How to make predictions for specific metal ion binding sites?

[linonetwo]

Is the only way to get a result is to run a complete forecast? Will that get the desired results?

I didn't see a parameter about metal ion. Only motifs.

[josan82]

The current version (v1.0) of BioMetAll only allows the search by residues and motifs.

To address the specificity of metal ions (to some extent), we make searches by the most common residues coordinating that metal (Table S3 of the article).

For that, we use the --residues parameter. For example, for the most common ions:

• Zn: --residues [CYS,HIS,ASP,GLU]
• Ca: --residues [ASP,GLU,ASN]
• Mg: --residues [ASP,GLU,HIS,THR] (--residues [ASP,GLU,HIS,THR,ASN,SER,GLN] for a looser search)
• Fe: --residues [HIS,CYS,GLU] (--residues [HIS,CYS,GLU,ASP,MET,TYR] for a looser search)
• Mn: --residues [ASP,HIS,GLU]
• Cu: --residues [HIS,CYS] (--residues [HIS,CYS,MET,GLU,ASP] for a looser search)

In the near future (hopefully very near), we are aiming to incorporate the search for metal ion.

[linonetwo]

Many thanks for the quick reply!

As you can see I'm a web developer, I know little about this, I'm helping my wife to do the research. I will send this message to her.

Looking forward to the update! Let me give you a star!

[linonetwo]

Understood, this table summarized the information about the relationship between metal ion and residues, is basically a reverse-index of them.

So using following command means biometall --metal-looser Mg --pdb mypdb.pdb (If you are going to add a --metal argument in next version):

biometall --residues [ASP,GLU,HIS,THR,ASN,SER,GLN] --pdb mypdb.pdb

This can serve as a temporary workaround, and I've test it is working for her. She will cite you in the paper.

[josan82]

Thank you for using the app, I hope it brings good results to your wife's project!

That's the point, with v.1.0 we work that way, with the --residues parameter.

For the next version we are working on additional statistical models in addition to the amino acid propensity of each metal.