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

Bidirectional path-based non-equilibrium simulations for binding free energy

Andrea Cavalli

Estimating free energy is a fundamental computational challenge, especially in complex biological systems characterised by numerous degrees of freedom. In this study, we investigate the potential of leveraging non-equilibrium free energy estimators within ...

Taylor & Francis2024

AMCG: a graph dual atomic-molecular conditional molecular generator

Andrea Cavalli

Drug design is both a time consuming and expensive endeavour. Computational strategies offer viable options to address this task; deep learning approaches in particular are indeed gaining traction for their capability of dealing with chemical structures. A ...

IOP Publishing2024

An 19F NMR fragment-based approach for the discovery and development of BRCA2-RAD51 inhibitors to pursuit synthetic lethality in combination with PARP inhibition in pancreatic cancer

Andrea Cavalli

The BRCA2-RAD51 interaction remains an intriguing target for cancer drug discovery due to its vital role in DNA damage repair mechanisms, which cancer cells become particularly reliant on. Moreover, RAD51 has many synthetically lethal partners, including P ...

Elsevier France-Editions Scientifiques Medicales Elsevier2024

Preomic profile of BxPC-3 cells after treatment with BRC4

Andrea Cavalli

BRCA2 and RAD51 are two proteins that play a central role in homologous recombination (HR) and DNA double strand break (DSB) repair. BRCA2 assists RAD51 fibrillation and defibrillation through binding with its eight BRC repeats, with BRC4 being one of the ...

ELSEVIER2023

Multiomic analysis of HER2-enriched and AR-positive breast carcinoma with apocrine differentiation and an oligometastatic course: a case report

Andrea Cavalli

Breast carcinoma is the most prevalent cancer among women globally. It has variable clinical courses depending on the stage and clinical-biological features. This case report describes a 56-year-old female with invasive breast cancer without estrogen or pr ...

FRONTIERS MEDIA SA2023

Expert recommendation from the Swiss Amyloidosis Network (SAN) for systemic AL-amyloidosis

Alessio Mylonas, Andrea Cavalli, Martin Meyer

Systemic amyloidosis is a heterogeneous group of diseases associated with protein misfolding into insoluble beta-sheet rich structures that deposit extracellularly in different organs, eventually compromising their function. There are more than 30 differen ...

E M H SWISS MEDICAL PUBLISHERS LTD2020

Endoplasmic Reticulum and Lysosomal Quality Control of Four Nonsense Mutants of Iduronate 2-Sulfatase Linked to Hunter's Syndrome

Maurizio Molinari, Andrea Cavalli

Hunter's syndrome (mucopolysaccharidosis type II) is a rare X-linked lysosomal storage disorder caused by mutations in the iduronate-2-sulfatase (IDS) gene. Motivated by the case of a child affected by this syndrome, we compared the intracellular fate of w ...

2020

Molecular Simulations Integrated with Experiments Unravel the Key Factors of Lipid Selection in Fatty Acid Amide Hydrolase and Suggest A General Mechanism of Lipid-Processing in the Parent Enzymes

Ursula Röthlisberger, Pablo Campomanes Ramos, Giulia Palermo, Andrea Cavalli

Cell Press2016

Catalytic Metal Ions and Enzymatic Processing of DNA and RNA

Matteo Dal Peraro, Giulia Palermo, Andrea Cavalli

Two-metal-ion-dependent nucleases cleave the phosphodiester bonds of nucleic acids via the two-metal-ion (2M) mechanism. Several high-resolution X-ray structures portraying the two-metal-aided catalytic site, together with mutagenesis and kinetics studies, ...

Amer Chemical Soc2015

Anandamide Hydrolysis in FAAH Reveals a Dual Strategy for Efficient Enzyme-Assisted Amide Bond Cleavage via Nitrogen Inversion

Ursula Röthlisberger, Pablo Campomanes Ramos, Giulia Palermo, Andrea Cavalli

Herein, we combined classical molecular dynamics (MD) and quantum mechanical/molecular mechanics (QM/MM) simulations to unravel the whole catalytic cycle of fatty acid amide hydrolase (FAAH) in complex with anandamide, the main neurotransmitters involved i ...

2015