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benchmark.md

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Benchmark

The BinaryCIF format has been applied to encode macromolecular data stored using mmCIF data format (mmCIF is a schema of categories and fields that desribe a macromolecular structure stored using the CIF format). The raw data for the benchmark are included in this repository.

  • The "CoordinateServer" results were obtained using the corresponding query of the CoordinateServer.
  • The "MMTF" results were obtained using MMTF version 1.0.

HIV-1 Capsid size

Encoding the currenly largest structure in the PDB.org archive, the HIV-1 Capsid with 2.44M atoms, BinaryCIF achieves very good results.

3j3q size

Whole PDB archive size

  • (*) RCSB PDB: 122333 Entries, some 404'ed; recompressed using the same compression level as the other data.
  • (**) reduced = alpha + phosphate trace + HET

PDB Size

Read and write performance

This is the performance of BinaryCIF implementation of the CIFTools.js library, LiteMol, and the CoordinateServer.

Parse

Write