RECOORD ensembles

pdbe.org/nmr

Database of recalculated structure ensembles (RECOORD)

RECOORD is a database that contains recalculated structures for 500+ protein entries from the Protein Data Bank (PDB). Use the search box below to access RECOORD reports by PDB code.

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).


You can also download the scripts used for the recalculation and ftp all files directly as CCPN projects (size 2GB) or coordinate files in CNS format (size 1.6GB).

Reference

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