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af3cli: Streamlining AlphaFold3 Input Preparation.

Philipp Döpner¹, Stefan Kemnitz², Mark Doerr³

¹Department of Medicinal and Pharmaceutical Chemistry, Institute of Pharmacy, University of Greifswald, Friedrich-Ludwig-Jahn-Straße 17, 17489 Greifswald, Germany.

Journal of Chemical Information and Modeling

|April 9, 2025

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Researchers can now easily generate complex biomolecular modeling input files for AlphaFold3 using af3cli. This open-source tool simplifies the process, enabling broader access to advanced computational biology features.

Area of Science:

Computational Biology
Structural Biology
Bioinformatics

Background:

AlphaFold3 expands biomolecular modeling beyond proteins to include nucleic acids, ions, and small molecules.
Generating input files for complex AlphaFold3 assemblies is challenging for researchers lacking computational expertise.
The AlphaFold Server GUI offers limited functionality compared to the standalone AlphaFold3.

Purpose of the Study:

To introduce af3cli, an open-source command-line tool for simplifying AlphaFold3 input file generation.
To provide a user-friendly yet flexible solution for researchers using the standalone AlphaFold3.
To facilitate the creation of input data for diverse and complex biomolecular systems.

Main Methods:

Developed af3cli, a command-line interface and Python library.

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Implemented features for direct FASTA file incorporation, ID tracking, and JSON validation.

Demonstrated af3cli's utility through practical examples with various biological structures.

Main Results:

af3cli successfully simplifies the generation of AlphaFold3 input files.
The tool supports diverse biological structures, from simple proteins to complex assemblies.
af3cli integrates seamlessly into both manual and automated research workflows.

Conclusions:

af3cli enhances accessibility to AlphaFold3's full capabilities for biomolecular modeling.
The tool is valuable for researchers needing to generate numerous input files efficiently.
af3cli empowers a wider range of scientists to perform advanced structural biology analyses.