FAQ: Introduction

What is CATH-Funvar?

The Orengo group has developed the CATH-FunVar (Functional Variation) platform, to utilise the Functional Families (FunFams) in CATH along with structural annotations, to understand host-pathogen interactions associated with important infections and diseases. The FunVar platform identifies variants (residue mutations) lying on or close to known or predicted functional sites and likely to be modifying the function of the protein.

Data on which pathogens is currently provided in CATH-FunVar?

Currently, CATH FunVar provides data associated with proteins of SARS-CoV-2 and its host interactors as well as cancer driver mutations. In the future, the data on other important infections/diseases such as tuberculosis, will also be made available.

FAQ: Data and annotations in CATH-FunVar

What is the dataset of human interactors of SARS-CoV-2, used for CATH-FunVar?

The data is currently made available for the dataset of 332 human interactors is compiled from Gordon et al., 2020 [ref]. In the future, this dataset will be expanded to include additional host interactors from new experimental studies, where available.

What types of data and annotations are currently provided in CATH FunVar?

For the dataset of SARS-CoV-2 proteins and its 332 host interactors, CATH FunVar currently provides the following:

• Associated Functional Family (FunFam) ID in CATH
• 3D structures in PDB/predicted 3D models (generated using out in-house FunMod pipeline)
• Mapped structural domains in CATH
• Annotations based on species, GO term, EC number
• Drugs from ChEMBL
• Associated KEGG ID

How many Host Interactors / Functional Family data is available in CATH v4.3?

255 of the 332 human host proteins in the Krogan set are mapped to FunFams.

FAQs Key papers/suggested reading

Has the FunVar protocol been used previously to study human proteins?

Yes. Orengo group has utilised the FunVar protocol to identify driver genes in cancer types. Please refer to the paper: Ashford et al., 2019 [ref].

Where can I read more details about FunFams in CATH?

Please refer to our papers on FunFams, as listed below:

• Das et al., 2015 10.1093/bioinformatics/btv398
• Sillitoe et al., 2013 10.1093/nar/gks1211

FAQ: Downloads/data access

Is the data freely available at CATH-FunVar?

The data is freely available and can be downloaded via FTP.