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.
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 setuptools or tox:
python setup.py test
or simply run
toxInstallation is via the program pip.
pip install rcsb.utils.insilico3d
or for the local repository:
pip install .- 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).
- ModBase
- MODBASE, a database of annotated comparative protein structure models and associated resources. Ursula Pieper, Benjamin M. Webb, Guang Qiang Dong, Dina Schneidman-Duhovny, Hao Fan, Seung Joong Kim, Natalia Khuri, Yannick G. Spill, Patrick Weinkam, Michal Hammel, John A. Tainer, Michael Nilges, Andrej Sali Nucleic Acids Research 42, D336-46, 2014.
- SWISS-MODEL Repository
- Bienert, S., Waterhouse, A., de Beer, T.A.P., Tauriello, G., Studer, G., Bordoli, L., Schwede, T. The SWISS-MODEL Repository - new features and functionality. Nucleic Acids Res. 45, D313-D319 (2017).
- Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F.T., de Beer, T.A.P., Rempfer, C., Bordoli, L., Lepore, R., Schwede, T. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46(W1), W296-W303 (2018).