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pxq 庞雪芹 pxq at dicp.ac.cn
Mon Apr 6 23:49:29 PDT 2009


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======= 2009-04-03 22:18:24 您在来信中写道:=======

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>Today's Topics:
>
>   1.  (no subject) (Avni P Nimani)
>   2.  Autodock results. (awantika shrivastava)
>   3. Re:  How to make a flexible chain staying in the active
>      pocket (Jun-Wei)
>   4. Re:  How to make a flexible chain staying in the active
>      pocket (Gavin Seddon)
>   5. Re:  How to make a flexible chain staying in the active
>      pocket (Gavin Seddon)
>   6. Re:  Including water molecules in docking (Douglas Houston)
>   7. Re:  Including water molecules in docking (Florian Nachon)
>   8. Re:  Including water molecules in docking (Douglas Houston)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Thu, 2 Apr 2009 22:30:42 -0500 (EST)
>From: Avni P Nimani <animani at nmu.edu>
>Subject: ADL: (no subject)
>To: autodock at scripps.edu
>Message-ID: <2358988.1238729442698.JavaMail.animani at nmu.edu>
>Content-Type: text/plain; charset=UTF-8
>
>            I am a graduate student working on his thesis involving 
>docking using AutoDock 4.0 and ran into an interesting circumstance.  
>The docking of the ligand using a rigid body macromolecule gives a 
>rather weak Ki of 10^-4 M; however, I made 5 residues flexible in the 
>macromolecule binding pocket and the strength of the Ki increased to 
>10^-11 M.  Much of the binding energy is being contributed by internal 
>energy.  I was wondering on how to deal with this consequence, as it 
>seems that much of the increase in energy is a result of the flexible 
>macrolecule residues as opposed to an increase in intermolecular 
>interactions with the ligand.  What would you suggest?  And is there 
>any references or literature available that addresses this issue or at 
>least papers in which flexible macromolecule residues are used?  I only 
>found one paper in PubMed that reported using four flexible 
>macromolecule residues, but I don't think they reported how they dealt 
>with the internal energy issues.
>           The protein was generated by homology modeling.  The 
>structure was minimized by L-BFGS method to RMS of 0.1.  The gradient 
>of 0.1 was chosen simply because the desired effect was to leave the 
>model as close to crystallographic data as possible, in which major 
>problems such as bond distances were fixed.  The minimized model was 
>assessed for peculiarities by PROCHECK, in which the model was found to 
>have no steric clashes and 99% of residues were in allowed 
>conformational regions.  The final receptor protein conformation was 
>highly energetically favorable.
>         Flexible receptor docking without a ligand is not possible 
>since nothing is actually docking.  The rigid receptor docking shows 
>the internal energy due to the ligand to be small relative to the 
>intramolecular energies.  This control serves the purpose of comparison 
>the best because you can approximate how much contribution to the 
>internal is coming from the flexible residues in the binding pocket as 
>opposed to the ligand.  I appreciate advice anyone can provide 
>regarding this issue knowing that the residues of interest are not 
>clashing.                  
>
>                                       Sincerely,
>                                                  Avni
>
>
>------------------------------
>
>Message: 2
>Date: Fri, 3 Apr 2009 09:17:33 +0530
>From: awantika shrivastava <awantika31 at hotmail.com>
>Subject: ADL: Autodock results.
>To: <autodock at scripps.edu>
>Message-ID: <BLU107-W22E9477C4540E03EE69C43C3890 at phx.gbl>
>Content-Type: text/plain; charset="iso-8859-1"
>
>
>hi all!!!
>
> 
>
> 
>
>I am facing problem in reproducing  the autodock vina result , although i am using same random seed and same parameters. Although binding energy is same...
>
> 
>
> 
>
>Plz help ..
>
> 
>
> 
>
>Best regards
>
>Awantika shrivastava
>
> 
>
>_________________________________________________________________
>How fun is this? IMing with Windows Live Messenger just got better.
