From owner-chemistry@ccl.net Sun Dec 12 01:14:01 2010
From: "Shirin Seifert shirin.seifert : gmail.com" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian Linux
Message-Id: <-43341-101212010750-14435-zmtyfL830AnpBQ1SEEkRpw%%server.ccl.net>
X-Original-From: Shirin Seifert <shirin.seifert_-_gmail.com>
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Date: Sun, 12 Dec 2010 09:37:43 +0330
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Sent to CCL by: Shirin Seifert [shirin.seifert]_[gmail.com]
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Dear CCL'ers

Which of these Os'es do you recommend to install for Gaussian 09 (64bit) ?
(The CPUs are Intel (R) Xeon(R))
 Thanks for your recommendations in advance:
1- SuSE Linux 9.3, 10.3, 11.1, 11.2;
2- Fedora
3- Red Hat Enterprise Linux 5.2
4- Red Hat Enterprise Linux 4.7, 5.3, 5.4, 5.5;
5- SuSE Linux Enterprise Server
9 and 10

Regards,
SS

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Dear CCL&#39;ers<br><br>Which of these Os&#39;es do you recommend to instal=
l for Gaussian 09 (64bit) ?=A0 (The CPUs are Intel (R) Xeon(R))<br>=A0Thank=
s for your recommendations in advance:<br>1- <font size=3D"-1">SuSE  Linux =
 9.3, 10.3, 11.1, 11.2;<br>
</font><font size=3D"-1">2- Fedora <br>3- </font><font color=3D"#000000" si=
ze=3D"-1">Red Hat Enterprise Linux   5.2<br>4- </font><font size=3D"-1"><fo=
nt color=3D"#000000">Red Hat Enterprise Linux 4.7, 5.3, 5.4, 5.5</font>;<br=
>5- </font><font size=3D"-1">SuSE Linux Enterprise Server <br>

      9 and 10<br><br>Regards,<br>SS<br></font>

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From owner-chemistry@ccl.net Sun Dec 12 06:04:01 2010
From: "Inbal Tuvi-Arad inbaltu{=}openu.ac.il" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL: Freeware Molecular Mechanics
Message-Id: <-43342-101212060214-17134-ARmof1Uer7tYW3WEbq6v/g]_[server.ccl.net>
X-Original-From: "Inbal Tuvi-Arad" <inbaltu{}openu.ac.il>
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Date: Sun, 12 Dec 2010 13:00:52 +0200
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Sent to CCL by: "Inbal Tuvi-Arad" [inbaltu~!~openu.ac.il]
Hi Peter, 
You might one to check Webmo  - it is a web-based GUI for Tinker as well
as other packages (e.g., GAMESS, GUSSIAN, etc.)  http://www.webmo.net/

Best wishes,
Inbal


-----Original Message-----
> From: owner-chemistry+inbaltu==openu.ac.il _ ccl.net
[mailto:owner-chemistry+inbaltu==openu.ac.il _ ccl.net] On Behalf Of Peter
D Jarowski p.d.jarowski^^^surrey.ac.uk
Sent: Friday, December 10, 2010 4:49 PM
To: Inbal Tuvi-Arad
Subject: CCL: Freeware Molecular Mechanics


Sent to CCL by: "Peter D Jarowski" [p.d.jarowski!A!surrey.ac.uk]
Hello,

Anyone know of a freeware molecular mechanics package with a reasonable
GUI that runs on Mac 
intel? All I need is to run some preliminary minimizations and/or
conformational searches before 
submitting to the cluster for QM. I know about Tinker, but I do not see
a GUI for that one.

Best,

Peterhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Sun Dec 12 06:39:00 2010
From: "sina rastegar sina_rastegAR1979||YAHOO.COM" <owner-chemistry,server.ccl.net>
To: CCL
Subject: CCL: Ab Initio Molecular Dynamic
Message-Id: <-43343-101212051753-31236-E6crDHqgNHE/cWGbsuUmzQ,server.ccl.net>
X-Original-From: "sina  rastegar" <sina_rastegAR1979|a|YAHOO.COM>
Date: Sun, 12 Dec 2010 05:17:52 -0500


Sent to CCL by: "sina  rastegar" [sina_rastegAR1979%YAHOO.COM]
Hello Everybody
I am interested in abinitio simulation,and I am really confused about differences between vasp & cpmd packages.
Could anybody tell me what is the main methodology s aspects between these two software?
It is better to say that if a job which is completed with vasp ,could be done with cpmd with same results or not?(with same plane wave cutoff and same cell characteristic in DFT and GGA with PW91 Basis set usages.)

