[HTML][HTML] Deep learning path-like collective variable for enhanced sampling molecular dynamics

T Fröhlking, L Bonati, V Rizzi… - The Journal of Chemical …, 2024‏ - pubs.aip.org
Several enhanced sampling techniques rely on the definition of collective variables to
effectively explore free energy landscapes. The existing variables that describe the …

Boosting Ensemble Refinement with Transferable Force-Field Corrections: Synergistic Optimization for Molecular Simulations

I Gilardoni, T Fröhlking, G Bussi - The Journal of Physical …, 2024‏ - ACS Publications
A novel method combining the force-field fitting approach and ensemble refinement by the
maximum entropy principle is presented. Its formulation allows us to continuously interpolate …

Frontiers in integrative structural modeling of macromolecular assemblies

K Majila, S Arvindekar, M **dal, S Viswanath - QRB discovery, 2025‏ - cambridge.org
Integrative modeling enables structure determination for large macromolecular assemblies
by combining data from multiple experiments with theoretical and computational predictions …

MDRefine: a Python package for refining Molecular Dynamics trajectories with experimental data

I Gilardoni, V Piomponi, T Fröhlking, G Bussi - arxiv preprint arxiv …, 2024‏ - arxiv.org
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying
conformational dynamics of molecular systems. However, their capability to correctly …

Automatic Forward Model Parameterization with Bayesian Inference of Conformational Populations

RM Raddi, T Marshall, VA Voelz - Ar**v, 2024‏ - pmc.ncbi.nlm.nih.gov
To quantify how well theoretical predictions of structural ensembles agree with experimental
measurements, we depend on the accuracy of forward models. These models are …

Model selection using replica averaging with Bayesian inference of conformational populations

RM Raddi, T Marshall, Y Ge, V Voelz - 2023‏ - chemrxiv.org
Bayesian Inference of Conformational Populations (BICePs) is a reweighting algorithm that
reconciles simulated ensembles with sparse and/or noisy observables, by sampling the full …