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3.  Structure validation in chemical crystallography 
This paper reports on the current status of structure validation in chemical crystallography.
Automated structure validation was introduced in chemical crystallography about 12 years ago as a tool to assist practitioners with the exponential growth in crystal structure analyses. Validation has since evolved into an easy-to-use checkCIF/PLATON web-based IUCr service. The result of a crystal structure determination has to be supplied as a CIF-formatted computer-readable file. The checking software tests the data in the CIF for completeness, quality and consistency. In addition, the reported structure is checked for incomplete analysis, errors in the analysis and relevant issues to be verified. A validation report is generated in the form of a list of ALERTS on the issues to be corrected, checked or commented on. Structure validation has largely eliminated obvious problems with structure reports published in IUCr journals, such as refinement in a space group of too low symmetry. This paper reports on the current status of structure validation and possible future extensions.
doi:10.1107/S090744490804362X
PMCID: PMC2631630  PMID: 19171970
validation; checkCIF; PLATON
4.  Notes for authors 2012 
Notes for authors.
doi:10.1107/S1600536811047003
PMCID: PMC3254267
Notes for authors
5.  Applied and implied semantics in crystallographic publishing 
Background
Crystallography is a data-rich, software-intensive scientific discipline with a community that has undertaken direct responsibility for publishing its own scientific journals. That community has worked actively to develop information exchange standards allowing readers of structure reports to access directly, and interact with, the scientific content of the articles.
Results
Structure reports submitted to some journals of the International Union of Crystallography (IUCr) can be automatically validated and published through an efficient and cost-effective workflow. Readers can view and interact with the structures in three-dimensional visualization applications, and can access the experimental data should they wish to perform their own independent structure solution and refinement. The journals also layer on top of this facility a number of automated annotations and interpretations to add further scientific value.
Conclusions
The benefits of semantically rich information exchange standards have revolutionised the scholarly publishing process for crystallography, and establish a model relevant to many other physical science disciplines.
doi:10.1186/1758-2946-4-19
PMCID: PMC3497589  PMID: 22932420
Information exchange standard; Semantics; Ontology; Scholarly publishing; CIF; Crystallography
6.  Retraction of articles 
Retraction of articles.
This article reports the retraction of articles published in Acta Crystallographica Section E between 2005 and 2009.
doi:10.1107/S1600536811037603
PMCID: PMC3393136  PMID: 22807693
7.  Retraction of articles 
Retraction of articles.
This article reports the retraction of articles published in Acta Crystallographica Section E between 2007 and 2009.
doi:10.1107/S1600536811037597
PMCID: PMC3343774  PMID: 22589748
8.  Retraction of articles 
Retraction of five articles.
This article reports the retraction of five articles published in Acta Crystallographica Section E between 2004 and 2011.
doi:10.1107/S1600536811030649
PMCID: PMC3201258  PMID: 22058679
9.  Retraction of articles  
Retraction of 11 articles.
This article reports the retraction of 11 articles published in Acta Crystallographica Section E between 2005 and 2009.
doi:10.1107/S1600536810053882
PMCID: PMC3052007  PMID: 21522227
10.  Notes for authors 2011 
Notes for authors.
doi:10.1107/S1600536810045265
PMCID: PMC3050349
Notes for authors
11.  Retraction of articles 
Retraction of 39 articles.
This article reports the retraction of 39 articles published in Acta Crystallographica Section E between 2004 and 2009.
doi:10.1107/S1600536809054300
PMCID: PMC2983827  PMID: 21580459
12.  Notes for authors 2010 
Notes for authors.
doi:10.1107/S1600536809047825
PMCID: PMC2980098
Notes for authors
13.  Notes for authors 2009 
Notes for authors.
doi:10.1107/S1600536808035794
PMCID: PMC3009433
Notes for authors
14.  Notes for authors 2008 
Notes for authors.
doi:10.1107/S1600536807066421
PMCID: PMC2914877
Notes for authors
16.  Editorial 
doi:10.1107/S174430910601774X
PMCID: PMC2243099
Editorial
17.  Fragment approaches in structure-based drug discovery 
Journal of Synchrotron Radiation  2008;15(Pt 3):227-230.
