemical Society (ACS)2025

Rational Optimization of D3r/gsk-3(3 Dual Target-directed Ligands as Potential Treatment for Bipolar Disorder: Design, Synthesis, X-ray Crystallography, Molecular Dynamics Simulations, In Vitro Adme, And In Vivo Pharmacokinetic Studies

Andrea Cavalli

Bipolar disorder is a complex neuropsychiatric condition with a significant unmet medical need, as current treatments lack disease-modifying properties and multimodal therapeutic effects. To overcome the limitations of single-target drugs, we designed dual ...

ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER2025

Path-Based Nonequilibrium Binding Free Energy Estimation, from Protein–Ligand to RNA-Ligand Binding

Andrea Cavalli

In this study, we addressed the challenge of estimating binding free energies in complex biological systems of pharmaceutical relevance, including both protein-ligand and RNA-ligand complexes. As case studies, we examined the intricate binding of the drug ...

American Chemical Society (ACS)2025

Investigating synthetic lethality and PARP inhibitor resistance in pancreatic cancer through enantiomer differential activity

Andrea Cavalli

The RAD51-BRCA2 interaction is central to DNA repair through homologous recombination. Emerging evidence indicates RAD51 overexpression and its correlation with chemoresistance in various cancers, suggesting RAD51-BRCA2 inhibition as a compelling avenue fo ...

SPRINGERNATURE2025

Label Critic: Design Data Before Models

Andrea Cavalli

As medical datasets rapidly expand, creating detailed annotations of different body structures becomes increasingly expensive and time-consuming. We consider that requesting radiologists to create detailed annotations is unnecessarily burdensome and that p ...

IEEE Computer Society2025

The Need to Implement Fair Principles in Biomolecular Simulations

Ursula Röthlisberger, Matteo Dal Peraro, Andrea Cavalli

NATURE PORTFOLIO2025