Bringing Structure to Biology
Recalculated NMR data
RECOORD is a database that contains recalculated structures for 500+ protein entries from the Protein Data Bank (PDB).
For each entry, the originally deposited restraints were remediated, converted to a standardised form and filtered for redundancies. They are currently available from the NMR Restraints Grid (NRG), hosted by the Biological Magnetic Resonance Bank (BMRB). CCPN FormatConverter was used for import and export of data into CYANA and CNS formats. Next, four new structure ensembles were generated as follows, in addition to the originally deposited one:
|Label||Structure generation software|
|CNS||CNS without refinement|
|CNW||CNS followed by CNS refinement in aqueous environment|
|CYA||CYANA without refinement|
|CYW||CYANA followed by CNS refinement in aqueous environment|
Finally, quality scores were calculated for all five ensembles (four recalculated and the originally deposited).
A.J. Nederveen, J.F. Doreleijers, W.F. Vranken, Z. Miller, C.A.E.M. Spronk, S.B. Nabuurs, P. Güntert, M. Livny, J.L. Markley, M. Nilges, E.L. Ulrich, R. Kaptein and A.M.J.J. Bonvin. RECOORD: a REcalculated COORdinates Database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins (2005) 59:662-672. DOI: 10.1002/prot.20408
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.
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).
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