Interactive comparison and remediation of collections of macromolecular structures: Interactive Comparison and Remediation

Moriarty, Nigel W.; Liebschner, Dorothee; Klei, Herbert E.; Echols, Nathaniel; Afonine, Pavel V.; Headd, Jeffrey J.; Poon, Billy K.; Adams, Paul D.

doi:10.1002/pro.3296

Interactive comparison and remediation of collections of macromolecular structures: Interactive Comparison and Remediation

Journal Article · Wed Sep 13 00:00:00 EDT 2017 · Protein Science

DOI:https://doi.org/10.1002/pro.3296· OSTI ID:1506289

^[1]; Liebschner, Dorothee ^[1]; Klei, Herbert E. ^[1]; Echols, Nathaniel ^[1]; Afonine, Pavel V. ^[1]; Headd, Jeffrey J. ^[1]; Poon, Billy K. ^[1]; Adams, Paul D. ^[2]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging; Univ. of California, Berkeley, CA (United States). Dept. of Bioengineering

Often similar structures need to be compared to reveal local differences throughout the entire model or between related copies within the model. Therefore, a program to compare multiple structures and enable correction any differences not supported by the density map was written within the Phenix framework (Adams et al., Acta Cryst 2010; D66:213–221). This program, called Structure Comparison, can also be used for structures with multiple copies of the same protein chain in the asymmetric unit, that is, as a result of non-crystallographic symmetry (NCS). Structure Comparison was designed to interface with Coot(Emsley et al., Acta Cryst 2010; D66:486–501) and PyMOL(DeLano, PyMOL 0.99; 2002) to facilitate comparison of large numbers of related structures. Structure Comparison analyzes collections of protein structures using several metrics, such as the rotamer conformation of equivalent residues, displays the results in tabular form and allows superimposed protein chains and density maps to be quickly inspected and edited (via the tools in Coot) for consistency, completeness and correctness.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: National Institutes of Health (NIH); USDOE; USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1506289

Alternate ID(s):: OSTI ID: 1421245

Journal Information:: Protein Science, Journal Name: Protein Science Journal Issue: 1 Vol. 27; ISSN 0961-8368

Publisher:: The Protein SocietyCopyright Statement

Country of Publication:: United States

Language:: English

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