65 citations · 71 across the 7 of their papers we have counts for
7 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…
Transferring Chemical and Energetic Knowledge Between Molecular Systems with Machine Learning
Sajjad Heydari, Stefano Raniolo, Lorenzo Livi +1
Predicting structural and energetic properties of a molecular system is one of the fundamental tasks in molecular simulations, and it has use cases in chemistry, biology, and medic…
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…