ADL: autodock Digest, Vol 50, Issue 9

曾志平 zengzhiping at xmu.edu.cn
Mon May 12 19:48:57 PDT 2008


i think the RMSD value is not the key problem for our docking.
how to evaluate that our result is resonable or not? the binding model of 
the ligand to the receptor is crucial
what do you think about it?
----- Original Message ----- 
From: "Rohit Tiwari" <tiwari at pharmacy.ohio-state.edu>
To: <autodock at scripps.edu>
Sent: Monday, May 12, 2008 11:17 AM
Subject: Re: ADL: autodock Digest, Vol 50, Issue 9


>I had the similar problem earlier, in my case at least it was due to the
> alignment. Try aligning the molecule which you are docking with the
> original reference molecule.
>
> Alternatively, you can see for yourself whether the "reference molecule"
> and the molecule you are docking are in the same "fields" or not by
> opening them together along with the enzyme.
>
> I hope you see what I am trying to convey here.
>
>
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>> Today's Topics:
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>>    1.  I get very high reference RMSD value (anantha ramanan)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Sun, 11 May 2008 03:35:03 -0700
>> From: "anantha ramanan" <ananthu.bioinfo at gmail.com>
>> Subject: ADL: I get very high reference RMSD value
>> To: autodock at scripps.edu
>> Message-ID:
>> <3ec817200805110335n4a0b5a8ct5851feb05691678c at mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Dear All
>>
>>                I get very high ref rms value in my docking studies but 
>> the
>> ligand binds almost near to the crystal binding site. Then i tried to
>> specify  the crystal ligand using "refrms" command in DPF but still i am
>> getting the same high RMSD value.
>> Could anybody let me know the procedure to get low RMSD value.
>> Thanks in advance
>>
>> --
>> Best Regards
>> Anantha ramanan.R
>> Junior Scientist,
>>
>> Institute Of Computational Biology,
>> #1101,First Floor , OTC Road,
>> Near Corporation Circle,
>> Bangalore - 560002
>> Visit us at : www.iocbindia.org
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>> Call us on : 080 - 41571426 / 27
>>
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>> End of autodock Digest, Vol 50, Issue 9
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>
>
> Rohit Tiwari
> Graduate Student
> Division of Medicinal Chemistry
> The Ohio State University
> Columbus, OH 43210
> Phone: 614-688-3149
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