[QuteMol] another molecular viewer

I learned a new molecular viewer called QuteMol. Like the name, it displays the molecules in a cute way. I like the way QuteMol simulates SEM-like structure. It’s good for a manual assembeled supramolecules (e.g. GroEL+GroES); you can display the PDB structure in a SEM-like picture.

So far, QuteMol supports platform includes MS-Win and Mac OS.

Here is my example using 1XQ8:

Or 2C7D, a GroEL+GroES complex.

[PyMOL] give your protein a box!

Here is a nice script to draw a minimu bounding box of your target PDB.
Author: Jason Vertrees

Example of 2GB1, using stereo view:

usage:
run PATH/drawMinBoundingBox.py
drawMinBoundingBox.py 2GB1, 3, r=0.3, g=0.3, b=0.3
======
drawMinBoundingBox [selection, [lineWidth, [redColor, [greenColor, [blueColor]]]]]

Download this script at pymolwiki.

[IDP] Cytoplasmic Domain of the T Cell Receptor zeta

Title:  The Intrinsically Disordered Cytoplasmic Domain of the T Cell Receptor ζ Chain Binds to the Nef Protein of Simian Immunodeficiency Virus without a Disorder-to-Order Transition

Authors: Alexander B. Sigalov, Walter M. Kim, Maria Saline and Lawrence J. Stern

Journal: Biochemistry, 2008, 47 (49), pp 12942–12944

Not fully labeled in HSQC

[IDP] RTX calcium-binding motifs

Title:RTX calcium-binding motifs are intrinsically disordered in the absence of calcium: Implication for protein secretion

Authors: Alexandre Chenal, J. Iñaki Guijarro, Bertrand Raynal, Muriel Delepierre, and Daniel Ladant

Journal: J. Biol. Chem, 10.1074/jbc.M807312200 (online publish first)

Note: Not an NMR-based study.

[IDP] Human Securin

Title:Structural and Dynamic Characterization of Intrinsically Disordered Human Securin by NMR Spectroscopy

Authors: Veronika Csizmok, Isabella C. Felli, Peter Tompa, Lucia Banci and Ivano Bertin

Journal: J. Am. Chem. Soc., 2008, 130 (50), pp 16873–16879

Assignment table is provided within the supplementary file.

[IDP]The Intrinsically Disordered RNR Inhibitor Sml1 Is a Dynamic Dimer

Title:The Intrinsically Disordered RNR Inhibitor Sml1 Is a Dynamic Dimer

Biochemistry, 2008, 47 (50), pp 13428–13437

NO HSQC spectrum available.
NO BMRB code provided.

The Ramachandran Plot Explorer

Here is a good molecular viewer which instantly displays the phi/psi/chi angles of the residues you select and display the ramachandran space in the plot. The Ramachandran plot can be magnified easily. To me, it’s a very nice program because I don’t need to open PyMOL or MOLMOL to run scripts getting the angles.

The official site is “here“, written by Bosco Ho.

[IDP]A Disease State Mutation Unfolds the Parkin Ubiquitin-like Domain

Title: A Disease State Mutation Unfolds the Parkin Ubiquitin-like Domain
Journal: Biochemistry. 2007 Dec 11;46(49):14162-9. Epub 2007 Nov 16.
Authors:Safadi SS, Shaw GS.

HSQC spectra:

[IDP] Human C/EBP Homologous Protein

Title: Intrinsically Disordered Human C/EBP Homologous Protein Regulates Biological Activity of Colon Cancer Cells during Calcium Stress

Authors: Vinay K. Singh, Ivan Pacheco, Vladimir N. Uversky, Steven P. Smith, R. John MacLeod, Zongchao Jia

Journal: Journal of Molecular Biology, Volume 380, Issue 2, 4 July 2008, Pages 313-326

[IDP] tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain

Title: Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain

Authors: 1. Mark Wells, 2. Henning Tidow, 3. Trevor J. Rutherford, 4. Phineus Markwick, 5. Malene Ringkjobing Jensen, 6. Efstratios Mylonas, 7. Dmitri I. Svergun, 8. Martin Blackledge, and 9. Alan R. Fersht

Journal: PNAS April 15, 2008 vol. 105 no. 15 5762-5767

p53 NTD