rcsb.utils.insilico3d 0.38

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 setuptools or tox:

python setup.py test

or simply run

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. 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.
3. 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).