Interactive visualization tools for the structural biologist

We have developed two software plugins for the Mac OSX operating system that allow rapid and convenient visualization of PDB files and X-ray diffraction images directly within the file browser, without the need of full-featured applications.  We have just published a paper describing this work:

Porebski BT, Ho BK, Buckle AM. (2013) Interactive visualization tools for the structural biologist. J. Appl. Cryst. (2013). 46, 1518-1520.

Project page and download

Shown below are views of a folder containing PDB files. Shown on the right is a Finder window of a folder containing PDB files with the PyMol rendered cartoon thumbnail. On the left is a QuickLook popup of the same PDB file using the Jolecule viewer.

New papers published

Yersinia enterocolitica Provides the Link between Thyroid-Stimulating Antibodies and Their Germline Counterparts in Graves’ Disease.

Hargreaves CE, Grasso M, Hampe CS, Stenkova A, Atkinson S, Joshua GW, Wren BW, Buckle AM, Dunn-Walters D, Banga JP.

Molecular determinants of the substrate specificity of the complement initiating protease, C1r.

Wijeyewickrema LC, Yongqing T, Tran TP, Thompson PE, Viljoen JE, Coetzer TH, Duncan RC, Kass I, Buckle AM, Pike RN.

J Biol Chem. 2013 Apr 15. [Epub ahead of print]

Mechanism-based selection of a potent kallikrein-related peptidase 7 inhibitor from a versatile library based on the sunflower trypsin inhibitor SFTI-1.

de Veer SJ, Ukolova SS, Munro CA, Swedberg JE, Buckle AM, Harris JM.

Biopolymers. 2013 Mar 11. doi: 10.1002/peps.22231. [Epub ahead of print]

Structural characterization of the mechanism through which human glutamic acid decarboxylase auto-activates.

Langendorf CG, Tuck KL, Key TL, Fenalti G, Pike RN, Rosado CJ, Wong AS, Buckle AM, Law RH, Whisstock JC.

Biosci Rep. 2013 Jan 11;33(1):137-44. doi: 10.1042/BSR20120111.

2 New Papers

The Rate of PolyQ-Mediated Aggregation Is Dramatically Affected by the Number and Location of Surrounding Domains

Amy L. Robertson, Mark A. Bate, Ashley M. Buckle, Stephen P. Bottomley

J Mol Biol. 2011 Nov 4;413(4):879-87. Epub 2011 Sep 16.

Computational methods for studying serpin conformational change and structural plasticity.

Kass I, Reboul CF, Buckle AM.

Methods Enzymol. 2011;501:295-323.

New Paper Published!

PolyQ: a database describing the sequence and domain context of polyglutamine repeats in proteins

Amy L. Robertson, Mark A. Bate, Steve G. Androulakis, Stephen P. Bottomley, and Ashley M. Buckle

Nucl. Acids Res. (2010) doi: 10.1093/nar/gkq1100
First published online: November 8, 2010
This article is Open Access

Download the PDF

The polyglutamine diseases are caused in part by a gain-of-function mechanism of neuronal toxicity involving protein conformational changes that result in the formation and deposition of β-sheet rich aggregates. Recent evidence suggests that the misfolding mechanism is context-dependent, and that properties of the host protein, including the domain architecture and location of the repeat tract, can modulate aggregation. In order to allow the bioinformatic investigation of the context of polyglutamines, we have constructed a database, PolyQ.   We have collected the sequences of all human proteins containing runs of seven or more glutamine residues and annotated their sequences with domain information. PolyQ can be interrogated such that the sequence context of polyglutamine repeats in disease and non-disease associated proteins can be investigated.

TARDIS article on P212121

The crystallography blog P212121 have posted an article on TARDIS  entitled “TARDIS for the Storage of X-ray Diffraction Images“.

This comes as a follow-up to their recent poll “Do we need an X-ray Diffraction Image Data Bank?“.

The poll is still open, but currently 81% of P212121 readers are voting for that the crystallography community does need an open, freely available diffraction image data bank.

Be sure to head over to P212121 and have your say.