Thanks 

Sincerely yours 
Sina Rastegar


From owner-chemistry@ccl.net Sun Dec 12 07:14:00 2010
From: "eurisco1%pochta.ru" <owner-chemistry]|[server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian Linux
Message-Id: <-43344-101212062057-25211-N+VUxF7tiQkQYi11YMx0+A]|[server.ccl.net>
X-Original-From: <eurisco1^pochta.ru>
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Date: Sun, 12 Dec 2010 14:20:30 +0300
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Sent to CCL by: [eurisco1()pochta.ru]
]rn  qnnayemhe hg meqjnk|jhu w`qrei b tnpl`re MIME.

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Dear Shirin Seifert,

I suggest you to install the OS that you know better or is known by the =
expert who works in your Department or Lab.
Personally,  I would suggest to install OpenSuse (SuSE Linux 11.1 11.2). =
It is free and well behaved on different platforms.

Sincerely,
Ol Ga




> From: Shirin Seifert shirin.seifert : gmail.com=20
Sent: Sunday, December 12, 2010 9:07 AM
To: Ga, Ol =20
Subject: CCL:G: Gaussian Linux

Dear CCL'ers

Which of these Os'es do you recommend to install for Gaussian 09 (64bit) =
?  (The CPUs are Intel (R) Xeon(R))
Thanks for your recommendations in advance:
1- SuSE Linux 9.3, 10.3, 11.1, 11.2;
2- Fedora=20
3- Red Hat Enterprise Linux 5.2
4- Red Hat Enterprise Linux 4.7, 5.3, 5.4, 5.5;
5- SuSE Linux Enterprise Server=20
9 and 10

Regards,
SS

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	charset="ISO-8859-1"
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<HTML><HEAD></HEAD>
<BODY dir=3Dltr>
<DIV dir=3Dltr>
<DIV style=3D"FONT-FAMILY: 'Calibri'; COLOR: #000000; FONT-SIZE: 12pt">
<DIV>Dear Shirin Seifert,</DIV>
<DIV>&nbsp;</DIV>
<DIV>I suggest you to install the OS that you know better or is known by =
the=20
expert who works in your Department or Lab.<BR>Personally,&nbsp; I would =
suggest=20
to install OpenSuse (SuSE Linux 11.1 11.2). It is free and well behaved =
on=20
different platforms.<BR></DIV>
<DIV>Sincerely,</DIV>
<DIV>Ol Ga</DIV>
<DIV>&nbsp;</DIV>
<DIV>&nbsp;</DIV>
<DIV>&nbsp;</DIV>
<DIV=20
style=3D"FONT-STYLE: normal; DISPLAY: inline; FONT-FAMILY: 'Calibri'; =
COLOR: #000000; FONT-SIZE: small; FONT-WEIGHT: normal; TEXT-DECORATION: =
none">
<DIV style=3D"FONT: 10pt tahoma">
<DIV>&nbsp;</DIV>
<DIV style=3D"BACKGROUND: #f5f5f5">
<DIV style=3D"font-color: black"><B>From:</B> <A =
title=3Downer-chemistry(~)ccl.net=20
href=3D"mailto:owner-chemistry(~)ccl.net">Shirin Seifert shirin.seifert :=20
gmail.com</A> </DIV>
<DIV><B>Sent:</B> Sunday, December 12, 2010 9:07 AM</DIV>
<DIV><B>To:</B> <A title=3Deurisco1(~)pochta.ru =
href=3D"mailto:eurisco1(~)pochta.ru">Ga,=20
Ol </A> </DIV>
<DIV><B>Subject:</B> CCL:G: Gaussian Linux</DIV></DIV></DIV>
<DIV>&nbsp;</DIV></DIV>
<DIV=20
style=3D"FONT-STYLE: normal; DISPLAY: inline; FONT-FAMILY: 'Calibri'; =
COLOR: #000000; FONT-SIZE: small; FONT-WEIGHT: normal; TEXT-DECORATION: =
none">Dear=20
CCL'ers<BR><BR>Which of these Os'es do you recommend to install for =
Gaussian 09=20
(64bit) ?&nbsp; (The CPUs are Intel (R) Xeon(R))<BR>Thanks for your=20
recommendations in advance:<BR>1- <FONT size=3D-1>SuSE Linux 9.3, 10.3, =
11.1,=20
11.2;<BR></FONT><FONT size=3D-1>2- Fedora <BR>3- </FONT><FONT =
color=3D#000000=20
size=3D-1>Red Hat Enterprise Linux 5.2<BR>4- </FONT><FONT =
size=3D-1><FONT=20
color=3D#000000>Red Hat Enterprise Linux 4.7, 5.3, 5.4, =
5.5</FONT>;<BR>5-=20
</FONT><FONT size=3D-1>SuSE Linux Enterprise Server <BR>9 and=20
10<BR><BR>Regards,<BR>SS<BR></FONT></DIV></DIV></DIV></BODY></HTML>