>http://www.microsoft.com/india/windows/windowslive/messenger.aspx
>
>------------------------------
>
>Message: 3
>Date: Fri, 3 Apr 2009 16:10:45 +0800 (CST)
>From: Jun-Wei <zhaojunwei2004 at 126.com>
>Subject: Re: ADL: How to make a flexible chain staying in the active
>	pocket
>To: autodock at scripps.edu
>Message-ID:
>	<14609455.279871238746245146.JavaMail.coremail at bj126app92.126.com>
>Content-Type: text/plain; charset=gbk
>
>Yes. I choose "center on the ligand" and the ligand is placed right in the pocket.
>
>
>
>
>2009-04-02?18:07:40?"Gavin?Seddon"?<home at gavsed.net>??
>>Jun-Wei?wrote:
>>>?Dear?AutoDockers,
>>>??
>>>?I'm?trying?to?dock?a?ligand?to?a?metalloenzyme?containing?zinc?ion?by?AutoDock4.?The?zinc?is?in?the?active?pocket?of?the?protein.?My?ligand?has?a?sidechain?containing?five?C-C?single?bonds,?which?should?be?located?in?the?active?pocket?theoretically.
>>>???The?question:?when?checking?the?docking?results,?all?the?docked?poses?bind?to?the?protein?surface?around?the?pocket,?instead?of?binding?into?the?zinc?pocket?with?the?five?C-C?single?bonds.?What?should?I?do?to?get?the?sidechain?into?the?pocket??Thanks?in?advance!
>>>??
>>>???The?grid?box?is?properly?set?around?the?pocket?and?different?zinc?parameters?have?been?tried.
>>>
>>>?Best?wishes,
>>>?Junwei?Zhao
>>>?________________________________________________
>>>?---?ADL:?AutoDock?List??---?http://autodock.scripps.edu/mailing_list?---
>>>
>>>???
>>Have?you?placed?the?gridcenter?inside?pocket?
>>________________________________________________
>>---?ADL:?AutoDock?List??---?http://autodock.scripps.edu/mailing_list?---
>
>
>------------------------------
>
>Message: 4
>Date: Fri, 03 Apr 2009 09:53:15 +0100
>From: Gavin Seddon <home at gavsed.net>
>Subject: Re: ADL: How to make a flexible chain staying in the active
>	pocket
>To: autodock at scripps.edu
>Message-ID: <49D5CE7B.9000702 at gavsed.net>
>Content-Type: text/plain; charset=gbk; format=flowed
>
>Jun-Wei wrote:
>> Yes. I choose "center on the ligand" and the ligand is placed right in the pocket.
>>
>>
>>
>>
>> 2009-04-02?18:07:40?"Gavin?Seddon"?<home at gavsed.net>??
>>   
>>> Jun-Wei?wrote:
>>>     
>>>> ?Dear?AutoDockers,
>>>> ??
>>>> ?I'm?trying?to?dock?a?ligand?to?a?metalloenzyme?containing?zinc?ion?by?AutoDock4.?The?zinc?is?in?the?active?pocket?of?the?protein.?My?ligand?has?a?sidechain?containing?five?C-C?single?bonds,?which?should?be?located?in?the?active?pocket?theoretically.
>>>> ???The?question:?when?checking?the?docking?results,?all?the?docked?poses?bind?to?the?protein?surface?around?the?pocket,?instead?of?binding?into?the?zinc?pocket?with?the?five?C-C?single?bonds.?What?should?I?do?to?get?the?sidechain?into?the?pocket??Thanks?in?advance!
>>>> ??
>>>> ???The?grid?box?is?properly?set?around?the?pocket?and?different?zinc?parameters?have?been?tried.
>>>>
>>>> ?Best?wishes,
>>>> ?Junwei?Zhao
>>>> ?________________________________________________
>>>> ?---?ADL:?AutoDock?List??---?http://autodock.scripps.edu/mailing_list?---
>>>>
>>>> ???
>>>>       
>>> Have?you?placed?the?gridcenter?inside?pocket?
