Literature DB >> 28573584

Acknowledging Errors: Advanced Molecular Replacement with Phaser.

Airlie J McCoy1.   

Abstract

Molecular replacement is a method for solving the crystallographic phase problem using an atomic model for the target structure. State-of-the-art methods have moved the field significantly from when it was first envisaged as a method for solving cases of high homology and completeness between a model and target structure. Improvements brought about by application of maximum likelihood statistics mean that various errors in the model and pathologies in the data can be accounted for, so that cases hitherto thought to be intractable are standardly solvable. As a result, molecular replacement phasing now accounts for the lion's share of structures deposited in the Protein Data Bank. However, there will always be cases at the fringes of solvability. I discuss here the approaches that will help tackle challenging molecular replacement cases.

Entities:  

Keywords:  LLGI; Maximum likelihood; Molecular replacement

Mesh:

Substances:

Year:  2017        PMID: 28573584     DOI: 10.1007/978-1-4939-7000-1_18

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  13 in total

1.  Structural Insights into Interaction Mechanisms of Alternative Piperazine-urea YEATS Domain Binders in MLLT1.

Authors:  Xiaomin Ni; David Heidenreich; Thomas Christott; James Bennett; Moses Moustakim; Paul E Brennan; Oleg Fedorov; Stefan Knapp; Apirat Chaikuad
Journal:  ACS Med Chem Lett       Date:  2019-11-25       Impact factor: 4.345

2.  Design, Synthesis, and Characterization of an Orally Active Dual-Specific ULK1/2 Autophagy Inhibitor that Synergizes with the PARP Inhibitor Olaparib for the Treatment of Triple-Negative Breast Cancer.

Authors:  Huiyu Ren; Nicole A Bakas; Mitchell Vamos; Apirat Chaikuad; Allison S Limpert; Carina D Wimer; Sonja N Brun; Lester J Lambert; Lutz Tautz; Maria Celeridad; Douglas J Sheffler; Stefan Knapp; Reuben J Shaw; Nicholas D P Cosford
Journal:  J Med Chem       Date:  2020-11-17       Impact factor: 7.446

3.  Structural basis for recruitment of the CHK1 DNA damage kinase by the CLASPIN scaffold protein.

Authors:  Matthew Day; Sarah Parry-Morris; Jack Houghton-Gisby; Antony W Oliver; Laurence H Pearl
Journal:  Structure       Date:  2021-03-30       Impact factor: 5.006

4.  On the application of the expected log-likelihood gain to decision making in molecular replacement.

Authors:  Robert D Oeffner; Pavel V Afonine; Claudia Millán; Massimo Sammito; Isabel Usón; Randy J Read; Airlie J McCoy
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-04-04       Impact factor: 7.652

5.  Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement.

Authors:  Airlie J McCoy; Robert D Oeffner; Claudia Millán; Massimo Sammito; Isabel Usón; Randy J Read
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-04-03       Impact factor: 7.652

6.  [b]-Annulated Halogen-Substituted Indoles as Potential DYRK1A Inhibitors.

Authors:  Christian Lechner; Maren Flaßhoff; Hannes Falke; Lutz Preu; Nadége Loaëc; Laurent Meijer; Stefan Knapp; Apirat Chaikuad; Conrad Kunick
Journal:  Molecules       Date:  2019-11-13       Impact factor: 4.411

7.  Discovery of a Novel Class of Covalent Dual Inhibitors Targeting the Protein Kinases BMX and BTK.

Authors:  Michael Forster; Xiaojun Julia Liang; Martin Schröder; Stefan Gerstenecker; Apirat Chaikuad; Stefan Knapp; Stefan Laufer; Matthias Gehringer
Journal:  Int J Mol Sci       Date:  2020-12-04       Impact factor: 5.923

8.  Phasertng: directed acyclic graphs for crystallographic phasing.

Authors:  Airlie J McCoy; Duncan H Stockwell; Massimo D Sammito; Robert D Oeffner; Kaushik S Hatti; Tristan I Croll; Randy J Read
Journal:  Acta Crystallogr D Struct Biol       Date:  2021-01-01       Impact factor: 7.652

Review 9.  Introduction to molecular replacement: a time perspective.

Authors:  Eleanor Dodson
Journal:  Acta Crystallogr D Struct Biol       Date:  2021-06-18       Impact factor: 7.652

10.  Comparative structural analyses and nucleotide-binding characterization of the four KH domains of FUBP1.

Authors:  Xiaomin Ni; Stefan Knapp; Apirat Chaikuad
Journal:  Sci Rep       Date:  2020-08-10       Impact factor: 4.379

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