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From owner-chemistry@ccl.net Sun Dec 12 08:31:00 2010
From: "Michael Dimitrov mich.dimitrov()gmail.com" <owner-chemistry]![server.ccl.net>
To: CCL
Subject: CCL:G: Is SMD/IEFPCM appropiate for charged transition metal complex?
Message-Id: <-43345-101212082747-17365-KEQd/SIj26adDR6Wr9MtQg]![server.ccl.net>
X-Original-From: Michael Dimitrov <mich.dimitrov#,#gmail.com>
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Date: Sun, 12 Dec 2010 16:27:41 +0300
MIME-Version: 1.0


Sent to CCL by: Michael Dimitrov [mich.dimitrov/a\gmail.com]
Dear Sayed,

As far as I remember, calculations of reactions of charged metal
complexes without taking into account solvent may give huge errors,
like 30-40 kcal/mol.
I have an example with Pt complexes in my literature archive:
Organometallics 2001, 20, 1652 (http://dx.doi.org/10.1021/om001073u).
It was reported that PCM improved the results very much and it was
possible to get dG.

Best regards,
Michael Dimitrov.


On 12/3/10, Sayed Mesa elsayed.elmes#yahoo.com <owner-chemistry- -ccl.net> wrote:
>
> Sent to CCL by: "Sayed  Mesa" [elsayed.elmes]*[yahoo.com]
> Dear CCL community;
>
> I want to study the thermochemistry of the following reaction in water using
> B3LYP/mixed basis set as implemented in Gaussian 09 :
>
> [Cu2L]4+  + OH-  ----> [Cu2LOH]3+
>
> Where [Cu2L]4+ is dinuclear copper complex. L is macrocyclic complex.
>
> I have two questions:
>
> 1- Is SMD/IEFPCM appropriate for charged transition metal complex? If not
> please let me know which solvation model is better?
>
> 2- Can I calculate Delta G and Delta H of this reaction using SMD/IEFPCM?
>
> N.B. I read that SMD the reommended choice for calculation the delta G of
> solavation
>  http://www.gaussian.com/g_tech/g_ur/k_scrf.htm
>
> Thanks beforehand,
> Sayed>
>
>


From owner-chemistry@ccl.net Sun Dec 12 10:25:00 2010
From: "Phil Hasnip pjh503+*+york.ac.uk" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL: Ab Initio Molecular Dynamic
Message-Id: <-43346-101212100058-11730-2Fsauh+3JhF8rsUR7G7rPA,+,server.ccl.net>
X-Original-From: Phil Hasnip <pjh503^_^york.ac.uk>
Content-Type: text/plain; format=flowed; charset=ISO-8859-1
Date: 12 Dec 2010 15:00:47 +0000
Mime-Version: 1.0


Sent to CCL by: Phil Hasnip [pjh503*york.ac.uk]
Dear Sina,

I can't comment on any specific differences between vasp and cmpd as I 
develop a different ab initio program (castep), but in general different 
packages will have different approximations and functionality -- of course 
they will all do groundstate calculations with LDA and some GGAs, and if 
you use good pseudopotentials and convergence criteria in each then you 
should get very similar answers regardless of your program. In my 
experience the differences in fundamental approximations between progams 
are small enough that you should get pretty much the same answer with the 
same quality of calculation.

Where ab initio programs differ is in the more advanced features, so you 
may need to think about what you want to do. I don't know what your 
research is, but some of the things you might like to think about are:

1) Will they optimise crystal lattices? (Most will optimise atomic 
positions within a fixed unit cell, but not all will optimise the cell size 
and shape)

2) Do they come with a good, accurate set of pseudopotentials (it's not a 
disaster if not, but you will have to make and test your own)

3) Will they compute experimentally accessible properties (NMR spectra, 
EELS, IR, Raman etc.)

