BeEM: fast and faithful conversion of mmCIF format structure files to PDB format

Abstract

AbstractAlthough mmCIF is the current official format for deposition of protein and nucleic acid structures to the Protein Data Bank (PDB) database, the legacy PDB format is still the primary supported format for many structural bioinformatics tools. Therefore, reliable software to convert mmCIF structure files to PDB files is needed. Unfortunately, existing conversion programs fail to correctly convert many mmCIF files, especially those with many atoms and/or long chain identifies. This study proposed BeEM, which converts any mmCIF format structure files to PDB format. BeEM conversion faithfully retains all atomic and chain information, including chain IDs with more than 2 characters, which are not supported by any existing mmCIF to PDB converters. The conversion speed of BeEM is at least ten times faster than existing converters such as MAXIT and Phenix. BeEM is available under the BSD licence athttps://github.com/kad-ecoli/BeEM/.