Molecular File Converter
Convert between chemical file formats with our web-based tool
Was this tool helpful?
AlphaFold structure predictions are commonly distributed in mmCIF format, which can store rich structural and metadata information, including per-residue confidence scores. Despite these advantages, many molecular visualization, modeling, and simulation tools still rely on the traditional Protein Data Bank (PDB) format as their primary or exclusive input format. For a detailed explanation of the structural and practical differences between these formats, see our in-depth guide on CIF vs mmCIF and CIF vs PDB.
The AlphaFold CIF to PDB Converter enables researchers to convert AlphaFold-generated CIF files to the standard PDB format while preserving essential structural features, including atomic coordinates, chain identifiers, residue numbering, and prediction confidence values.
How to Use This Tool
- Select CIF / mmCIF as the input format and PDB as the output format.
- Upload your AlphaFold CIF file or paste the file content directly into the input field.
- Click Convert File to start the conversion process.
- Download the generated PDB file and use it in your preferred molecular analysis software or online viewers such as the ScienceCodons PDB Viewer for quick 3D inspection.
About AlphaFold
AlphaFold is a deep learning system developed by DeepMind to predict protein three-dimensional structures from amino acid sequences. The original AlphaFold proved the feasibility of AI-driven structure prediction, while AlphaFold2 achieved near-experimental accuracy for many proteins and set a new standard in structural bioinformatics. Later versions, such as AlphaFold-Multimer, expanded the approach to protein–protein complexes and multi-chain assemblies. Community-driven projects like ColabFold improved accessibility and computational efficiency, allowing more researchers to generate high-quality structure predictions. AlphaFold models include per-residue confidence scores (pLDDT), which are used to assess prediction reliability and are typically stored in mmCIF files.
How the Conversion Works
The conversion engine operates by systematically reading the structural definitions stored in the mmCIF file and translating them into the fixed-column syntax required by the PDB format. During this process, atomic coordinates, element symbols, residue names, and connectivity information are interpreted according to established macromolecular structure standards to ensure consistency and correctness in the resulting file.
Since mmCIF is more flexible than PDB, the conversion applies normalization rules to fit PDB constraints. These include standardized atom naming, adjusting coordinate precision, and managing chain identifiers and residue numbering. If AlphaFold confidence scores (pLDDT) are present, they are mapped to the B-factor column so downstream tools can visualize structural confidence using standard color schemes.
The conversion process is deterministic and format-focused; it does not perform structural optimization, energy minimization, or coordinate modification. The output PDB file is a direct translation of the input CIF file, formatted for compatibility with common molecular visualization and analysis software.
Key Features
- Converts AlphaFold mmCIF / CIF files to standard PDB format
- Preserves atomic coordinates and residue connectivity
- Retains chain identifiers and residue numbering where possible
- Maps AlphaFold pLDDT confidence scores to the PDB B-factor column
- Supports drag-and-drop upload as well as direct content pasting
- Designed for fast, browser-based conversion with no installation required
FAQ
Meet the Authors
Mahdi Morshedi Yekta
Founder & Bioinformatics Developer
Mahdi is the founder of ScienceCodons and a Medical Biotechnologist with a deep passion for computational biology. Holding an M.Sc. in Medical Biotechnology, he specializes in transforming complex biological algorithms into accessible, high-performance web tools, bridging the gap between laboratory sciences and software engineering.
Fatemeh Faryadras
Medical Biotechnologist & Researcher
Fatemeh is a Medical Biotechnologist and researcher. With extensive expertise in genetic engineering, molecular cloning, and cancer biology, she combines her rigorous laboratory background with intuitive design principles to create reliable, user-centered scientific calculators and tools.
Dr. Mosayeb Rostamian
Assistant Professor, Infectious Diseases Research Center
Certified Scientific Reviewer
Google ScholarExpert Review Process
To ensure the highest quality and scientific accuracy, this tool's underlying algorithms, formulas, and edge-case handling have been thoroughly reviewed and validated by Dr. Mosayeb Rostamian.
The "Reviewed By" badge signifies that an independent expert has evaluated the tool's logic to guarantee accuracy and alignment with the current consensus in the scientific community.