4) Will they work efficiently in parallel (i.e. on multicore machines, 
clusters and supercomputers)?

5) If you're interested in systems with hydrogen or other light atoms, will 
they handle the nuclear quantum effects?

Of course I am completely biased and would recommend castep to you 
(www.castep.org) but in all honesty when you're thinking about getting 
different programs you need to think about what you need for your 
simulations, and what you don't need but would like.

Finally, remember that if a program does almost everything you need but 
there are one or two things missing, you can always contact a developer 
like me and ask about either putting the extra bit in yourself or whether 
they might consider putting it in.

I hope that's helped a bit.

Yours,

Phil Hasnip

On Dec 12 2010, sina rastegar sina_rastegAR1979||YAHOO.COM wrote:

>
> Sent to CCL by: "sina rastegar" [sina_rastegAR1979%YAHOO.COM] Hello 
> Everybody I am interested in abinitio simulation,and I am really confused 
> about differences between vasp & cpmd packages. Could anybody tell me 
> what is the main methodology s aspects between these two software? It is 
> better to say that if a job which is completed with vasp ,could be done 
> with cpmd with same results or not?(with same plane wave cutoff and same 
> cell characteristic in DFT and GGA with PW91 Basis set usages.)
>
>Thanks 
>
>Sincerely yours 
>Sina Rastegar>
>
>

-- 
-------------------------------------------------------
Dr Phil Hasnip                 Email: pjh503(_)york.ac.uk
Dept of Physics                   
University of York             Tel:  +44 (0)1904 434624
York YO10 5DD


From owner-chemistry@ccl.net Sun Dec 12 10:59:01 2010
From: "Deepangi Pandit deepangi.pandit++gmail.com" <owner-chemistry|server.ccl.net>
To: CCL
Subject: CCL: Prediction & Identification of protein-ligand binding sites
Message-Id: <-43347-101212105336-26805-IjGPtZdnRh5hn9Pq31LHhA|server.ccl.net>
X-Original-From: Deepangi Pandit <deepangi.pandit{=}gmail.com>
Content-Transfer-Encoding: 8bit
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Date: Sun, 12 Dec 2010 10:53:27 -0500
MIME-Version: 1.0


Sent to CCL by: Deepangi Pandit [deepangi.pandit|,|gmail.com]
Thank you Peter, for your detailed reply. I would just like to clarify
my case based on your questions.

> 1 : Do you want to apply this method on a database of proteins or just a few structures?

I am looking at just a few structures to identify the putative drug
binding site. I have PDB files of protein structures (of course,
without the compound) and have experimental data which suggests the
compound is binding but do not know where.

> 2 : Do you want to identify putative drug binding sites or whatever binding site a method could find (general purpose pocket prediction)

I am trying to identify the putative drug binding sites not general
purpose pocket prediction


> 3 : Do you want to find conserved pockets among homologs?

This is not my primary goal.

