Calculating classical bioinformatics features from protein sequences

Question

[Sergio Martínez Cuesta]

Hi all,

I hope this finds you well

I was wondering if you are familiar of any integrated tool that I could use to calculate bioinformatics features from protein sequences e.g. physicochemical properties (e.g. disorder and secondary structure features), amino acid composition ... There are multiple tools to calculate features individually however I am looking for a tool that I can use to calculate many features at once rather than relying on each tool separately.

I am asking this in the context of an assessment work studying how language models perform at representing proteins in comparison with representing proteins using classical features.

Any suggestions/comments would be much appreciated.

Thanks,
Sergio

Answer 1

[Jiyao Wang]

For SwissProt sequences, you can use iCn3D Node.js script to output sequence-based annotations (such as Conserved Domains, SNP, ClinVar, etc) and structure-based annotations (such as 3D domains). The example script "annotation.js" is listed at https://github.com/ncbi/icn3d/tree/master/icn3dnode. This script retrieves all annotations from iCn3D UI: https://structure.ncbi.nlm.nih.gov/icn3d/share.html?LRpYHQU55gi5XUwb7

Answer 2

[Jeremy]

Check out Expasy ProtParam. Given an amino acid sequence, it returns 14 parameters, including molecular weight, isoelectric point, and amino acid composition.

Expasy ProtParam