>>> ________________________________________________
>>> ---?ADL:?AutoDock?List??---?http://autodock.scripps.edu/mailing_list?---
>>>     
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>I had an idea last night. Rather than using a genetic biorhythms for 
>dckg, try simulated annealing and pls let me know how you get on since I 
>have other interests in sa.
>
>
>------------------------------
>
>Message: 5
>Date: Fri, 03 Apr 2009 09:57:49 +0100
>From: Gavin Seddon <home at gavsed.net>
>Subject: Re: ADL: How to make a flexible chain staying in the active
>	pocket
>To: autodock at scripps.edu
>Message-ID: <49D5CF8D.7080808 at gavsed.net>
>Content-Type: text/plain; charset=gbk; format=flowed
>
>Gavin Seddon wrote:
>> Jun-Wei wrote:
>>> Yes. I choose "center on the ligand" and the ligand is placed right 
>>> in the pocket.
>>>
>>>
>>>
>>>
>>> 2009-04-02?18:07:40?"Gavin?Seddon"?<home at gavsed.net>??
>>>> Jun-Wei?wrote:
>>>>> ?Dear?AutoDockers,
>>>>> ??
>>>>> ?I'm?trying?to?dock?a?ligand?to?a?metalloenzyme?containing?zinc?ion?by?AutoDock4.?The?zinc?is?in?the?active?pocket?of?the?protein.?My?ligand?has?a?sidechain?containing?five?C-C?single?bonds,?which?should?be?located?in?the?active?pocket?theoretically. 
>>>>>
>>>>> ???The?question:?when?checking?the?docking?results,?all?the?docked?poses?bind?to?the?protein?surface?around?the?pocket,?instead?of?binding?into?the?zinc?pocket?with?the?five?C-C?single?bonds.?What?should?I?do?to?get?the?sidechain?into?the?pocket??Thanks?in?advance! 
>>>>>
>>>>> ??
>>>>> ???The?grid?box?is?properly?set?around?the?pocket?and?different?zinc?parameters?have?been?tried. 
>>>>>
>>>>>
>>>>> ?Best?wishes,
>>>>> ?Junwei?Zhao
>>>>> ?________________________________________________
>>>>> ?---?ADL:?AutoDock?List??---?http://autodock.scripps.edu/mailing_list?--- 
>>>>>
>>>>>
>>>>> ???
>>>> Have?you?placed?the?gridcenter?inside?pocket?
>>>> ________________________________________________
>>>> ---?ADL:?AutoDock?List??---?http://autodock.scripps.edu/mailing_list?--- 
>>>>
>>> ________________________________________________
>>> --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list ---
>> I had an idea last night. Rather than using a genetic biorhythms for 
>> dckg, try simulated annealing and pls let me know how you get on since 
>> I have other interests in sa.
>> ________________________________________________
>> --- ADL: AutoDock List --- http://autodock.scripps.edu/mailing_list ---
>that should be genetic algorhythm, spell checker!!!
>sorry
>
>
>------------------------------
>
>Message: 6
>Date: Fri, 03 Apr 2009 14:37:08 +0100
>From: Douglas Houston <dhouston at staffmail.ed.ac.uk>
>Subject: Re: ADL: Including water molecules in docking
>To: autodock at scripps.edu
>Message-ID: <20090403143708.4s23ttjrwgk4gsow at www.staffmail.ed.ac.uk>
>Content-Type: text/plain;	charset=ISO-8859-1;	DelSp="Yes";
>	format="flowed"
>
>Thanks Gavin,
>
>If I use
>
>/prepare_receptor4.py -U nphs_lps_nonstdres -r receptor.pdb
>
>it seems to keep the waters while still doing everything else,
>
>cheers,
>
>Doug
>
>
>Quoting Gavin Seddon <home at gavsed.net>:
>
>> Douglas Houston wrote:
>>> Hi all,
>>>
>>> I've noticed that in one of my structures there's a very   
>>> stable-looking water molecule that might well allow for   
>>> water-mediated hydrogen bonding when ligands bind. I also notice   
>>> all water molecules get removed when converting the receptor pdb to  
>>>  pdbq. Is there any way to get Autodock to use this water molecule,  
>>>  for example perhaps by treating it as part of the binding site?
