af3cli: Streamlining AlphaFold3 Input Preparation

With the release of AlphaFold3, modeling capabilities
have expanded
beyond protein structure prediction to embrace the inherent complexity
of biomolecular systems, including nucleic acids, ions, small molecules,
and their interactions. The increased complexity of these assemblies
is reflected in the input file generation process, presenting a significant
hurdle for researchers without advanced computational expertise. While
AlphaFold Server comes with a user-friendly graphical user interface,
it supports only a subset of the features of AlphaFold3. To address
this, we present af3cli, an open-source tool designed to facilitate
the generation of AlphaFold3 input files, specifically tailored to
the standalone version of AlphaFold3 and its unrestricted functionality.
Featuring a user-friendly command-line interface and an accompanying
Python library, af3cli simplifies the input generation process while
maintaining flexibility and customization, which makes af3cli especially
useful for fast (automated) generation of a large number of input
files since it enables direct incorporation of FASTA files, keeps
track of IDs, and validates the JSON file. Through practical examples,
we demonstrate its capabilities for constructing input data for diverse
biological structures, ranging from simple proteins to complex systems,
and demonstrate its seamless integration into both manual and automated
workflows.