Fragment-based methods are successfully generating novel and selective drug-like inhibitors of protein targets, with a number of groups reporting compounds entering clinical trials. This paper summarizes the key features of the approach as one of the tools in structure-guided drug discovery.
There has been considerable interest recently in what is known as ‘fragment-based lead discovery’. The novel feature of the approach is to begin with small low-affinity compounds. The main advantage is that a larger potential chemical diversity can be sampled with fewer compounds, which is particularly important for new target classes. The approach relies on careful design of the fragment library, a method that can detect binding of the fragment to the protein target, determination of the structure of the fragment bound to the target, and the conventional use of structural information to guide compound optimization. In this article the methods are reviewed, and experiences in fragment-based discovery of lead series of compounds against kinases such as PDK1 and ATPases such as Hsp90 are discussed. The examples illustrate some of the key benefits and issues of the approach and also provide anecdotal examples of the patterns seen in selectivity and the binding mode of fragments across different protein targets.
doi:10.1107/S090904950705666X
PMCID: PMC2394783  PMID: 18421145
18.  Current events 
Journal of Synchrotron Radiation  2008;15(Pt 3):319-321.
doi:10.1107/S0909049508009175
PMCID: PMC2394788  PMID: 18421169
19.  A degradation signal recognition in prokaryotes 
Journal of Synchrotron Radiation  2008;15(Pt 3):246-249.
Substrates tagged with ssrA are recognized and degraded by a subset of the Clp family, ATP-dependent proteases in prokaryotes. This paper describes the mechanism of intracellular breakdown of ssrA-tagged substrates by ClpXP and its adaptor protein, SspB.
The degradation of ssrA-tagged substrates in prokaryotes is conducted by a subset of ATP-dependent proteases, including ClpXP complex. More than 630 sequences of ssrA have been identified from 514 species, and are conserved in a wide range of prokaryotes. SspB protein markedly stimulates the degradation of these ssrA-tagged substrates by the ClpXP proteolytic machine. The dimeric SspB protein is composed of a compact ssrA-binding domain, which has a dimerization surface and a flexible C-terminal tail with a ClpX-binding motif at its very end. Since SspB is an adaptor protein for the ClpXP complex, designed mutagenesis, fluorescence spectroscopy, biochemistry and X-ray crystallography have been used to investigate the mechanism of delivery of ssrA-tagged proteins. In this paper the structural basis of ssrA-tag recognition by ClpX and SspB, as well as SspB-tail recognition by ZBD, is described.
doi:10.1107/S0909049507062826
PMCID: PMC2394798  PMID: 18421150
adaptor; ClpX; ClpXP complex; SspB; ssrA; zinc-binding domain
21.  GenOVa: a computer program to generate orientational variants 
Journal of Applied Crystallography  2007;40(Pt 6):1179-1182.
This computer program calculates the orientational variants, the operators and the composition table of a groupoid.
A computer program called GenOVa, written in Python, calculates the orientational variants, the operators (special types of misorientations between variants) and the composition table associated with a groupoid structure. The variants can be represented by three-dimensional shapes or by pole figures.
doi:10.1107/S0021889807048741
PMCID: PMC2483482  PMID: 19461844
variants; orientation; groupoids; pole figures; simulations; computer programs; GenOVa
22.  Parametric Rietveld refinement 
Journal of Applied Crystallography  2007;40(Pt 1):87-95.
The use of ‘parametric Rietveld refinement’ to extract information from large numbers of powder diffraction patterns using a single evolving structural model is described.
In this paper the method of parametric Rietveld refinement is described, in which an ensemble of diffraction data collected as a function of time, temperature, pressure or any other variable are fitted to a single evolving structural model. Parametric refinement offers a number of potential benefits over independent or sequential analysis. It can lead to higher precision of refined parameters, offers the possibility of applying physically realistic models during data analysis, allows the refinement of ‘non-crystallographic’ quantities such as temperature or rate constants directly from diffraction data, and can help avoid false minima.
doi:10.1107/S0021889806043275
PMCID: PMC2483475  PMID: 19461841
powder diffraction; non-ambient; Rietveld refinement

Results 1-22 (22)