cath-funsite-predictor

This is the code base for generating protein functional site predictions using the CATH Funsite predictor.

This git repository contains the following:

datasets This contains all the datasets mentioned in the Funsite manuscript along with jupyter notebooks showing the steps for generating them. Some dataset files are very large, these can be downloaded from ftp://orengoftp.biochem.ucl.ac.uk/cath/supplementary-materials/2020-cath-funsite-predictor/
funsite_models This contains the Funsite model generation, prediction scripts and benchmark results using the dataset files that are reported in the Funsite manuscript.
scripts This contains all scripts used for generating Funsite models and predictions.

Python environment for Funsite predictor

virtualenv -p python3.6 FunsiteEnv
source FunsiteEnv/bin/activate

# install dependencies
pip install -r scripts/FunsiteEnv_requirements.txt

Note that in order to install XGBoost on Mac may require the installation of Xcode (developer tools) and Xcode Command Line Tools.

Getting CATH FunFam assignments for proteins

To get CATH FunFam assignments for proteins, one can use the online search tool for few sequences or the cath-genomescan tool for getting assignments for large sequence datasets.

External softwares

This repository uses external bioinformatics tools that are not written and maintained by the authors of this project. If you use the results of these tools, please reference the relevant papers.

GroupSim

Characterization and Prediction of Residues Determining Protein Functional Specificity. Capra JA and Singh M (2008). Bioinformatics, 24(13): 1473-1480, 2008.

Scorecons

Scoring residue conservation. Valdar WSJ (2002) Proteins: Structure, Function, and Genetics. 43(2): 227-241, 2002.

DSSP

Kabsch, W, and C Sander. 1983. ‘DSSP: Definition of Secondary Structure of Proteins given a Set of 3D Coordinates’. Biopolymers 22: 2577–2637.

NACCESS

Hubbard, S J. 1992. ‘NACCESS: Program for Calculating Accessibilities’. Department of Biochemistry and Molecular Biology, University College of London.

Speedfill

Laskowski, R A. 1995. ‘SURFNET: A Program for Visualizing Molecular Surfaces, Cavities, and Intermolecular Interactions’. J. Mol. Graph. 13 (5): 307-308,323-330.

Schymkowitz, Joost, Jesper Borg, Francois Stricher, Robby Nys, Frederic Rousseau, and Luis Serrano. 2005. ‘The FoldX Web Server: An Online Force Field’. Nucleic Acids Res. 33 (Web Server issue): W382-8.

bio3d

Skjærven, Lars, Shashank Jariwala, Xin-Qiu Yao, Julien Idé, and Barry J Grant. 2016. ‘The Bio3D Project: Interactive Tools for Structural Bioinformatics’. Biophys. J. 110 (3): 379a.

PSAIA

Mihel, Josip, Mile Sikić, Sanja Tomić, Branko Jeren, and Kristian Vlahovicek. 2008. ‘PSAIA - Protein Structure and Interaction Analyzer’. BMC Struct. Biol. 8 (April): 21.

PSI-BLAST

Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J., 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research, 25(17), pp.3389-3402.

Centre of mass

References

The most recent papers describing the CATH protein structure database and CATH FunFams:

JudeWells/cath-funsite-predictor