7 papers
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…
MIMIC: A Generative Multimodal Foundation Model for Biomolecules
Siavash Golkar, Jake Kovalic, Irina Espejo Morales +28
Biological function emerges from coupled constraints across sequence, structure, regulation, evolution, and cellular context, yet most foundation models in biology are trained with…
Cryo-em images are intrinsically low dimensional
Luke Evans, Octavian-Vlad Murad, Lars Dingeldein +3
Simulation-based inference provides a powerful framework for cryo-electron microscopy, employing neural networks in methods like CryoSBI to infer biomolecular conformations via lea…
CryoBench: Diverse and challenging datasets for the heterogeneity problem in cryo-EM
Minkyu Jeon, Rishwanth Raghu, Miro Astore +6
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining high-resolution 3D biomolecular structures from imaging data. Its unique ability to capture structural va…
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…
Estimating the tails of the spectrum of the Hessian of the log-likelihood for \textit{ab-initio} single-particle reconstruction in electron cryomicroscopy
Aaditya V. Rangan, Wai-Shing Tang, Pilar Cossio +2
Electron cryomicroscopy (cryo-EM) is a technique in structural biology used to reconstruct accurate volumetric maps of molecules. One step of the cryo-EM pipeline involves solving…