ModelArchive: A Deposition Database for Computational Macromolecular Structural Models

Abstract

A wide range of applications in life science research benefit from the availability of three-dimensional structures of biological macromolecules as they provide valuable insights into their molecular function. Recent advances in structure prediction techniques have made it possible to generate high quality computational macromolecular structural models for almost all known proteins.

In this context, ModelArchive (https://modelarchive.org/) serves as a deposition database for computational models, complementing the Protein Data Bank (PDB) and PDB-IHM, which require experimental data, and specialised databases such as the AlphaFold DB. ModelArchive contains over 600,000 models contributed by researchers using a variety of modelling techniques. It supports single biological macromolecules and complexes, including any combination of polymers and small molecules. Each deposited model can be referenced in manuscripts using an immutable accession code provided by ModelArchive. Depositors are required to provide a minimal set of information about the modelling process and the expected accuracy of the resulting model, enabling scientific reproducibility and maximising the potential reuse of the models. The vast majority of models in ModelArchive use the ModelCIF format which includes coordinates and metadata, allows for programmatic validation of the models, and makes the models interoperable with structures obtained from other sources such as the PDB. The ModelArchive web service provides access to the models and search queries. Model findability is also provided in external services either through APIs or by importing data from ModelArchive.