Journal ArticleDOI
Molecular replacement with MOLREP
Alexei A. Vagin,Alexei Teplyakov +1 more
TLDR
MOLREP is an automated program for molecular replacement that utilizes a number of original approaches to rotational and translational search and data preparation that includes weighting of the X-ray data and search models, multi-copy search, fitting the model into electron density, structural superposition of two models and rigid-body refinement.Abstract:
MOLREP is an automated program for molecular replacement that utilizes a number of original approaches to rotational and translational search and data preparation. Since the first publication describing the program, MOLREP has acquired a variety of features that include weighting of the X-ray data and search models, multi-copy search, fitting the model into electron density, structural superposition of two models and rigid-body refinement. The program can run in a fully automatic mode using optimized parameters calculated from the input data.read more
Citations
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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.
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Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors
Linlin Zhang,Daizong Lin,Xinyuanyuan Sun,Ute Curth,Christian Drosten,Lucie Sauerhering,Stephan Becker,Katharina Rox,Rolf Hilgenfeld +8 more
TL;DR: The pharmacokinetic characterization of the optimized inhibitor reveals a pronounced lung tropism and suitability for administration by the inhalative route and work that may provide a basis for development of anticoronaviral drugs.
Journal ArticleDOI
Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease
TL;DR: A crystal structure of Streptococcus pyogenes Cas9 in complex with a single-molecule guide RNA and a target DNA containing a canonical 5′-NGG-3′ PAM is reported, revealing that the PAM motif resides in a base-paired DNA duplex.
Journal ArticleDOI
Latent TGF-β structure and activation
TL;DR: Crystals of dimeric porcine proTGF-β1 reveal a ring-shaped complex, a novel fold for the pro domain, and show how the prodomain shields the growth factor from recognition by receptors and alters its conformation.
Journal ArticleDOI
Phosphorylation of p62 activates the Keap1-Nrf2 pathway during selective autophagy.
Yoshinobu Ichimura,Satoshi Waguri,Yu-shin Sou,Shun Kageyama,Jun Hasegawa,Ryosuke Ishimura,Tetsuya Saito,Yinjie Yang,Tsuguka Kouno,Toshiaki Fukutomi,Takayuki Hoshii,Atsushi Hirao,Kenji Takagi,Tsunehiro Mizushima,Hozumi Motohashi,Myung-Shik Lee,Tamotsu Yoshimori,Keiji Tanaka,Masayuki Yamamoto,Masaaki Komatsu +19 more
TL;DR: It is shown that phosphorylation of the autophagy-adaptor protein p62 markedly increases p62's binding affinity for Keap1, an adaptor of the Cul3-ubiquitin E3 ligase complex responsible for degrading Nrf2, and that inhibitors of the interaction between phosphorylated p62 and Keap 1 have potential as therapeutic agents against human HCC.
References
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Journal ArticleDOI
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Journal ArticleDOI
Phaser crystallographic software
Airlie J. McCoy,Ralf W. Grosse-Kunstleve,Paul D. Adams,Martyn Winn,Laurent C. Storoni,Randy J. Read +5 more
TL;DR: A description is given of Phaser-2.1: software for phasing macromolecular crystal structures by molecular replacement and single-wavelength anomalous dispersion phasing.
Journal ArticleDOI
The CCP4 suite: programs for protein crystallography
TL;DR: The CCP4 (Collaborative Computational Project, number 4) program suite is a collection of programs and associated data and subroutine libraries which can be used for macromolecular structure determination by X-ray crystallography.
Journal ArticleDOI
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
Axel T. Brunger,Axel T. Brunger,Paul D. Adams,G M Clore,W. L. DeLano,Piet Gros,R.W. Grosse-Kunstleve,R.W. Grosse-Kunstleve,Jiansheng Jiang,J. Kuszewski,Michael Nilges,Navraj S. Pannu,Randy J. Read,Luke M. Rice,Thomas Simonson,Gregory L. Warren +15 more
TL;DR: The Crystallography & NMR System (CNS) as mentioned in this paper is a software suite for macromolecular structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy.
Journal ArticleDOI
MOLREP: an Automated Program for Molecular Replacement
Alexei A. Vagin,Alexei Teplyakov +1 more
TL;DR: MOLREP as mentioned in this paper is an automated program for molecular replacement which utilizes effective new approaches in data processing and rotational and translational searching, such as automatic choice of all parameters, scaling by Patterson origin peaks and soft resolution cut-off.
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