Best,
Deepa

On Sat, Dec 11, 2010 at 4:45 PM, Peter Schmidtke
pschmidtke[-]mmb.pcb.ub.es <owner-chemistry[A]ccl.net> wrote:
>
> Sent to CCL by: Peter Schmidtke [pschmidtke[*]mmb.pcb.ub.es]
> Dear Deepangi,
>
> protein-ligand binding site detection is a very active field and there
> is a large variety of methods out there.
> Since the publication of PocketPicker
> (http://www.journal.chemistrycentral.com/content/1/1/7/abstract/) lots
> of newer methods used the comparative table that was published with
> PocketPicker (table 2). A very recent example is the paper by Andrea
> Volkamer, where you have an update of this table with a few more recent
> methods (http://pubs.acs.org/doi/full/10.1021/ci100241y).
>
> This comparison is definitely arguable, but at least it gives some hint
> on general pocket prediction performance. In order to find the perfect
> method for your purpose you should maybe clarify what is the
> functionality your are seeking. There are lots of webservers out there,
> methods you have to pay and also free methods.
>
> Some questions that could influence your choice :
>
> 1 : Do you want to apply this method on a database of proteins or just a
> few structures?
> 2 : Do you want to identify putative drug binding sites or whatever
> binding site a method could find (general purpose pocket prediction)
> 3 : Do you want to find conserved pockets among homologs?
>
> Concerning question 1, if you just need a method for a few structures
> you can go for slower programs (mostly energy based algorithms) like
> SiteMap from Schrödinger (but you need a license) Q-SiteFinder or
> PocketPicker or Vice (I think it's sold by Tripos) There are surely more
> than that.
> If you need to process a large number of structures, considering
> geometry based methods might become an interesting choice. Choices could
> be Ligsite, fpocket, PASS, SiteFinder (included in MOE by CCG) ...
>
> Regarding question 2. Pocket prediction is not equal drug binding site
> prediction. Recent druggability prediction methods have been published
> and some scores are available ready for use in SiteMap (I don't know if
> you still have to calculate it or if they finally included it into the
> SiteMap distribution) and fpocket. I suspect also QSiteFinder might give
> indications on druggability (I extrapolate from the methodology I just
> read very quickly, so maybe I'm wrong here ;) ).
>
> Regarding question 3, I think ligsite csc can help there
> (http://projects.biotec.tu-dresden.de/pocket/), or else hpocket, which
> is part of the fpocket webserver :
> http://bioserv.rpbs.univ-paris-diderot.fr/fpocket/
>
> I hope that this gives you at least a direction, there are really lots
> of methods and it is indeed not easy to know which one to use ;)
>
> Ah, I nearly forgot, metapocket2.0 is a sort of consensus pocket
> prediction method that makes use of LIGSITEcsc, PASS, Q-SiteFinder,
> SURFNET, Fpocket, GHECOM and ConCavity. This has again advantages and
> disadvantages, but well, at least you know that it exists ;)
>
> Good luck.
>
> Peter Schmidtke
>
>
>
>
> On 12/11/2010 06:44 PM, Deepangi Pandit deepangi.pandit~!~gmail.com wrote:
>> Sent to CCL by: Deepangi Pandit [deepangi.pandit(!)gmail.com]
>> Dear All:
>> I tried to search literature and Internet to find a reliable method
>> that I can use to identify protein-ligand binding site. I came across
>> number of papers but I am unable to evaluate the methods before I
>> start using them. I was also unable to find a review which compares
>> the methods. It seems method can be broadly classified as "Geometry
>> based" and "Energy Based". Could you please recommend from your own
>> experience which method gives reasonable results. Also, feel free to
>> share pros and cons of the method.
>>
>> Thank you.
>> Deepa
>>
>> List of methods I came across
>>
>> Q-Site Finder
>> http://www.bioinformatics.leeds.ac.uk/qsitefinder
>>
>> Surface triplet propensities
>> http://opus.bch.ed.ac.uk/stp
>>
>> Screen
>> http://interface.bioc.columbia.edu/screen>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt>
>
>


From owner-chemistry@ccl.net Sun Dec 12 11:34:00 2010
From: "Peter Schmidtke pschmidtke~!~mmb.pcb.ub.es" <owner-chemistry~~server.ccl.net>
To: CCL
Subject: CCL: Prediction & Identification of protein-ligand binding sites
Message-Id: <-43348-101212111343-32362-7q4kQbJAoDVmMy33BG3Rng~~server.ccl.net>
X-Original-From: Peter Schmidtke <pschmidtke:+:mmb.pcb.ub.es>
Content-Type: multipart/alternative; boundary=Apple-Mail-2-330577573
Date: Sun, 12 Dec 2010 17:13:10 +0100
Mime-Version: 1.0 (Apple Message framework v1081)


Sent to CCL by: Peter Schmidtke [pschmidtke(!)mmb.pcb.ub.es]

--Apple-Mail-2-330577573
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Content-Type: text/plain;
	charset=iso-8859-1


On 12/12/2010, at 16:53, Deepangi Pandit wrote:

> Thank you Peter, for your detailed reply. I would just like to clarify
> my case based on your questions.
>=20
>> 1 : Do you want to apply this method on a database of proteins or =
just a few structures?
>=20
> I am looking at just a few structures to identify the putative drug
> binding site. I have PDB files of protein structures (of course,
> without the compound) and have experimental data which suggests the
> compound is binding but do not know where.
>=20
>> 2 : Do you want to identify putative drug binding sites or whatever =
binding site a method could find (general purpose pocket prediction)
>=20
> I am trying to identify the putative drug binding sites not general
> purpose pocket prediction
>=20

>> 3 : Do you want to find conserved pockets among homologs?
>=20
> This is not my primary goal.

