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Gorgon and pathwalking: Macromolecular modeling tools for subnanometer resolution density maps
Author(s) -
Baker Matthew L.,
Baker Mariah R.,
Hryc Corey F.,
Ju Tao,
Chiu Wah
Publication year - 2012
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.22065
Subject(s) - resolution (logic) , macromolecule , low resolution , cryo electron microscopy , high resolution , identification (biology) , chemistry , nanotechnology , function (biology) , range (aeronautics) , computational biology , computer science , biological system , artificial intelligence , materials science , biology , geography , biochemistry , botany , remote sensing , evolutionary biology , composite material
The complex interplay of proteins and other molecules, often in the form of large transitory assemblies, are critical to cellular function. Today, X‐ray crystallography and electron cryo‐microscopy (cryo‐EM) are routinely used to image these macromolecular complexes, though often at limited resolutions. Despite the rapidly growing number of macromolecular structures, few tools exist for modeling and annotating structures in the range of 3–10 Å resolution. To address this need, we have developed a number of utilities specifically targeting subnanometer resolution density maps. As part of the 2010 Cryo‐EM Modeling Challenge, we demonstrated two of our latest de novo modeling tools, Pathwalking and Gorgon, as well as a tool for secondary structure identification (SSEHunter) and a new rigid‐body/flexible fitting tool in Gorgon. In total, we submitted 30 structural models from ten different subnanometer resolution data sets in four of the six challenge categories. Each of our utlities produced accurate structural models and annotations across the various density maps. In the end, the utilities that we present here offer users a robust toolkit for analyzing and modeling protein structure in macromolecular assemblies at non‐atomic resolutions. © 2012 Wiley Periodicals, Inc. Biopolymers 97: 655–668, 2012.