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
3D-TROSY-based backbone and ILV-methyl resonance assignments of a 319-residue homodimer from a single protein sample
3D-TROSY-based backbone and ILV-methyl resonance assignments of a 319-residue homodimer from a single protein sample
Abstract The feasibility of practically complete backbone and ILV methyl chemical shift assignments from a single -labeled protein sample of the truncated form of ligand-free Bst-Tyrosyl tRNA Synthetase (Bst-Î?YRS), a 319-residue predominantly helical homodimer, is established. Protonation of ILV residues at methyl positions does not appreciably detract from the quality of TROSY triple resonance data. The assignments are performed at 40 °C to improve the sensitivity of...
nmrlearner
Journal club
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09-10-2012 01:48 AM
[Question from NMRWiki Q&A forum] Looking for hsqc-based ZZ exchange bruker pulse program
Looking for hsqc-based ZZ exchange bruker pulse program
hi nmrwikier !
Anyone know if the hsqc-based zz exchange pulse prog developed by Farrow et al. (1994) is available on standart bruker pulse prog library and what is its name ?
Many thanks !
nmrlearner
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CING: an integrated residue-based structure validation program suite
Linear Mode
