Faculty, Staff and Student Publications
Publication Date
6-2-2022
Journal
Biomolecules
Abstract
Single-particle electron cryomicroscopy (cryoEM) has become an indispensable tool for studying structure and function in macromolecular assemblies. As an integral part of the cryoEM structure determination process, computational tools have been developed to build atomic models directly from a density map without structural templates. Nearly a decade ago, we created Pathwalking, a tool for de novo modeling of protein structure in near-atomic resolution cryoEM density maps. Here, we present the latest developments in Pathwalking, including the addition of probabilistic models, as well as a companion tool for modeling waters and ligands. This software was evaluated on the 2021 CryoEM Ligand Challenge density maps, in addition to identifying ligands in three IP3R1 density maps at ~3 Å to 4.1 Å resolution. The results clearly demonstrate that the Pathwalking de novo modeling pipeline can construct accurate protein structures and reliably localize and identify ligand density directly from a near-atomic resolution map.
Keywords
Cryoelectron Microscopy, Ligands, Models, Molecular, Protein Conformation, Proteins, Software, cryoEM, Pathwalking, de novo modeling, near-atomic resolution, density map, probabilistic models, ligand modeling
DOI
10.3390/biom12060773
PMID
35740898
PMCID
PMC9220806
PubMedCentral® Posted Date
6-2-2022
PubMedCentral® Full Text Version
Post-print
Published Open-Access
yes