>>>
>>> thanks for any input,
>>>
>>> Doug
>>>
>> Hi
>> the python script
>> prepare_receptor4.py
>> uses a '-U' ARGUMENT that removes water, use scrpts, without -U and do
>> other cleanup with alternate software; or prep molecule another way.
>> This is a really interesting point.
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>
>
>
>_____________________________________________
>Dr. Douglas R. Houston
>Room 3.23
>Institute of Structural and Molecular Biology
>Michael Swann Building
>King's Buildings
>University of Edinburgh
>Edinburgh, EH9 3JR, UK
>Tel. 0131 650 7358
>
>-- 
>The University of Edinburgh is a charitable body, registered in
>Scotland, with registration number SC005336.
>
>
>
>
>
>------------------------------
>
>Message: 7
>Date: Fri, 3 Apr 2009 16:03:03 +0200
>From: Florian Nachon <mailinglist at nachon.net>
>Subject: Re: ADL: Including water molecules in docking
>To: autodock at scripps.edu
>Message-ID: <A0DD69DC-A2FE-4CEC-BCD7-C574E8DB5841 at nachon.net>
>Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
>
>On 3 Apr 2009, at 15:37, Douglas Houston wrote:
>
>> Thanks Gavin,
>>
>> If I use
>>
>> /prepare_receptor4.py -U nphs_lps_nonstdres -r receptor.pdb
>>
>> it seems to keep the waters while still doing everything else,
>
>You'll miss the protons, i.e. H-Bond donor atoms, but H-Bond acceptor  
>is already a drastic improvement over no water molecule at all!
>Any software to predict the most likely position of these protons?
>
>
>------------------------------
>
>Message: 8
>Date: Fri, 03 Apr 2009 15:18:13 +0100
>From: Douglas Houston <dhouston at staffmail.ed.ac.uk>
>Subject: Re: ADL: Including water molecules in docking
>To: autodock at scripps.edu
>Message-ID: <20090403151813.enb83jxv4ookck40 at www.staffmail.ed.ac.uk>
>Content-Type: text/plain;	charset=ISO-8859-1;	DelSp="Yes";
>	format="flowed"
>
>The waters already have hydrogens added using PDB2PQR (which I also  
>use to add hydrogens to the receptor). This tries to predict positions  
>based on optimal H-bonding network.
>
>
>Quoting Florian Nachon <mailinglist at nachon.net>:
>
>>
>> On 3 Apr 2009, at 15:37, Douglas Houston wrote:
>>
>>> Thanks Gavin,
>>>
>>> If I use
>>>
>>> /prepare_receptor4.py -U nphs_lps_nonstdres -r receptor.pdb
>>>
>>> it seems to keep the waters while still doing everything else,
>>
>> You'll miss the protons, i.e. H-Bond donor atoms, but H-Bond acceptor
>> is already a drastic improvement over no water molecule at all!
>> Any software to predict the most likely position of these protons?
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>
>
>
>_____________________________________________
>Dr. Douglas R. Houston
>Room 3.23
>Institute of Structural and Molecular Biology
>Michael Swann Building
>King's Buildings
>University of Edinburgh
>Edinburgh, EH9 3JR, UK
>Tel. 0131 650 7358
>
>-- 
>The University of Edinburgh is a charitable body, registered in
>Scotland, with registration number SC005336.
>
>
>
>
>
>------------------------------
>
>________________________________________________
>--- ADL: AutoDock List  --- http://www.scripps.edu/pub/olson-web/doc/autodock/ ---
>
>End of autodock Digest, Vol 56, Issue 5
>***************************************

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

        致
礼!
 
				 
        pxq 庞雪芹
        pxq at dicp.ac.cn
          2009-04-07




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