11 citations · 27 across the 10 of their papers we have counts for
11 papers
Learning the Shared Latent Structure of Cryo-EM Inverse Problems
Nithin Chalapathi, Theo Sternlieb, Ethan Han +4
Understanding biomolecular function requires characterizing three-dimensional structure and conformational variability, for which cryogenic electron microscopy (cryo-EM) is a power…
On the discretization of the object space in inverse problems with application to cryo-electron microscopy
Gilles Mordant, Luke Evans, David Silva-Sánchez +2
In many inverse problems, the aim is to recover a probability distribution on a latent (or object state) space from indirect, noisy observations. When the observations can be model…
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…
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…
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…
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…
Simulation-based inference of single-molecule experiments
Lars Dingeldein, Pilar Cossio, Roberto Covino
Single-molecule experiments are a unique tool to characterize the structural dynamics of biomolecules. However, reconstructing molecular details from noisy single-molecule data is…
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…
Good rates from bad coordinates: the exponential average time-dependent rate approach
Nicodemo Mazzaferro, Subarna Sasmal, Pilar Cossio +1
Our ability to calculate rates of biochemical processes using molecular dynamics simulations is severely limited by the fact that the time scales for reactions, or changes in confo…
Active learning of Boltzmann samplers and potential energies with quantum mechanical accuracy
Ana Molina-Taborda, Pilar Cossio, Olga Lopez-Acevedo +1
Extracting consistent statistics between relevant free-energy minima of a molecular system is essential for physics, chemistry and biology. Molecular dynamics (MD) simulations can…