SCOPe Funding Alert: SCOPe support from the NIH ended in April 2016. John-Marc Chandonia is the primary maintainer and has continued to develop SCOPe using vacation time. Three proposals to the NIH for continued funding have been unsuccessful. If our current NIH proposal is not funded, SCOPe will shut down permanently in Summer 2017 as Dr. Chandonia will need to seek a new position.

Summary PDB ASTRAL Check Index (SPACI)

The Summary PDB ASTRAL Check Index (SPACI) provides a numeric score that provides some insight into the reliability and precision of a crystallographically-determined structure in a PDB file. The SPACI score includes three components: the quality of the experimental data (the resolution), how well the model fits the collected data (the R-factor), and the theoretical quality of the model (stereochemical checks from PROCHECK and WHAT_CHECK).

The SPACI scores are intended approximate the reciprocal of the resolution, which is the dominant component of the index, with adjustments for the model quality. Consequently, structures with SPACI scores greater than 0.4 are generally quite good.

As of version 1.57, structural representatives are now selected according to Aberrant Entry Re-Ordered (AERO) SPACI scores, which are SPACI scores scores with penalties for aberrant structures. In this release, aberrant structures were identified using human-curated comments in SCOPe regarding each PDB chain. PDB chains with comments including one or more of the following keywords were penalized by lowering their AEROSPACI score by 2.0:

  chimer circular disorder error incorrect interrupted
  misfolded missing mistraced mutant permut truncat

Also, theoretical structures (which are not present in SCOPe or Astral domains, but still assigned SPACI and AEROSPACI scores) receive an additional 5.0 penalty to their AEROSPACI score.

Warning! The SPACI scores are valid only for atomic resolution crystallographically determined molecular structures where both PROCHECK and WHAT_CHECK were able to provide valid reports. When these reports were not available, the SPACI score assumes the worst. For non-crystallographic structures, lack of information about how to evaluate the structure means that poor scores are assigned. We hope that as the NMR community grows and BioMagResBank is more fully used, it will be possible to assign more meaningful scores to these structures in the future. Moreover, even for crystallographic structures, the SPACI score is only one heuristic for the quality of a structure. It is no substitute for a detailed knowledge of the experiment that was performed and the complexity of the model.

Get SPACI and AEROSPACI scores for PDB Entry (e.g., 2cro)

Note: files containing all SPACI and AEROSPACI scores are available upon request.