Literature DB >> 34783106

Optimal structure determination from sub-optimal diffraction data.

Wladek Minor1, Marcin Cymborowski1, Dominika Borek2,3, David R Cooper1, Maksymilian Chruszcz4, Zbyszek Otwinowski2,3.   

Abstract

Herein we present the newest version of the HKL-3000 system that integrates data collection, data reduction, phasing, model building, refinement, and validation. The system significantly accelerates the process of structure determination and has proven its high value for the determination of very high-quality structures. The heuristic for choosing the best approach for every step of structure determination for various quality samples and diffraction data has been optimized. The latest modifications increase the likelihood of a successful structure determination with challenging data. The HKL-3000 is a successor of HKL and HKL-2000 programs. The use of the HKL family of programs has been reported for over 73,000 PDB deposits, that is, almost 50% of macromolecular structures determined with X-ray diffraction.
© 2021 The Protein Society.

Entities:  

Keywords:  high-quality macromolecular structures; macromolecular structure determination; optimal structure determination

Mesh:

Year:  2021        PMID: 34783106      PMCID: PMC8740829          DOI: 10.1002/pro.4235

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  44 in total

1.  Molecular replacement with MOLREP.

Authors:  Alexei Vagin; Alexei Teplyakov
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-12-21

2.  The top 100 papers.

Authors:  Richard Van Noorden; Brendan Maher; Regina Nuzzo
Journal:  Nature       Date:  2014-10-30       Impact factor: 49.962

Review 3.  Against Method: Table 1-Cui Bono?

Authors:  Bernhard Rupp
Journal:  Structure       Date:  2018-05-31       Impact factor: 5.006

4.  Data management in the modern structural biology and biomedical research environment.

Authors:  Matthew D Zimmerman; Marek Grabowski; Marcin J Domagalski; Elizabeth M Maclean; Maksymilian Chruszcz; Wladek Minor
Journal:  Methods Mol Biol       Date:  2014

Review 5.  Data to knowledge: how to get meaning from your result.

Authors:  Helen M Berman; Margaret J Gabanyi; Colin R Groom; John E Johnson; Garib N Murshudov; Robert A Nicholls; Vijay Reddy; Torsten Schwede; Matthew D Zimmerman; John Westbrook; Wladek Minor
Journal:  IUCrJ       Date:  2015-01-01       Impact factor: 4.769

6.  Automated refinement of macromolecular structures at low resolution using prior information.

Authors:  Oleg Kovalevskiy; Robert A Nicholls; Garib N Murshudov
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-09-30       Impact factor: 7.652

7.  Data publication with the structural biology data grid supports live analysis.

Authors:  Peter A Meyer; Stephanie Socias; Jason Key; Elizabeth Ransey; Emily C Tjon; Alejandro Buschiazzo; Ming Lei; Chris Botka; James Withrow; David Neau; Kanagalaghatta Rajashankar; Karen S Anderson; Richard H Baxter; Stephen C Blacklow; Titus J Boggon; Alexandre M J J Bonvin; Dominika Borek; Tom J Brett; Amedeo Caflisch; Chung-I Chang; Walter J Chazin; Kevin D Corbett; Michael S Cosgrove; Sean Crosson; Sirano Dhe-Paganon; Enrico Di Cera; Catherine L Drennan; Michael J Eck; Brandt F Eichman; Qing R Fan; Adrian R Ferré-D'Amaré; J Christopher Fromme; K Christopher Garcia; Rachelle Gaudet; Peng Gong; Stephen C Harrison; Ekaterina E Heldwein; Zongchao Jia; Robert J Keenan; Andrew C Kruse; Marc Kvansakul; Jason S McLellan; Yorgo Modis; Yunsun Nam; Zbyszek Otwinowski; Emil F Pai; Pedro José Barbosa Pereira; Carlo Petosa; C S Raman; Tom A Rapoport; Antonina Roll-Mecak; Michael K Rosen; Gabby Rudenko; Joseph Schlessinger; Thomas U Schwartz; Yousif Shamoo; Holger Sondermann; Yizhi J Tao; Niraj H Tolia; Oleg V Tsodikov; Kenneth D Westover; Hao Wu; Ian Foster; James S Fraser; Filipe R N C Maia; Tamir Gonen; Tom Kirchhausen; Kay Diederichs; Mercè Crosas; Piotr Sliz
Journal:  Nat Commun       Date:  2016-03-07       Impact factor: 14.919

8.  Highly accurate protein structure prediction with AlphaFold.

Authors:  John Jumper; Richard Evans; Alexander Pritzel; Tim Green; Michael Figurnov; Olaf Ronneberger; Kathryn Tunyasuvunakool; Russ Bates; Augustin Žídek; Anna Potapenko; Alex Bridgland; Clemens Meyer; Simon A A Kohl; Andrew J Ballard; Andrew Cowie; Bernardino Romera-Paredes; Stanislav Nikolov; Rishub Jain; Demis Hassabis; Jonas Adler; Trevor Back; Stig Petersen; David Reiman; Ellen Clancy; Michal Zielinski; Martin Steinegger; Michalina Pacholska; Tamas Berghammer; Sebastian Bodenstein; David Silver; Oriol Vinyals; Andrew W Senior; Koray Kavukcuoglu; Pushmeet Kohli
Journal:  Nature       Date:  2021-07-15       Impact factor: 49.962

9.  Covid-19.bioreproducibility.org: A web resource for SARS-CoV-2-related structural models.

Authors:  Dariusz Brzezinski; Marcin Kowiel; David R Cooper; Marcin Cymborowski; Marek Grabowski; Alexander Wlodawer; Zbigniew Dauter; Ivan G Shabalin; Miroslaw Gilski; Bernhard Rupp; Mariusz Jaskolski; Wladek Minor
Journal:  Protein Sci       Date:  2020-10-08       Impact factor: 6.993

10.  Small Molecule Microcrystal Electron Diffraction for the Pharmaceutical Industry-Lessons Learned From Examining Over Fifty Samples.

Authors:  Jessica F Bruhn; Giovanna Scapin; Anchi Cheng; Brandon Q Mercado; David G Waterman; Thejusvi Ganesh; Sargis Dallakyan; Brandon N Read; Travis Nieusma; Kyle W Lucier; Megan L Mayer; Nicole J Chiang; Nicole Poweleit; Philip T McGilvray; Timothy S Wilson; Michael Mashore; Camille Hennessy; Sean Thomson; Bo Wang; Clinton S Potter; Bridget Carragher
Journal:  Front Mol Biosci       Date:  2021-07-12
View more
  1 in total

1.  Optimal structure determination from sub-optimal diffraction data.

Authors:  Wladek Minor; Marcin Cymborowski; Dominika Borek; David R Cooper; Maksymilian Chruszcz; Zbyszek Otwinowski
Journal:  Protein Sci       Date:  2021-11-24       Impact factor: 6.725

  1 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.