Ok, in this case I'd say that you could use either SiteMap if you have a =
license or fpocket (I can assist you off list on fpocket as I am the =
co-developper of the software), which is free (GNU GPL).
More info on fpocket and it's druggability score :=20
http://pubs.acs.org/doi/abs/10.1021/jm100574m
http://fpocket.sourceforge.net

And on SiteMaps Dscore :
http://pubs.acs.org/doi/abs/10.1021/ci800324m

These are two methods that couple automatic pocket detection with a =
druggability estimation out of the box.=20
Ah depending on what type of molecule you have, the methods might work =
more or less well. They are particularly suited for oral druglike =
molecules. So if you have a prodrug or a covalent binder you could =
potentially use another method (consensus pocket prediction or so).

Best regards.

Peter Schmidtke


>=20
> Best,
> Deepa
>=20
> On Sat, Dec 11, 2010 at 4:45 PM, Peter Schmidtke
> pschmidtke[-]mmb.pcb.ub.es <owner-chemistry[a]ccl.net> wrote:
>>=20
>> Sent to CCL by: Peter Schmidtke [pschmidtke[*]mmb.pcb.ub.es]
>> Dear Deepangi,
>>=20
>> protein-ligand binding site detection is a very active field and =
there
>> is a large variety of methods out there.
>> Since the publication of PocketPicker
>> (http://www.journal.chemistrycentral.com/content/1/1/7/abstract/) =
lots
>> of newer methods used the comparative table that was published with
>> PocketPicker (table 2). A very recent example is the paper by Andrea
>> Volkamer, where you have an update of this table with a few more =
recent
>> methods (http://pubs.acs.org/doi/full/10.1021/ci100241y).
>>=20
>> This comparison is definitely arguable, but at least it gives some =
hint
>> on general pocket prediction performance. In order to find the =
perfect
>> method for your purpose you should maybe clarify what is the
>> functionality your are seeking. There are lots of webservers out =
there,
>> methods you have to pay and also free methods.
>>=20
>> Some questions that could influence your choice :
>>=20
>> 1 : Do you want to apply this method on a database of proteins or =
just a
>> few structures?
>> 2 : Do you want to identify putative drug binding sites or whatever
>> binding site a method could find (general purpose pocket prediction)
>> 3 : Do you want to find conserved pockets among homologs?
>>=20
>> Concerning question 1, if you just need a method for a few structures
>> you can go for slower programs (mostly energy based algorithms) like
>> SiteMap from Schr=F6dinger (but you need a license) Q-SiteFinder or
>> PocketPicker or Vice (I think it's sold by Tripos) There are surely =
more
>> than that.
>> If you need to process a large number of structures, considering
>> geometry based methods might become an interesting choice. Choices =
could
>> be Ligsite, fpocket, PASS, SiteFinder (included in MOE by CCG) ...
>>=20
>> Regarding question 2. Pocket prediction is not equal drug binding =
site
>> prediction. Recent druggability prediction methods have been =
published
>> and some scores are available ready for use in SiteMap (I don't know =
if
>> you still have to calculate it or if they finally included it into =
the
>> SiteMap distribution) and fpocket. I suspect also QSiteFinder might =
give
>> indications on druggability (I extrapolate from the methodology I =
just
>> read very quickly, so maybe I'm wrong here ;) ).
>>=20
>> Regarding question 3, I think ligsite csc can help there
>> (http://projects.biotec.tu-dresden.de/pocket/), or else hpocket, =
which
>> is part of the fpocket webserver :
>> http://bioserv.rpbs.univ-paris-diderot.fr/fpocket/
>>=20
>> I hope that this gives you at least a direction, there are really =
lots
>> of methods and it is indeed not easy to know which one to use ;)
>>=20
>> Ah, I nearly forgot, metapocket2.0 is a sort of consensus pocket
>> prediction method that makes use of LIGSITEcsc, PASS, Q-SiteFinder,
>> SURFNET, Fpocket, GHECOM and ConCavity. This has again advantages and
>> disadvantages, but well, at least you know that it exists ;)
>>=20
>> Good luck.
>>=20
>> Peter Schmidtke
>>=20
>>=20
>>=20
>>=20
>> On 12/11/2010 06:44 PM, Deepangi Pandit deepangi.pandit~!~gmail.com =
wrote:
>>> Sent to CCL by: Deepangi Pandit [deepangi.pandit(!)gmail.com]
>>> Dear All:
>>> I tried to search literature and Internet to find a reliable method
>>> that I can use to identify protein-ligand binding site. I came =
across
>>> number of papers but I am unable to evaluate the methods before I
>>> start using them. I was also unable to find a review which compares
>>> the methods. It seems method can be broadly classified as "Geometry
>>> based" and "Energy Based". Could you please recommend from your own
>>> experience which method gives reasonable results. Also, feel free to
>>> share pros and cons of the method.
>>>=20
>>> Thank you.
>>> Deepa
>>>=20
>>> List of methods I came across
>>>=20
>>> Q-Site Finder
>>> http://www.bioinformatics.leeds.ac.uk/qsitefinder
>>>=20
>>> Surface triplet propensities
>>> http://opus.bch.ed.ac.uk/stp
>>>=20
>>> Screen
>>> http://interface.bioc.columbia.edu/screen>
>>>=20
>>>=20
>>=20
>>=20
>>=20
>> -=3D This is automatically added to each message by the mailing =
script =3D-
>> To recover the email address of the author of the message, please =
change>>=20>>=20>>=20>>=20>>=20>> Conferences: =
http://server.ccl.net/chemistry/announcements/conferences/
>>=20>>=20>>=20>>=20
>>=20
>>=20

