Literature DB >> 15572770

Liking likelihood.

Airlie J McCoy1.   

Abstract

Maximum-likelihood methods have now been applied to most areas of macromolecular crystallography, including data reduction, molecular replacement, experimental phasing and refinement. However, students of macromolecular crystallography are predominantly taught only traditional crystallographic methods and therefore have little understanding of the methods underlying the modern software that they routinely use in structure determination. This situation arises, at least in part, because maximum likelihood is considered to be too difficult to be taught to students who lack substantial mathematical training within the limited time frame of undergraduate/graduate courses. A method of introducing maximum-likelihood concepts with the help of dice is described here and it is then shown how these concepts can form the core of understanding maximum-likelihood refinement, molecular replacement and experimental phasing. Within the framework described, the crystallographic maximum-likelihood techniques are all reduced to the same basic concepts and become easier and less time-consuming to teach than traditional methods, which rely on disparate concepts.

Mesh:

Year:  2004        PMID: 15572770     DOI: 10.1107/S0907444904016038

Source DB:  PubMed          Journal:  Acta Crystallogr D Biol Crystallogr        ISSN: 0907-4449


  16 in total

1.  Assessment of protein structure refinement in CASP9.

Authors:  Justin L MacCallum; Alberto Pérez; Michael J Schnieders; Lan Hua; Matthew P Jacobson; Ken A Dill
Journal:  Proteins       Date:  2011-08-30

2.  Experimental phasing: best practice and pitfalls.

Authors:  Airlie J McCoy; Randy J Read
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

3.  Crystal structure of a eukaryotic phosphate transporter.

Authors:  Bjørn P Pedersen; Hemant Kumar; Andrew B Waight; Aaron J Risenmay; Zygy Roe-Zurz; Bryant H Chau; Avner Schlessinger; Massimiliano Bonomi; William Harries; Andrej Sali; Atul K Johri; Robert M Stroud
Journal:  Nature       Date:  2013-03-31       Impact factor: 49.962

4.  A smooth and differentiable bulk-solvent model for macromolecular diffraction.

Authors:  T D Fenn; M J Schnieders; A T Brunger
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-08-13

5.  Solving structures of protein complexes by molecular replacement with Phaser.

Authors:  Airlie J McCoy
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2006-12-13

Review 6.  Serial femtosecond crystallography: the first five years.

Authors:  Ilme Schlichting
Journal:  IUCrJ       Date:  2015-02-03       Impact factor: 4.769

7.  Improved crystal orientation and physical properties from single-shot XFEL stills.

Authors:  Nicholas K Sauter; Johan Hattne; Aaron S Brewster; Nathaniel Echols; Petrus H Zwart; Paul D Adams
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2014-11-28

8.  X-ray structures of Na-GST-1 and Na-GST-2 two glutathione S-transferase from the human hookworm Necator americanus.

Authors:  Oluwatoyin A Asojo; Kohei Homma; Meghan Sedlacek; Michelle Ngamelue; Gaddam N Goud; Bin Zhan; Vehid Deumic; Oluyomi Asojo; Peter J Hotez
Journal:  BMC Struct Biol       Date:  2007-06-26

9.  An introduction to molecular replacement.

Authors:  Philip Evans; Airlie McCoy
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2007-12-05

10.  Phaser crystallographic software.

Authors:  Airlie J McCoy; Ralf W Grosse-Kunstleve; Paul D Adams; Martyn D Winn; Laurent C Storoni; Randy J Read
Journal:  J Appl Crystallogr       Date:  2007-07-13       Impact factor: 3.304

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