ADL: Protein Protonation patterns

chaitanya koppisetty kak_chaitanya at
Wed Jun 3 05:56:27 PDT 2009

Please refer to the following publication. 

of arylsulfatase-A (ASA) with its natural sulfoglycolipid substrates: a
computational and site-directed mutagenesis study.Schenk M, Koppisetty CA, Santos DC, Carmona E, Bhatia S, Nyholm PG, Tanphaichitr N.Glycoconj J. 2009 Apr 18. [Epub ahead of print]PMID: 19381802 [PubMed - as supplied by publisher]
We performed docking on a protein, arylsulfatase-A at pH 5.
Initially, the pKa values for the residues in the protein were calculated using Whatif and DelPhi programs. The protonation states at pH 5 were assigned based in the pKa values. Later charges were added and the resulting stuctures were used for dockings. 

----- Original Message ----- 

From: "Hassan Thomas Mamdani" <h.mamdani at>

To: <autodock at>

Sent: Wednesday, May 27, 2009 6:55 PM

Subject: ADL: Protein Protonation patterns

Hi All

I am interested in studying the effect of pH on protein ligand binding and

I was wondering if anyone knows of a way to change the protonation pattern

of a protein prior to setting up the protein in ADT and how ADT would

treat such an input?

Would propka be an appropriate tool to use to generate alternate

protonation states or is there something else I should be looking at?

Also, if I wanted to fiddle around with the dielectric constant used by

AutoDock or create new atom types, do I need to recompile the program

before use, or is there just a file somewhere I can edit the values that

autodock will read?

Looking forward to your responses.



Hassan Mamdani MSci MPhil MRSC

Research Engineer

Dept of Biochemical Engineering

University College London


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