Integrated AlphaFold2 and DEER investigation of the conformational dynamics of a pH-dependent APC antiporter
D Del Alamo, L DeSousa, RM Nair… - Proceedings of the …, 2022 - National Acad Sciences
The Amino Acid–Polyamine-Organocation (APC) transporter GadC contributes to the
survival of pathogenic bacteria under extreme acid stress by exchanging extracellular …
survival of pathogenic bacteria under extreme acid stress by exchanging extracellular …
Ensemble reweighting using cryo-EM particle images
WS Tang, D Silva-Sánchez… - The Journal of …, 2023 - ACS Publications
Cryo-electron microscopy (cryo-EM) has recently become a leading method for obtaining
high-resolution structures of biological macromolecules. However, cryo-EM is limited to …
high-resolution structures of biological macromolecules. However, cryo-EM is limited to …
AlphaFold prediction of structural ensembles of disordered proteins
ZF Brotzakis, S Zhang, M Vendruscolo - bioRxiv, 2023 - biorxiv.org
Deep learning methods of predicting protein structures have reached an accuracy
comparable to that of high-resolution experimental methods. It is thus possible to generate …
comparable to that of high-resolution experimental methods. It is thus possible to generate …
Protein conformation generation via force-guided se (3) diffusion models
The conformational landscape of proteins is crucial to understanding their functionality in
complex biological processes. Traditional physics-based computational methods, such as …
complex biological processes. Traditional physics-based computational methods, such as …
Score-based enhanced sampling for protein molecular dynamics
The dynamic nature of proteins is crucial for determining their biological functions and
properties, and molecular dynamics (MD) simulations stand as a predominant tool to study …
properties, and molecular dynamics (MD) simulations stand as a predominant tool to study …