Journal ArticleDOI
A graphical user interface to the CCP4 program suite.
TLDR
CCP4i is a graphical user interface that makes running programs from the CCP4 suite simpler and quicker and is particularly directed at inexperienced users and tightly linked to introductory and scientific documentation.Abstract:
CCP4i is a graphical user interface that makes running programs from the CCP4 suite simpler and quicker. It is particularly directed at inexperienced users and tightly linked to introductory and scientific documentation. It also provides a simple project-management system and visualization tools. The system is readily extensible and not specific to CCP4 software.read more
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Journal ArticleDOI
PHENIX: a comprehensive Python-based system for macromolecular structure solution
Paul D. Adams,Paul D. Adams,Pavel V. Afonine,Gábor Bunkóczi,Vincent B. Chen,Ian W. Davis,Nathaniel Echols,Jeffrey J. Headd,Li-Wei Hung,Gary J. Kapral,Ralf W. Grosse-Kunstleve,Airlie J. McCoy,Nigel W. Moriarty,Robert D. Oeffner,Randy J. Read,David S. Richardson,Jane S. Richardson,Thomas C. Terwilliger,Peter H. Zwart +18 more
TL;DR: The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.
Journal ArticleDOI
Overview of the CCP4 suite and current developments.
Martyn Winn,Charles Ballard,Kevin Cowtan,Eleanor J. Dodson,Paul Emsley,Phil Evans,Ronan M. Keegan,Eugene Krissinel,Andrew G. W. Leslie,Airlie J. McCoy,Stuart McNicholas,Garib N. Murshudov,Navraj S. Pannu,E. Potterton,Harold R. Powell,Randy J. Read,Alexei A. Vagin,Keith S. Wilson +17 more
TL;DR: An overview of the CCP4 software suite for macromolecular crystallography is given.
Journal ArticleDOI
Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7.
TL;DR: ARP/wARP 7.0 tackles several tasks: iterative protein model building including a high-level decision-making control module; fast construction of the secondary structure of a protein; building flexible loops in alternate conformations; fully automated placement of ligands; and finding ordered water molecules.
Journal ArticleDOI
Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota
Jan-Hendrik Hehemann,Gaëlle Correc,Gaëlle Correc,Tristan Barbeyron,Tristan Barbeyron,William Helbert,William Helbert,Mirjam Czjzek,Mirjam Czjzek,Gurvan Michel,Gurvan Michel +10 more
TL;DR: It is shown that porphyranases and agarases are frequent in the Japanese population and that they are absent in metagenome data from North American individuals, which indicates that contact with non-sterile food may be a general factor in CAZyme diversity in human gut microbes.
Journal ArticleDOI
BALBES: a molecular-replacement pipeline
TL;DR: The fully automated pipeline, BALBES, integrates a redesigned hierarchical database of protein structures with their domains and multimeric organization, and solves molecular-replacement problems using only input X-ray and sequence data.
References
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On the application of phase relationships to complex structures. XX. RANTAN for large structures and fragment development
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