CING: an integrated residue-based structure validation program suite
 

CING: an integrated residue-based structure validation program suite


Abstract We present a suite of programs, named CING for Common Interface for NMR Structure Generation that provides for a residue-based, integrated validation of the structural NMR ensemble in conjunction with the experimental restraints and other input data. External validation programs and new internal validation routines compare the NMR-derived models with empirical data, measured chemical shifts, distance- and dihedral restraints and the results are visualized in a dynamic Web 2.0 report. A redâ??orangeâ??green score is used for residues and restraints to direct the user to those critiques that warrant further investigation. Overall green scores below ~20 % accompanied by red scores over ~50 % are strongly indicative of poorly modelled structures. The publically accessible, secure iCing webserver (https://nmr.le.ac.uk) allows individual users to upload the NMR data and run a CING validation analysis.

• Content Type Journal Article
• Category Article
• Pages 1-17
• DOI 10.1007/s10858-012-9669-7
• Authors
  • Jurgen F. Doreleijers, CMBI, Radboud University Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands
  • Alan W. Sousa da Silva, UniProt, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD UK
  • Elmar Krieger, YASARA Biosciences GmbH, Wagramer Strasse 25/3/45, 1220 Vienna, Austria
  • Sander B. Nabuurs, CMBI, Radboud University Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands
  • Christian A. E. M. Spronk, Spronk NMR Consultancy UAB, Palangos gatvÄ? 4, 01402 Vilnius, Lithuania
  • Tim J. Stevens, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA UK
  • Wim F. Vranken, Department of Structural Biology, VIB, Building E, 4th Floor, Pleinlaan 2, 1050 Brussels, Belgium
  • Gert Vriend, CMBI, Radboud University Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands
  • Geerten W. Vuister, Department of Biochemistry, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 9HN UK

• • Journal Journal of Biomolecular NMR
  • Online ISSN 1573-5001
  • Print ISSN 0925-2738

Source: Journal of Biomolecular NMR