2 citations · 2 across the 3 of their papers we have counts for
6 papers
PHASE: encoding global protein ensembles with local Hamiltonians and all-atom backmapping
Daniele Angioletti, Marco Nobile, Matteo Carli +1
Protein function is governed by conformational ensembles, which can be viewed as high-dimensional probability distributions over molecular conformations. Yet the statistical organi…
GEqTrain: A Configuration-Driven Framework for Retargeting Equivariant Graph Neural Networks Across 3D Scientific Tasks
Daniele Angioletti, Marco Nobile, Vittorio Limongelli
Equivariant graph neural networks provide a powerful modeling language for three-dimensional scientific data, but their reuse is often limited by implementations tied to specific t…
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
Gareth A. Tribello, Massimiliano Bonomi, Giovanni Bussi +60
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific p…
The need to implement FAIR principles in biomolecular simulations
Rommie Amaro, Johan Åqvist, Ivet Bahar +125
This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necess…
HEroBM: a deep equivariant graph neural network for universal backmapping from coarse-grained to all-atom representations
Daniele Angioletti, Stefano Raniolo, Vittorio Limongelli
Molecular simulations have assumed a paramount role in the fields of chemistry, biology, and material sciences, being able to capture the intricate dynamic properties of systems. W…
The free energy landscape of GABA binding to a pentameric ligand-gated ion channel and its disruption by mutations
Federico Comitani, Vittorio Limongelli, Carla Molteni
Pentameric ligand-gated ion channels (pLGICs) of the Cys-loop superfamily are important neuroreceptors that mediate fast synaptic transmission. They are activated by the binding of…