Since I am working with an enzyme, I need to know a reliable way to predict the metal binding sites. what would be the best way. Any recommended tools?
If your enzyme is related to others that have known metal binding sites, the information may be available in the literature and/or in the structural databases for the related enzymes, such as https://www.rcsb.org/
As Adam B Shapiro has mentioned your protein could have them predicted by using databases, but be aware that variants of well known folds can be challenging to identify. e.g. TET proteins (2-OG oxygenase) where the fold was not identified earlier because it as split by very large interdomains.
MIB server can be used to dock various metal ions into proteins.
http://combio.life.nctu.edu.tw/MIB2/
Might be helpful for you.
Navindu Dinara Gajanayaka
Check this also might be interesting for you.
Preprint PinMyMetal: A hybrid learning system to accurately model met...
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