Efficient protein structure archiving using ProteStAr.

ABSTRACT:

Motivation

The introduction of Deep Minds' Alpha Fold 2 enabled the prediction of protein structures at an unprecedented scale. AlphaFold Protein Structure Database and ESM Metagenomic Atlas contain hundreds of millions of structures stored in CIF and/or PDB formats. When compressed with a general-purpose utility like gzip, this translates to tens of terabytes of data, which hinders the effective use of predicted structures in large-scale analyses.

Results

Here, we present ProteStAr, a compressor dedicated to CIF/PDB, as well as supplementary PAE files. Its main contribution is a novel approach to predicting atom coordinates on the basis of the previously analyzed atoms. This allows efficient encoding of the coordinates, the largest component of the protein structure files.

SUBMITTER: Deorowicz S 

PROVIDER: S-EPMC11239224 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature