rcsb.utils.insilico3d 0.44

RCSB Python In Silico Model Access Utilities

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

1. 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).
2. 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