Peter Schmidtke

-----------------
PhD Student
Department of Physical Chemistry
School of Pharmacy
University of Barcelona
Barcelona, Spain


--Apple-Mail-2-330577573
Content-Transfer-Encoding: quoted-printable
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	charset=iso-8859-1

<html><head></head><body style=3D"word-wrap: break-word; =
-webkit-nbsp-mode: space; -webkit-line-break: after-white-space; =
"><br><div><div>On 12/12/2010, at 16:53, Deepangi Pandit wrote:</div><br =
class=3D"Apple-interchange-newline"><blockquote type=3D"cite"><div>Thank =
you Peter, for your detailed reply. I would just like to clarify<br>my =
case based on your questions.<br><br><blockquote type=3D"cite">1 : Do =
you want to apply this method on a database of proteins or just a few =
structures?<br></blockquote><br>I am looking at just a few structures to =
identify the putative drug<br>binding site. I have PDB files of protein =
structures (of course,<br>without the compound) and have experimental =
data which suggests the<br>compound is binding but do not know =
where.<br><br><blockquote type=3D"cite">2 : Do you want to identify =
putative drug binding sites or whatever binding site a method could find =
(general purpose pocket prediction)<br></blockquote><br>I am trying to =
identify the putative drug binding sites not general<br>purpose pocket =
prediction<br><font class=3D"Apple-style-span" color=3D"#000000"><font =
class=3D"Apple-style-span" =
color=3D"#144FAE"><br></font></font></div></blockquote><br><blockquote =
type=3D"cite"><div><blockquote type=3D"cite">3 : Do you want to find =
conserved pockets among homologs?<br></blockquote><br>This is not my =
primary goal.<br></div></blockquote><div><br></div><div>Ok, in this case =
I'd say that you could use either SiteMap if you have a license or =
fpocket (I can assist you off list on fpocket as I am the co-developper =
of the software), which is free (GNU GPL).</div><div>More info on =
fpocket and it's druggability score :&nbsp;</div><div><a =
href=3D"http://pubs.acs.org/doi/abs/10.1021/jm100574m">http://pubs.acs.org=
/doi/abs/10.1021/jm100574m</a></div><div><a =
href=3D"http://fpocket.sourceforge.net">http://fpocket.sourceforge.net</a>=
</div><div><br></div><div>And on SiteMaps Dscore :</div><div><a =
href=3D"http://pubs.acs.org/doi/abs/10.1021/ci800324m">http://pubs.acs.org=
/doi/abs/10.1021/ci800324m</a></div><div><br></div><div>These are two =
methods that couple automatic pocket detection with a druggability =
estimation out of the box.&nbsp;</div><div>Ah depending on what type of =
molecule you have, the methods might work more or less well. They are =
particularly suited for oral druglike molecules. So if you have a =
prodrug or a covalent binder you could potentially use another method =
(consensus pocket prediction or so).</div><div><br></div><div>Best =
regards.</div><div><br></div><div>Peter =
Schmidtke</div><div><br></div><br><blockquote =
type=3D"cite"><div><br>Best,<br>Deepa<br><br>On Sat, Dec 11, 2010 at =
4:45 PM, Peter Schmidtke<br>pschmidtke[-]mmb.pcb.ub.es &lt;<a =
href=3D"mailto:owner-chemistry[a]ccl.net">owner-chemistry[a]ccl.net</a>&gt; =
wrote:<br><blockquote type=3D"cite"><br></blockquote><blockquote =
type=3D"cite">Sent to CCL by: Peter Schmidtke =
[pschmidtke[*]mmb.pcb.ub.es]<br></blockquote><blockquote =
type=3D"cite">Dear Deepangi,<br></blockquote><blockquote =
type=3D"cite"><br></blockquote><blockquote type=3D"cite">protein-ligand =
binding site detection is a very active field and =
there<br></blockquote><blockquote type=3D"cite">is a large variety of =
