[Blaster-fans] deletion of amino acids by the preparer

John Irwin jir322 at gmail.com
Sun Aug 29 09:19:27 PDT 2010

Hi Chris

We draw cut the receptor at ca. 20 A from the binding site. For all
practical purposes, atoms beyond this distance from the binding site
have no influence on the docking or the score.  In general, we have to
do this, because some people upload ribosomes or multidomain
complexes, and various scripts would fail if we did not truncate.

I realize it looks a little weird to have just a few residues
disappear, and I could imaging writing better code that would handle
this situation more gracefully (e.g. allow a few extra atoms, if that
is all there is).

If I miss understood (I am doing 100s of support emails), write again.


On Thu, Aug 26, 2010 at 7:20 AM, Christoph Hörth
<c.hoerth at mx.uni-saarland.de> wrote:
> Hi,
> first of all I want to thank you for designing this useful tool. I'm
> working on job 52675.
> To run DOCKBLASTER I uploaded my own receptor and ligand file.
> Comparing the by DOCKBLASTER prepared receptor file to the original
> input file some amino acids have been removed (e.g. Ala1, Arg,2 ,Thr3
> and Val4).
> Is this wanted?
> Thank you,
> Chris
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