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Title

 

 

 

 

 

CARON Average RMSD of NMR structure ensembles

Authors

 

Kresimir Sikic1,2, Oliviero Carugo1,3

Affiliation

 

1Departement of Structural and Computational Biology, Max F. Perutz Laboratories, Vienna University, 1030 Vienna, Austria; 2Faculty of Electrical Engineering and Computing, University of Zagreb, 10000 Zagreb, Croatia; 3Departement of General Chemistry, University of Pavia, I-27100 Pavia, Italy

 

Email

 

kresimir.sikic@univie.ac.at

Article Type

 

Web Server

Date

 

Received May 13, 2009; Accepted June 15, 2009; Published September 30, 2009

Abstract

The NMR protein structures are often deposited in the Protein Data Bank as ensembles of models that agree with the experimental restraints. Information about stereochemical variability and the molecular flexibility can be obtained by systematic comparison of all models. Here we describe CARON, a software that allows the computation of the root-mean-square-distances between equivalent atoms and residues in all models and introduces these values into the occupancy and the B-factor fields of PDB-formatted files. This tool allows the user to both get a quantitative estimation of the conformational homogeneity of the models and to exploit this information in common computer graphics programs.

 

Keywords

CARON, Bioinformatics software, conformational homogeneity, superposition, Root-Mean-Square Deviation, Protein Data Bank, NMR spectroscopy.

 

Citation

 

Sikic & Carugo, Bioinformation 4(3): 132-133 (2009)

Edited by

 

P. Kangueane

 

ISSN

 

0973-2063

 

Publisher

 

Biomedical Informatics

License

 

 

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.