Numbat: an interactive software tool for fitting Delta chi-tensors to molecular coordinates using pseudocontact shifts

Schmitz, C., Stanton-Cook, M., Su, X.-C., Otting, G. and Huber, T.L. (2008) Numbat: an interactive software tool for fitting Delta chi-tensors to molecular coordinates using pseudocontact shifts. Journal of Biomolecular NMR, 41 3: 179-189. doi:10.1007/s10858-008-9249-z


Author Schmitz, C.
Stanton-Cook, M.
Su, X.-C.
Otting, G.
Huber, T.L.
Title Numbat: an interactive software tool for fitting Delta chi-tensors to molecular coordinates using pseudocontact shifts
Formatted title
Numbat: an interactive software tool for fitting ∆X tensors to molecular coordinates using pseudocontact shifts
Journal name Journal of Biomolecular NMR   Check publisher's open access policy
ISSN 0925-2738
Publication date 2008-07-01
Year available 2008
Sub-type Article (original research)
DOI 10.1007/s10858-008-9249-z
Open Access Status
Volume 41
Issue 3
Start page 179
End page 189
Total pages 11
Place of publication Dordrecht, The Netherlands
Publisher Springer
Language eng
Subject C1
030105 Instrumental Methods (excl. Immunological and Bioassay Methods)
970106 Expanding Knowledge in the Biological Sciences
Abstract Pseudocontact shift (PCS) effects induced by a paramagnetic lanthanide bound to a protein have become increasingly popular in NMR spectroscopy as they yield a complementary set of orientational and long-range structural restraints. PCS are a manifestation of the χ-tensor anisotropy, the Δχ-tensor, which in turn can be determined from the PCS. Once the Δχ-tensor has been determined, PCS become powerful long-range restraints for the study of protein structure and protein–ligand complexes. Here we present the newly developed package Numbat (New User-friendly Method Built for Automatic Δχ-Tensor determination). With a Graphical User Interface (GUI) that allows a high degree of interactivity, Numbat is specifically designed for the computation of the complete set of Δχ-tensor parameters (including shape, location and orientation with respect to the protein) from a set of experimentally measured PCS and the protein structure coordinates. Use of the program for Linux and Windows operating systems is illustrated by building a model of the complex between the E. coli DNA polymerase III subunits ε186 and θ using PCS.
Keyword paramagnetic NMR
Pseudo-contact Shift
magnetic susceptibility tensor
software
program
unique tensor representation
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Published online: 24 June 2008. -- Electronic supplementary material The online version of this article (doi:10.1007/s10858-008-9249-z) contains supplementary material, which is available to authorized users.

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2009 Higher Education Research Data Collection
School of Chemistry and Molecular Biosciences
 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 93 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 96 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Thu, 26 Feb 2009, 01:56:36 EST by Jennifer Falknau on behalf of School of Chemistry & Molecular Biosciences