logRECOORD ensembles

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Database of structure ensembles recalculated with log-harmonic potential (logRECOORD)

logRECOORD is a database that contains recalculated structure ensembles for 300+ protein entries from the Protein Data Bank (PDB). Instead of usual distance constraints, a log-harmonic potential function was applied for NOE interpretation. Use the search field below to access individual entries.


Enter a PDB code: GO Example


Three approaches for structure calculation were using to generaqte the klogRECOORD database:

  • FBHW: Standard approach, which uses "flat-bottom harmonic-wall" potential for applying the restraints.
  • LogCstW: Applying log-harmonic potential with constant weighting of the restraints.
  • LogBayW: Applying log-harmonic potential with Bayesian weighting of the restraints.

You can ftp all logRECOORD files here (size 3.4GB).


References

  • A. Bernard, W.F. Vranken, B. Bardiaux, M. Nilges and T.E. Malliavin. Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures. Proteins (2011) 79:1525-1537. DOI: 10.1002/prot.22980
  • W. Rieping, M. Habeck and M. Nilges. Modeling errors in NOE data with a log-normal distribution improves the quality of NMR structures. J. Am. Chem. Soc. (2005) 127:16026-16027. DOI: 10.1021/ja055092c