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[HTML][HTML] Deep learning path-like collective variable for enhanced sampling molecular dynamics
Several enhanced sampling techniques rely on the definition of collective variables to
effectively explore free energy landscapes. The existing variables that describe the …
effectively explore free energy landscapes. The existing variables that describe the …
Boosting Ensemble Refinement with Transferable Force-Field Corrections: Synergistic Optimization for Molecular Simulations
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 …
maximum entropy principle is presented. Its formulation allows us to continuously interpolate …
Frontiers in integrative structural modeling of macromolecular assemblies
Integrative modeling enables structure determination for large macromolecular assemblies
by combining data from multiple experiments with theoretical and computational predictions …
by combining data from multiple experiments with theoretical and computational predictions …
MDRefine: a Python package for refining Molecular Dynamics trajectories with experimental data
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying
conformational dynamics of molecular systems. However, their capability to correctly …
conformational dynamics of molecular systems. However, their capability to correctly …
Automatic Forward Model Parameterization with Bayesian Inference of Conformational Populations
To quantify how well theoretical predictions of structural ensembles agree with experimental
measurements, we depend on the accuracy of forward models. These models are …
measurements, we depend on the accuracy of forward models. These models are …
Model selection using replica averaging with Bayesian inference of conformational populations
Bayesian Inference of Conformational Populations (BICePs) is a reweighting algorithm that
reconciles simulated ensembles with sparse and/or noisy observables, by sampling the full …
reconciles simulated ensembles with sparse and/or noisy observables, by sampling the full …