40 citations · 113 across the 11 of their papers we have counts for
11 papers
Robust Inference-Time Steering of Protein Diffusion Models via Embedding Optimization
Minhuan Li, Jiequn Han, Pilar Cossio +1
A core challenge in structural biophysics is generating biomolecular conformations that are both physically plausible and consistent with experimental measurements. While sequence-…
Microscopic Theory, Analysis, and Interpretation of Conductance Histograms in Molecular Junctions
Leopoldo Mejía, Pilar Cossio, Ignacio Franco
Molecular electronics break-junction experiments are widely used to investigate fundamental physics and chemistry at the nanoscale. Reproducibility in these experiments relies on m…
Ensemble reweighting using Cryo-EM particles
Wai Shing Tang, David Silva-Sánchez, Julian Giraldo-Barreto +5
Cryo-electron microscopy (cryo-EM) has recently become a premier method for obtaining high-resolution structures of biological macromolecules. However, it is limited to biomolecula…
Simulation-based inference of single-molecule force spectroscopy
Lars Dingeldein, Pilar Cossio, Roberto Covino
Single-molecule force spectroscopy (smFS) is a powerful approach to studying molecular self-organization. However, the coupling of the molecule with the ever-present experimental d…
Ab initio metadynamics determination of temperature-dependent free-energy landscape in ultrasmall silver clusters
Daniel Sucerquia, Cristian Parra, Pilar Cossio +1
Ab initio metadynamics enables extracting free-energy landscapes having the accuracy of first principles electronic structure methods. We introduce an interface between the PLUMED…
Transition rates, survival probabilities, and quality of bias from time-dependent biased simulations
Karen Palacio-Rodriguez, Hadrien Vroylandt, Lukas S. Stelzl +3
Simulations with an adaptive time-dependent bias, such as metadynamics, enable an efficient exploration of the conformational space of a system. However, the dynamic information of…
A Bayesian approach for extracting free energy profiles from cryo-electron microscopy experiments using a path collective variable
Julian Giraldo-Barreto, Sebastian Ortiz, Erik H. Thiede +4
Cryo-electron microscopy (cryo-EM) extracts single-particle density projections of individual biomolecules. Although cryo-EM is widely used for 3D reconstruction, due to its single…
PARCE: Protocol for Amino acid Refinement through Computational Evolution
Rodrigo Ochoa, Miguel A. Soler, Alessandro Laio +1
The in silico design of peptides and proteins as binders is useful for diagnosis and therapeutics due to their low adverse effects and major specificity. To select the most promisi…
Cross-validation tests for cryo-EM maps using an independent particle set
Sebastian Ortiz, Luka Stanisic, Boris A Rodriguez +3
Cryo-electron microscopy is a revolutionary technique that can provide 3D density maps at near-atomic resolution. However, map validation is still an open issue in the field. Despi…
Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors
Roberto Covino, Michael T. Woodside, Gerhard Hummer +2
In single-molecule force spectroscopy experiments, a biomolecule is attached to a force probe via polymer linkers, and the total extension -- of molecule plus apparatus -- is monit…
BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images
Pilar Cossio, David Rohr, Fabio Baruffa +3
In cryo-electron microscopy (EM), molecular structures are determined from large numbers of projection images of individual particles. To harness the full power of this single-mole…