ArticleBMC bioinformatics2023
BeEM: fast and faithful conversion of mmCIF format structure files to PDB format.
Article in BMC bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed.
- A structure-guided approach to noncoding variant evaluation for transcription factor binding using AlphaFold 3.Nucleic acids research · 2026Article
- LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank.Genomics, proteomics & bioinformatics · 2025Article
- FURNA: A database for functional annotations of RNA structures.PLoS biology · 2024Article
- BioLiP2: an updated structure database for biologically relevant ligand-protein interactions.Nucleic acids research · 2024Article
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1 author.
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Abstract
backgroundAlthough 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.
resultsThis 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. Part of the reason for the speed improvement is the avoidance of conversion between numerical values and text strings.
conclusionBeEM is a fast and accurate tool for mmCIF-to-PDB format conversion, which is a common procedure in structural biology. The source code is available under the BSD licence at https://github.com/kad-ecoli/BeEM/ .
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