Literature DB >> 15572769

Introduction to macromolecular refinement.

Dale E Tronrud1.   

Abstract

The process of refinement is such a large problem in function minimization that even the computers of today cannot perform the calculations to properly fit X-ray diffraction data. Each of the refinement packages currently under development reduces the difficulty of this problem by utilizing a unique combination of targets, assumptions and optimization methods. This review summarizes the basic methods and underlying assumptions in the commonly used refinement packages. This information can guide the selection of a refinement package that is best suited for a particular refinement project.

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Year:  2004        PMID: 15572769     DOI: 10.1107/S090744490402356X

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


  14 in total

1.  New method to compute Rcomplete enables maximum likelihood refinement for small datasets.

Authors:  Jens Luebben; Tim Gruene
Journal:  Proc Natl Acad Sci U S A       Date:  2015-07-06       Impact factor: 11.205

2.  Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic.

Authors:  Huili Yao; Huan Rui; Ritesh Kumar; Kate Eshelman; Scott Lovell; Kevin P Battaile; Wonpil Im; Mario Rivera
Journal:  Biochemistry       Date:  2015-02-17       Impact factor: 3.162

3.  Q|R: quantum-based refinement.

Authors:  Min Zheng; Jeffrey R Reimers; Mark P Waller; Pavel V Afonine
Journal:  Acta Crystallogr D Struct Biol       Date:  2017-01-01       Impact factor: 7.652

4.  Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package.

Authors:  Oleg Y Borbulevych; Joshua A Plumley; Roger I Martin; Kenneth M Merz; Lance M Westerhoff
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2014-04-26

5.  Cryo-electron microscopy modeling by the molecular dynamics flexible fitting method.

Authors:  Kwok-Yan Chan; Leonardo G Trabuco; Eduard Schreiner; Klaus Schulten
Journal:  Biopolymers       Date:  2012-09       Impact factor: 2.505

6.  Carrying out an optimal experiment.

Authors:  Zbigniew Dauter
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

7.  Model building, refinement and validation.

Authors:  Roberto A Steiner; Bernhard Rupp
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2012-03-16

8.  Crystallographic refinement of ligand complexes.

Authors:  Gerard J Kleywegt
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2006-12-13

9.  The N14 anti-afamin antibody Fab: a rare VL1 CDR glycosylation, crystallographic re-sequencing, molecular plasticity and conservative versus enthusiastic modelling.

Authors:  Andreas Naschberger; Barbara G Fürnrohr; Tihana Lenac Rovis; Suzana Malic; Klaus Scheffzek; Hans Dieplinger; Bernhard Rupp
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-11-29       Impact factor: 7.652

10.  Automatic multiple-zone rigid-body refinement with a large convergence radius.

Authors:  Pavel V Afonine; Ralf W Grosse-Kunstleve; Alexandre Urzhumtsev; Paul D Adams
Journal:  J Appl Crystallogr       Date:  2009-07-16       Impact factor: 3.304

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