Nucleic Acids Research Advance Access originally published online on April 22, 2007
Nucleic Acids Research 2007 35(Web Server issue):W375-W383; doi:10.1093/nar/gkm216
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W375-W383
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
1Department of Biochemistry, Duke University, Durham, NC, USA and 2Department of Computer Science, UNC Chapel Hill, Chapel Hill, NC, USA
*To whom correspondence should be addressed. Tel: +1-919-684-6010; Email: dcr{at}kinemage.biochem.duke.edu
Received January 26, 2007. Revised March 20, 2007. Accepted March 28, 2007.
MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu.
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J. D. Richards, K. A. Johnson, H. Liu, A.-M. McRobbie, S. McMahon, M. Oke, L. Carter, J. H. Naismith, and M. F. White Structure of the DNA Repair Helicase Hel308 Reveals DNA Binding and Autoinhibitory Domains J. Biol. Chem., February 22, 2008; 283(8): 5118 - 5126. [Abstract] [Full Text] [PDF]
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E. Severi, A. Muller, J. R. Potts, A. Leech, D. Williamson, K. S. Wilson, and G. H. Thomas Sialic Acid Mutarotation Is Catalyzed by the Escherichia coli {beta}-Propeller Protein YjhT J. Biol. Chem., February 22, 2008; 283(8): 4841 - 4849. [Abstract] [Full Text] [PDF]
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N. Mallorqui-Fernandez, S. P. Manandhar, G. Mallorqui-Fernandez, I. Uson, K. Wawrzonek, T. Kantyka, M. Sola, I. B. Thogersen, J. J. Enghild, J. Potempa, et al. A New Autocatalytic Activation Mechanism for Cysteine Proteases Revealed by Prevotella intermedia Interpain A J. Biol. Chem., February 1, 2008; 283(5): 2871 - 2882. [Abstract] [Full Text] [PDF]
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A. W. Barb, L. Jiang, C. R. H. Raetz, and P. Zhou Structure of the deacetylase LpxC bound to the antibiotic CHIR-090: Time-dependent inhibition and specificity in ligand binding PNAS, November 20, 2007; 104(47): 18433 - 18438. [Abstract] [Full Text] [PDF]
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