Literature DB >> 10713511

Validation of protein crystal structures.

G J Kleywegt1.   

Abstract

Since the process of building and refining a model of a biomacromolecule based on crystallographic data is subjective, quality-control techniques are required to assess the validity of such models. During the 1990s, much experience was gained; the methods used and some of the lessons learned are reviewed here. In addition, an extensive compendium of quality criteria and quality-control methods that are or have been used to validate models of biomacromolecules has been compiled. The emphasis in this compendium is on the validation of protein crystal structures.

Mesh:

Year:  2000        PMID: 10713511     DOI: 10.1107/s0907444999016364

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


  82 in total

1.  A geometry force field which converts low-resolution X-ray models to structures with properties found at ultra high resolution.

Authors:  Colin McMartin
Journal:  Protein Sci       Date:  2011-12-05       Impact factor: 6.725

2.  Dihedral-angle information entropy as a gauge of secondary structure propensity.

Authors:  Shi Zhong; Jeremy M Moix; Stephen Quirk; Rigoberto Hernandez
Journal:  Biophys J       Date:  2006-09-15       Impact factor: 4.033

3.  Models of protein-ligand crystal structures: trust, but verify.

Authors:  Marc C Deller; Bernhard Rupp
Journal:  J Comput Aided Mol Des       Date:  2015-02-10       Impact factor: 3.686

4.  Adsorption of human serum albumin on the chrysotile surface: a molecular dynamics and spectroscopic investigation.

Authors:  Roberto Artali; Antonio Del Pra; Elisabetta Foresti; Isidoro Giorgio Lesci; Norberto Roveri; Piera Sabatino
Journal:  J R Soc Interface       Date:  2008-03-06       Impact factor: 4.118

5.  Local quality assessment in homology models using statistical potentials and support vector machines.

Authors:  Marc Fasnacht; Jiang Zhu; Barry Honig
Journal:  Protein Sci       Date:  2007-06-28       Impact factor: 6.725

6.  Spectral fitting for signal assignment and structural analysis of uniformly 13C-labeled solid proteins by simulated annealing based on chemical shifts and spin dynamics.

Authors:  Yoh Matsuki; Hideo Akutsu; Toshimichi Fujiwara
Journal:  J Biomol NMR       Date:  2007-07-06       Impact factor: 2.835

7.  The war of tools: how can NMR spectroscopists detect errors in their structures?

Authors:  Edoardo Saccenti; Antonio Rosato
Journal:  J Biomol NMR       Date:  2008-03-05       Impact factor: 2.835

8.  Sorting the chaff from the wheat at the PDB.

Authors:  Dale E Tronrud; Brian W Matthews
Journal:  Protein Sci       Date:  2009-01       Impact factor: 6.725

9.  TM0486 from the hyperthermophilic anaerobe Thermotoga maritima is a thiamin-binding protein involved in response of the cell to oxidative conditions.

Authors:  Zorah Dermoun; Amélie Foulon; Mitchell D Miller; Daniel J Harrington; Ashley M Deacon; Corinne Sebban-Kreuzer; Philippe Roche; Daniel Lafitte; Olivier Bornet; Ian A Wilson; Alain Dolla
Journal:  J Mol Biol       Date:  2010-05-13       Impact factor: 5.469

10.  Structure of the orthorhombic form of human inosine triphosphate pyrophosphatase.

Authors:  Jason Porta; Carol Kolar; Stanislav G Kozmin; Youri I Pavlov; Gloria E O Borgstahl
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2006-10-25
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