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MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures
Anthony R Bradley1,2, Alexander S Rose1, Antonín Pavelka1
1Structural Bioinformatics Laboratory, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, United States of America.
Plos Computational Biology
|June 3, 2017
Summary
A new MacroMolecular Transmission Format (MMTF) offers faster macromolecular structure analysis. This compressed binary format significantly reduces file size and parsing time, improving structural bioinformatics workflows.
Area of Science:
- Structural Biology
- Computational Biology
- Biophysics
Background:
- Macromolecular structure data, particularly from the Protein Data Bank (PDB), is rapidly increasing in size and complexity.
- Existing file formats like PDBx/mmCIF present challenges in transfer speed, parsing efficiency, and integration with third-party software for visualization and analysis.
Purpose of the Study:
- To introduce a novel data representation, the MacroMolecular Transmission Format (MMTF), designed to overcome the limitations of current macromolecular structure file formats.
- To present software implementations supporting MMTF across multiple programming languages.
- To demonstrate the performance benefits of MMTF in terms of file size and parsing speed.
Main Methods:
- Development of a new binary and compressed data representation (MMTF).
- Creation of software APIs for MMTF.
- Comparative analysis of MMTF against PDBx/mmCIF for file size and parsing performance.
Main Results:
- MMTF files are approximately one-quarter the size of PDBx/mmCIF files.
- MMTF parsing is several times faster than PDBx/mmCIF parsing.
- Enables visualization of large macromolecular structures (millions of atoms) in web browsers and efficient processing of the entire PDB archive.
Conclusions:
- MMTF provides a significantly more efficient data representation for macromolecular structures.
- This advancement facilitates improved visualization, analysis, and algorithm development in structural bioinformatics.
- The PDB archive is now available in MMTF format, enabling enhanced accessibility and usability.
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