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niewenjuan-csu / TSNAPred

TSNAPred is an ensemble predictor first proposed to identify type-specific nucleic acid-binding residues.
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How to calculate ECO？ #2

Open Weikang-sun opened 1 year ago

Weikang-sun commented 1 year ago

I saw the ECO sample file in the feature folder, each residue has only one feature, but I have 30 columns of features in the HMM file output using HHblits, how to calculate the ECO value? Is it possible to provide code?

niewenjuan-csu commented 1 year ago

Actually, for the calculation of ECO, we refer to the method mentioned in Comprehensive review and empirical analysis of hallmarks of DNA-, RNA- and protein-binding residues in protein chains(PMID:29253082). The calculation formula is as follows, and you can find more details in "Computation of the three hallmarks of binding residues" section of Comprehensive review and empirical analysis of hallmarks of DNA-, RNA- and protein-binding residues in protein chains . 20230409194724