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Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters

Nucleic Acids Research
Oxford University Press
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gkm216 375..383 Nucleic Acids Research, 2007, Vol. 35, Web Server issue W375–W383 doi:10.1093/nar/gkm216 MolProbity: all-atom contacts and structure validation for proteins and nucleic acids Ian W. Davis1, Andrew Leaver-Fay2, Vincent B. Chen1, Jeremy N. Block1, Gary J. Kapral1, Xueyi Wang2, Laura W. Murray1, W. Bryan Arendall III1, Jack Snoeyink2, Jane S. Richardson1 and David C. Richardson1,* 1Department of Biochemistry, Duke University, Durham, NC, USA and 2Department of Computer Science, UNC Chapel Hill, Chapel Hill, NC, USA Received January 26, 2007; Revised March 20, 2007; Accepted March 28, 2007 ABSTRACT 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 INTRODUCTION The atomic models of proteins and nucleic acids that come from X-ray crystallography and NMR are our most accurate sources of 3D information about these molecules, far more reliable than computed structures from modeling or simulation. They are best when determined at high resolution or with many re

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