Extend-NMR: Extending NMR for Functional and Structural Genomics
Partner 4:Radboud University Nijmegen
People involved:Geerten W. Vuister, Jurgen Doreleijers & Gert Vriend

CING: Program Suite for Structure Validation

We have developed an open-source program suite called CING (pronounced king) for Common Interface for NMR structure Generation. Color-coding (ROG for red, orange, and green) and hyperlinking provide a friendly residue-based web interface to run and analyze the results and reports generated by programs such as WHAT IF, QUEEN, PROCHECK_NMR/Aqua, SHIFTX, Wattos, and DSSP. CING combines all these data and integrates this with its own routines to generate a comprehensive analysis of the NMR-derived structure ensemble in relation to its experimental data.

Using CING, we are now able to univocally identify a wrong monomer (PDB entry 1TGQ) that has since been replaced by a dimer interpretation of the experimental data. The iCing multi-lingual web-server allows individual NMR spectroscopists to upload their own NMR data and structural ensembles for verification with the CING program suite.

CING is a python-based suite with GWT java for the iCing web server. CING also provides for an API that allows easy access to the NMR data, structure ensemble and validation results. This API allows for straightforward implementation of new ideas using only a minimal coding effort. The program forms also a part of an integrated NMR structure determination pipeline developed in a collaborative, EU-funded Extend-NMR research effort.

CING Features

  • Residue-oriented, integrated analysis of data and results.
  • User-friendly, color-coded, hyperlinked html output.
  • Multi-lingual webserver.
  • CCPN integrated.
  • Scriptable.
  • API to data, structure and validation results.
  • Automated exports to multiple formats.

Main web page generated by a CING analysis
The multi-lingual iCing Server in Chinese, Deutsch, English, Nederlands & Portugues

Ribbon diagrams of the PDB entries 1Y4O and 1TGQ color coded red, orange, and green based on the outcome of the CING analysis. CING successfully identifies the incorrect 1TGQ monomer, that has since been replaced by the 1Y4O dimer interpretation of the experimental data.