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Interactive comparison and remediation of collections of macromolecular structures
Author(s) -
Moriarty Nigel W.,
Liebschner Dorothee,
Klei Herbert E.,
Echols Nathaniel,
Afonine Pavel V.,
Headd Jeffrey J.,
Poon Billy K.,
Adams Paul D.
Publication year - 2018
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.3296
Subject(s) - correctness , computer science , crystallography , consistency (knowledge bases) , protein structure , biomolecular structure , angstrom , chemistry , algorithm , artificial intelligence , biochemistry
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.