Journal
JOURNAL OF STRUCTURAL BIOLOGY
Volume 196, Issue 3, Pages 289-298Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.jsb.2016.06.004
Keywords
Protein structure; Backbone model
Funding
- National Institutes of Health [R21GM100229, R01GM079429, P41GM103832, R01GM080139]
- National Science Foundation [DBI-1408887]
- Direct For Biological Sciences
- Div Of Biological Infrastructure [1356388] Funding Source: National Science Foundation
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As electron cryo-microscopy (cryo-EM) can now frequently achieve near atomic resolution, accurate interpretation of these density maps in terms of atomistic detail has become paramount in deciphering macromolecular structure and function. However, there are few software tools for modeling protein structure from cryo-EM density maps in this resolution range. Here, we present an extension of our original Pathwalking protocol, which can automatically trace a protein backbone directly from a near-atomic resolution (3-6 angstrom) density map. The original Pathwalking approach utilized a Traveling Salesman Problem solver for backbone tracing, but manual adjustment was still required during modeling. In the new version, human intervention is minimized and we provide a more robust approach for backbone modeling. This includes iterative secondary structure identification, termini detection and the ability to model multiple subunits without prior segmentation. Overall, the new Pathwalking procedure provides a more complete and robust tool for annotating protein structure function in near-atomic resolution density maps. (C) 2016 Elsevier Inc. All rights reserved.
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