NRG-CING is created using code in CING. Please visit the this
for more information on CING.
The NRG-CING website is a collection of CING reports that has been pre-calculated for all PDB files solved by NMR.
In case the underlying experimental data is available, these have been cleaned up and made syntactically and
semantically correct and homogeneous.
This webserver is described in:
NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB,
J.F. Doreleijers, W.F. Vranken, C. Schulte, J.L. Markley, E.L. Ulrich, G. Vriend, and
G. W. Vuister
For many macromolecular NMR ensembles from the Protein Data Bank (PDB) the experiment-based restraint lists used in the structure calculation are accessible, while other experimental data, mainly chemical shift values, are often available from the BioMagResBank. Assessment of the quality of the structural result is paramount to their usage and a combined, integrated repository of both input data and structural results greatly facilitates such an analysis. In addition, the accuracy and precision of the coordinates in these macromolecular NMR ensembles can be improved by recalculations using the available experimental data and present-day software with improved protocols and force fields. Such efforts, however, generally fail on over half of all deposited structures due to the syntactic and semantic heterogeneity of the data and the wide variety of formats used for their deposition. We have combined the cleaned-up restraints information from the NMR Restraints Grid (NRG) database with available chemical shifts from the BioMagResBank in the weekly updated NRG-CING database. Eleven programs, in addition to CING itself, have been included in the NRG-CING production pipeline to arrive at validation reports that list for each entry the potential inconsistencies between the coordinates and the available restraint and chemical shift data. The longitudinal validation of this data yielded a set of indicators that can be used to judge the quality of every macromolecular structure solved with NMR. The cleaned up NMR experimental datasets and the validation reports are freely available.
The NRG-CING reports are based on a series of programs that are be tabulated below.
|CING||CING (pronounced 'king') for Common Interface for NMR Structure Generation, that provides for a residue-based, integrated validation of the structural ensemble in conjunction with the experimental restraints and input data. The program is optimized for, but not limited to, NMR-derived bio-molecular structures. *Vuister, et al., CING; an integrated residue-based structure validation program suite, Manuscript in preparation||*|
|CCPN||The Collaborative Computing Project for the NMR community (CCPN) created a 'Data Model' that describes all the different types of information needed in an NMR structural study, from molecular structure and NMR parameters to coordinates.|
|DSSP||DSSP compiles an overview of the primary structure, including SS bonds, secondary structure, and solvent exposure.|
|MatPlotLib||matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell (ala MATLAB or Mathematica), web application servers, and six graphical user interface toolkits.|
|MOLMOL||MOLMOL is a program for display and analysis of macromolecular structures|
|PROCHECK-NMR/Aqua||The AQUA and PROCHECK-NMR programs provide a means of validating the geometry and restraint violations of an ensemble of protein structures solved by solution NMR.|
|Povray||The Persistence of Vision Raytracer is a high-quality, totally free tool for creating stunning three-dimensional graphics.|
|ShiftX||SHIFTX predicts protein 1H, 13C and 15N chemical shifts from X-ray or NMR coordinate data of previously assigned proteins.|
|Talos+||TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts.|
|VASCO||VASCO corrects and validates protein chemical shift values in relation to their 3D structure coordinates.|
|Wattos||Wattos is a collection of Java programs for structural biology and NMR spectroscopy. It's programs analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors world wide into the PDB and BMRB.|
|WHAT_CHECK||The protein verification tools from the WHAT IF program are available as this free stand-alone program.|
The NRG-CING integrates with many database resources. NRG-CING and the related databases are be tabulated below.
|NRG-CING||NRG-CING is a collection of CING reports that has been pre-calculated for all PDB files solved by NMR. * NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB, Doreleijers et al, NAR DB (Manuscript submitted).||Manuscript submitted|
|wwPDB||The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The members are RCSB PDB (USA), PDBe (Europe), PDBj (Japan), and BMRB (USA).|
|RCSB-PDB||The PDB by RCSB.|
|PDBe||The Protein Data Bank in Europe.|
|PDBj||The Protein Data Bank in Japan.|
|BMRB||The BioMagResBank is a repository for experimental and derived data gathered from NMR spectroscopic studies of biological molecules.|
|NRG||The NMR Restraints Grid contains the original, parsed, processed, and filtered NMR data.|
|STAP||The Statistical Torsional Angles Potentials of NMR Refinement Database. Yang et al, NAR DB (Manuscript accepted).||Manuscript accepted|
|RECOORD||RECOORD is a recalculated coordinate database of 500+ proteins.|
|DRESS||DRESS is a Database of 100 REfined Solution NMR Structures.|
|WHY_NOT||Explains why entries in other databases cannot exist.|
|PDB_REDO||Re-refined PDB files solved by X-ray crystallography|
NRG-CING is the result of many years of work of many people. These have been listed under Credits .