From the 1 of 12 linked papers with an AI index.
12 papers
A differentiable photon-by-photon likelihood for continuous free-energy landscapes and diffusion coefficients from single-molecule FRET
Lars Dingeldein, Roberto Covino
Single-molecule FRET probes the conformational dynamics of biomolecules by measuring the distance between two dyes. The experiment produces a stream of coloured photons, which is o…
Committors and Reaction Rates from Trial Functions That Violate the Boundary Conditions
Magnus Petersen, Simon Lichtinger, Roberto Covino
The committor is the optimal reaction coordinate for a rare transition: it pinpoints the transition state and fixes the rate, and it governs events from protein folding to crystal…
Accelerated descriptor-free path sampling for protein-ligand binding kinetics
Simon M. Lichtinger, Roberto Covino
The paper introduces a descriptor‑free path‑sampling method that uses an equivariant graph neural network to model the committor and a static bias potential to accelerate convergen…
Protein Dynamics Beyond Structure Prediction
Juliette Griffié, Sviatlana Shashkova, Antonio Ciarlo +41
The ability to predict protein three-dimensional structures from amino acid sequences is a landmark achievement in molecular biology, where recent deep learning approaches such as…
Quantitative and Predictive Folding Models from Limited Single-Molecule Data Using Simulation-Based Inference
Lars Dingeldein, Aaron Lyons, Pilar Cossio +2
The study of biomolecular folding has been greatly advanced by single-molecule force spectroscopy (SMFS), which enables the observation of the dynamics of individual molecules. How…
A Machine-Learned Symbolic Committor for a Chemical Reaction: Retinal Isomerization
Kai Töpfer, Gianmarco Lazzeri, Vittoria Ossanna +4
The thermal cis-trans isomerization around the C=C double bond of retinal is a prototypical high-barrier reaction whose mechanism hinges on subtle out-of-plane bendin…