[gmx-users] Protein comparison

[Justin Lemkul]

On 11/17/14 8:09 AM, Onur Tuna wrote:
> Dear md,
>
> I mean that what kind of analysis I can perform? Should I perform binding
> energy calculation or rmsd calculation for protein stability change?
>
> You can perform binding energy calculation, of course. You have a docked
> structure. First make sure your docking simulation is reliable. It is
> important which software you have used and what kind of protein and ligand
> you have. After making sure your docking result is reliable you have to carry
> out MD simulation for testing whether your complex structure is stable. From
> MD simulations you are able to carry out analysis: what kind of interactions
> you have? Charged groups, Hydrogen bonding etc. After making sure your
> structure is stable during MD simulation (you can check RMSD values for this)
> you are able to calculate Potential of Mean Force using Umbrella Sampling or
> you can perform Free Energy Perturbation calculations.
>

In addition, one must take great care to properly parametrize the ligand for MD 
simulation if the results are to be of any use.

-Justin

> Please explore your structure and make sure your docking result is proper
> firstly.
>
> Best, Onur
>
>> On 17 Nov 2014, at 13:42, rama david <ramadavidgroup at gmail.com> wrote:
>>
>> Dear MD,
>>
>>
>> You are asking this question again. but let to tell you, the energy
>> comparison are made by docking software. Please see the manual of software
>> and mentioned the name of software you are using.
>>
>> By gromacs you can do the MD simulation and do analysis of other
>> interaction pattern.
>>
>> You cant compare just docking result  in gromacs.
>>
>>
>>
>>
>> On Mon, Nov 17, 2014 at 9:37 AM, md kashif <kashifzamir180.mk at gmail.com
>> <mailto:kashifzamir180.mk at gmail.com>> wrote:
>>
>>> Dear all I have protein pdb file and protein+ligand pdb file generated
>>> after docking. How can I compare them by using gromacs? With the word
>>> "compare " I mean that what kind of analysis I can perform? Should I
>>> perform binding energy calculation or rmsd calculation for protein
>>> stability change? Kindly suggest any tutorial for help.
>>>
>>> Thanks
>>>
>>>
>>> On Sun, Nov 16, 2014 at 3:13 PM, md kashif <kashifzamir180.mk at gmail.com>
>>> wrote:
>>>
>>>> Dear all I have protein pdb file and protein+ligand pdb file generated
>>>> after docking. How can I compare them by using gromacs?
>>>>
>>>> Thanks
>>>>
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>
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> e-posta mesaji size yanlislikla ulasmissa, icerigini hicbir sekilde
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>
>
> The information contained in this communication may contain confidential or
> legally privileged information. Hacettepe University doesn't accept any legal
> responsibility for the contents and attachments of this message. The sender
> does not accept any liability for any errors or omissions or any viruses in
> the context of this message which arise as a result of internet
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================