A5011547404- Computational Drug Discovery Methods
- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- SARS-CoV-2 and COVID-19 Research
- Retinal Development and Disorders
- Photoreceptor and optogenetics research
- Analytical Chemistry and Sensors
- Viral gastroenteritis research and epidemiology
- Quantum Computing Algorithms and Architecture
- Quantum Mechanics and Applications
- Influenza Virus Research Studies
- Machine Learning in Bioinformatics
- Molecular Sensors and Ion Detection
- Plant biochemistry and biosynthesis
- Noncommutative and Quantum Gravity Theories
- Neuroscience and Neuropharmacology Research
University of Geneva
2022-2024
SIB Swiss Institute of Bioinformatics
2023-2024
HES-SO University of Applied Sciences and Arts Western Switzerland
2023-2024
University of Verona
2017-2019
University of Trento
2019
Institute for Biomedicine
2017
Protein-protein interactions mediate most molecular processes in the cell, offering a significant opportunity to expand set of known druggable targets. Unfortunately, targeting these can be challenging due their typically flat and featureless interaction surfaces, which often change as complex forms. Such surface changes may reveal hidden (cryptic) pockets. Here, we analyze well-characterized protein-protein harboring cryptic pockets investigate predictive power current computational...
The calculation of absolute binding free energies (ABFEs) for protein-ligand systems has long been a challenge. Recently, refined force fields and algorithms have improved the quality ABFE calculations. However, achieving level accuracy required to inform drug discovery efforts remains difficult. Here, we present transferable enhanced sampling strategy accurately calculate using OneOPES with simple geometric collective variables. We tested on two protein targets, BRD4 Hsp90, complexed total...
Non-structural protein 1 (Nsp1) is a main pathogenicity factor of α- and β-coronaviruses. Nsp1 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) suppresses the host gene expression by sterically blocking 40S ribosomal subunits promoting mRNA degradation. This mechanism leads to downregulation translation-mediated innate immune response in cells, ultimately mediating observed evasion capabilities SARS-CoV-2. Here, combining extensive molecular dynamics simulations, fragment...
Cryptic binding sites in proteins, which are hidden the absence of a ligand, offer opportunities to modulate targets previously considered 'undruggable'. However, scarcity experimentally validated examples limits development predictive tools. Here, we introduce CryptoBank, large-scale database cryptic identified by applying machine learning model detect ligand-induced conformational changes over 5.5 million structural alignments unbound (apo) and bound (holo) protein pairs from Protein Data...
Recoverin (Rec) is a prototypical calcium sensor protein primarily expressed in the vertebrate retina. The binding of two Ca2+ ions to functional EF-hand motifs induces extrusion myristoyl group that increases affinity Rec for membrane and leads formation complex with rhodopsin kinase (GRK1). Here, unbiased all-atom molecular dynamics simulations were performed monitor spontaneous insertion into model multicomponent biological both isolated its peptide from GRK1 target. It was found...
CaF<sub>2</sub>nanoparticles constitute biocompatible nano-carriers for the calcium sensor protein GCAP1 preserving its biological function.
The calculation of absolute binding free energies (ABFEs) for protein-ligand systems has long been a challenge. Recently, refined force fields and algorithms have improved the quality ABFE calculations. However, achieving level accuracy required to inform drug discovery efforts remains difficult. Here, we present transferable enhanced sampling strategy accurately calculate using OneOPES with simple geometric collective variables. We tested on two protein targets, BRD4 Hsp90, complexed total...
The calculation of absolute binding free energies (ABFEs) for protein-ligand systems has long been a challenge. Recently, refined force fields and algorithms have improved the quality ABFE calculations. However, achieving level accuracy required to inform drug discovery efforts remains difficult. Here, we present transferable enhanced sampling strategy accurately calculate using OneOPES with simple geometric collective variables. We tested on two protein targets, BRD4 Hsp90, complexed total...
Abstract Non-structural protein 1 (Nsp1) is a main pathogenicity factor of α - and β -coronaviruses. Nsp1 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) suppresses the host gene expression by sterically blocking 40S ribosomal subunits promoting mRNA degradation. This mechanism leads to downregulation translation-mediated innate immune response in cells, ultimately mediating observed evasion capabilities SARS-CoV-2. Here, combining extensive Molecular Dynamics simulations,...
Abstract Protein-protein interactions mediate most molecular processes in the cell, offering a significant opportunity to expand set of known druggable targets. Unfortunately, targeting these can be challenging due their typically flat and featureless interaction surfaces, which often change as complex forms. Such surface changes may reveal hidden (cryptic) pockets. Here, we analyse well-characterised protein-protein harbouring cryptic pockets investigate predictive power current...