RCSB Python In Silico Model Access Utilities
Introduction
This module contains utility methods for accessing in silico 3D models and metadata from external data resources, including AlphaFold, ModBase, SWISS-MODEL, and Model Archive.
Installation
Download the library source software from the project repository:
git clone --recurse-submodules https://github.com/rcsb/py-rcsb_utils_insilico3d.git
Important: Setup will require an up-to-date version of cmake to be installed on the machine and the executable to be in the system's PATH.
Optionally, run test suite (Python versions 3.9) using tox:
tox
Installation is via the program pip.
pip install rcsb.utils.insilico3d
or for the local repository:
pip install .
References
- AlphaFold
- Jumper, J et al. Highly accurate protein structure prediction with AlphaFold. Nature (2021)
- Varadi, M et al. AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Research (2021).
- ModelArchive
- ModelArchive: A Deposition Database for Computational Macromolecular Structural Models. Gerardo Tauriello, Andrew M. Waterhouse, Juergen Haas, Dario Behringer, Stefan Bienert, Thomas Garello, Torsten Schwede. Journal of Molecular Biology (2025). https://doi.org/10.1016/j.jmb.2025.168996
Release files for rcsb.utils.insilico3d 0.44
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