137 citations · 183 across the 7 of their papers we have counts for
8 papers
NextGenPB: an analytically-enabled super resolution and local (de)refinement Poisson-Boltzmann Equation solver
Vincenzo Di Florio, Patrizio Ansalone, Sergii V. Siryk +3
The Poisson-Boltzmann equation (PBE) is a relevant partial differential equation commonly used in biophysical applications to estimate the electrostatic energy of biomolecular syst…
Theoretical Analysis of Divalent Cation Effects on Aptamer Recognition of Neurotransmitter Targets
Douaki Ali, Stuber Annina, Hengsteler Julien +6
Aptamer-based sensing of small molecules such as dopamine and serotonin in the brain, requires characterization of the specific aptamer sequences in solutions mimicking the in vivo…
SiteFerret: beyond simple pocket identification in proteins
Luca Gagliardi, Walter Rocchia
We present a novel method for the automatic detection of pockets on protein molecular surfaces. The algorithm is based on an ad hoc hierarchical clustering of virtual SES probe sph…
SHREC 2022: Protein-ligand binding site recognition
Luca Gagliardi, Andrea Raffo, Ulderico Fugacci +12
This paper presents the methods that have participated in the SHREC 2022 contest on protein-ligand binding site recognition. The prediction of protein-ligand binding regions is an…
SHREC 2021: Retrieval and classification of protein surfaces equipped with physical and chemical properties
Andrea Raffo, Ulderico Fugacci, Silvia Biasotti +21
This paper presents the methods that have participated in the SHREC 2021 contest on retrieval and classification of protein surfaces on the basis of their geometry and physicochemi…
Pandemic Drugs at Pandemic Speed: Infrastructure for Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers
Agastya P. Bhati, Shunzhou Wan, Dario Alfè +26
The race to meet the challenges of the global pandemic has served as a reminder that the existing drug discovery process is expensive, inefficient and slow. There is a major bottle…