From: Andrea Holfelder (andreaholfelder_at_gmx.com)
Date: Wed Aug 31 2011 - 21:51:27 CDT
I did not quite understand your last point though,
"than try with few snapshots from trajectory which have significantly different conformations in the region where Zn ion could bind well"
Are you suggesting to do a different MD for protein alone and then a different MD for metalloprotein and see the significant changes in region where Zn could bind well etc. ?
Care to elaborate,please Mr Branko?
----- Original Message -----
Sent: 09/01/11 01:58 AM
To: Andrea Holfelder, namd-l
Subject: Re: namd-l: Dock a metal ion into a peptide/protein
This is not a question for NAMD mailing list; anyway try with the GRID (http://www.moldiscovery.com/soft_grid.php ), there you have a Zn2+ probe, and you can estimate positions in your protein with high affinity for it. Good way is to perform classical MD simulation of the protein alone, than try with few snapshots from trajectory which have significantly different conformations in the region where Zn ion could bind well. Hope this will help
On 8/31/2011 9:29 PM, Andrea Holfelder wrote: Which is the best software to dock a metal ion into a protein .pdb file and generate a.pdb file of the "metalloprotein" ?
While not exactly, but by some experiments,I know of a possible binding site in my protein and it has like pico molar affinity towards Zn+2 .
Is there a good software to achieve this ?
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