Pilar Cossio

Nov 29, 2024 | cell.com | Pilar Cossio |Edward T. Eng

(A and B) Poster sessions were held over the 3 days of the symposium. The poster boards were a main place of gathering during breaks and also provided opportunities for trainees and in particular high school students in the region to present their work (B). (C–E) Eight hands-on practical sessions were held simultaneously during Workshop Wednesday, including vendor demonstrations (C), cryogenic electron microscopy (cryoEM) sample preparation tools (D), and instrumentation use (E).

Oct 22, 2024 | biorxiv.org | Wai Shing Tang |Aaditya V Rangan |Pilar Cossio |Jeff Soules

AbstractExtracting conformational heterogeneity from cryo-electron microscopy (cryo-EM) images is particularly challenging for flexible biomolecules, where traditional 3D classification approaches often fail. Over the past few decades, advancements in experimental and computational techniques have been made to tackle this challenge, especially Bayesian-based approaches that provide physically interpretable insights into cryo-EM heterogeneity.

Oct 11, 2024 | biorxiv.org | Miro Astore |Robert Blackwell |David Silva-Sanchez |Pilar Cossio

AbstractCryogenic electron microscopy (cryo-EM) has emerged as a powerful method for resolving the atomistic details of cellular components. In recent years, several computational methods have been developed to study the heterogeneity of molecules in single-particle cryo-EM. In this study, we analyzed a publicly available single-particle dataset of TRPV1 using five of these methods: 3D Flexible Refinement, 3D Variability Analysis, cryoDRGN, ManifoldEM, and Bayesian ensemble reweighting.

Oct 3, 2024 | biorxiv.org | Kexin Zhang |Pilar Cossio |Aaditya V Rangan |Bronwyn A Lucas

Abstract2D template matching (2DTM) can be used to detect molecules and their assemblies in cellular cryo-EM images with high positional and orientational accuracy. While 2DTM successfully detects spherical targets such as large ribosomal subunits, challenges remain in detecting smaller and more aspherical targets in various environments. In this work, a novel 2DTM metric, referred to as the 2DTM p-value, is developed to extend the 2DTM framework to more complex applications.

Mar 30, 2024 | dx.doi.org | Nicodemo Mazzaferro |Subarna Sasmal |Pilar Cossio |Glen M. Hocky

A major challenge in biomolecular simulation is to be able to accurately assess the transition rate constant (inverse of the mean residence time in a state) of complex processes, including conformational transitions and the binding/unbinding of macromolecules and their ligands.