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Title
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CARON – Average RMSD of NMR structure ensembles |
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Authors
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Kresimir Sikic1,2, Oliviero Carugo1,3 | |
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Affiliation
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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
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Article Type
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Web Server | |
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Date
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Received May 13, 2009; Accepted June 15, 2009; Published September 30, 2009 | |
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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.
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CARON, Bioinformatics software, conformational homogeneity, superposition, Root-Mean-Square Deviation, Protein Data Bank, NMR spectroscopy.
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Citation
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Sikic & Carugo, Bioinformation 4(3): 132-133 (2009) | |
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Edited by
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P. Kangueane
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ISSN
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0973-2063
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Publisher
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Biomedical Informatics | |
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License
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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. |