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Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source

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ModelArchive: A Deposition Database for Computational Macromolecular Structural Models.

Gerardo Tauriello¹, Andrew M Waterhouse¹, Juergen Haas¹

¹Biozentrum, University of Basel, Basel, Switzerland; Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland.

Journal of Molecular Biology

|February 13, 2025

Summary

This summary is machine-generated.

ModelArchive is a public database for over 600,000 computational macromolecular structures, enhancing life science research. It complements experimental databases by providing reproducible and reusable 3D structural models.

Keywords:

FAIR databases ModelArchive ModelCIF macromolecular structure prediction structural biology

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Area of Science:

Structural Biology
Bioinformatics
Computational Biology

Background:

Three-dimensional structures of biological macromolecules are crucial for understanding molecular function in life science research.
Advances in computational techniques enable the generation of high-quality protein structural models.
Existing databases like the Protein Data Bank (PDB) primarily focus on experimentally derived structures.

Purpose of the Study:

To introduce ModelArchive, a deposition database for computational macromolecular models.
To complement existing structural databases by archiving predicted models.
To facilitate the accessibility, reproducibility, and reuse of computational structural models.

Main Methods:

Collection and deposition of over 600,000 computational models from researchers.
Support for diverse biological entities including macromolecules, complexes, polymers, and small molecules.
Utilization of the ModelCIF format for storing coordinates and metadata, enabling validation and interoperability.

Main Results:

ModelArchive hosts a large collection of computational structural models, significantly expanding structural biology resources.
Deposited models are assigned immutable accession codes for citation.
Models include metadata on the modeling process and accuracy, promoting reproducibility.

Conclusions:

ModelArchive serves as a vital resource for computational structural models, supporting life science research.
The database enhances scientific reproducibility and model reuse through standardized formats and metadata.
ModelArchive improves model findability via its web service and external data integrations.