methods out there.<br></blockquote><blockquote type=3D"cite">Since the =
publication of PocketPicker<br></blockquote><blockquote type=3D"cite">(<a =
href=3D"http://www.journal.chemistrycentral.com/content/1/1/7/abstract/">h=
ttp://www.journal.chemistrycentral.com/content/1/1/7/abstract/</a>) =
lots<br></blockquote><blockquote type=3D"cite">of newer methods used the =
comparative table that was published with<br></blockquote><blockquote =
type=3D"cite">PocketPicker (table 2). A very recent example is the paper =
by Andrea<br></blockquote><blockquote type=3D"cite">Volkamer, where you =
have an update of this table with a few more =
recent<br></blockquote><blockquote type=3D"cite">methods (<a =
href=3D"http://pubs.acs.org/doi/full/10.1021/ci100241y">http://pubs.acs.or=
g/doi/full/10.1021/ci100241y</a>).<br></blockquote><blockquote =
type=3D"cite"><br></blockquote><blockquote type=3D"cite">This comparison =
is definitely arguable, but at least it gives some =
hint<br></blockquote><blockquote type=3D"cite">on general pocket =
prediction performance. In order to find the =
perfect<br></blockquote><blockquote type=3D"cite">method for your =
purpose you should maybe clarify what is the<br></blockquote><blockquote =
type=3D"cite">functionality your are seeking. There are lots of =
webservers out there,<br></blockquote><blockquote type=3D"cite">methods =
you have to pay and also free methods.<br></blockquote><blockquote =
type=3D"cite"><br></blockquote><blockquote type=3D"cite">Some questions =
that could influence your choice :<br></blockquote><blockquote =
type=3D"cite"><br></blockquote><blockquote type=3D"cite">1 : Do you want =
to apply this method on a database of proteins or just =
a<br></blockquote><blockquote type=3D"cite">few =
structures?<br></blockquote><blockquote type=3D"cite">2 : Do you want to =
identify putative drug binding sites or =
whatever<br></blockquote><blockquote type=3D"cite">binding site a method =
could find (general purpose pocket =
prediction)<br></blockquote><blockquote type=3D"cite">3 : Do you want to =
find conserved pockets among homologs?<br></blockquote><blockquote =
type=3D"cite"><br></blockquote><blockquote type=3D"cite">Concerning =
question 1, if you just need a method for a few =
structures<br></blockquote><blockquote type=3D"cite">you can go for =
slower programs (mostly energy based algorithms) =
like<br></blockquote><blockquote type=3D"cite">SiteMap from Schr=F6dinger =
(but you need a license) Q-SiteFinder or<br></blockquote><blockquote =
type=3D"cite">PocketPicker or Vice (I think it's sold by Tripos) There =
are surely more<br></blockquote><blockquote type=3D"cite">than =
that.<br></blockquote><blockquote type=3D"cite">If you need to process a =
large number of structures, considering<br></blockquote><blockquote =
type=3D"cite">geometry based methods might become an interesting choice. =
Choices could<br></blockquote><blockquote type=3D"cite">be Ligsite, =
fpocket, PASS, SiteFinder (included in MOE by CCG) =
...<br></blockquote><blockquote type=3D"cite"><br></blockquote><blockquote=
 type=3D"cite">Regarding question 2. Pocket prediction is not equal drug =
binding site<br></blockquote><blockquote type=3D"cite">prediction. =
Recent druggability prediction methods have been =
published<br></blockquote><blockquote type=3D"cite">and some scores are =
available ready for use in SiteMap (I don't know =
if<br></blockquote><blockquote type=3D"cite">you still have to calculate =
it or if they finally included it into the<br></blockquote><blockquote =
type=3D"cite">SiteMap distribution) and fpocket. I suspect also =
QSiteFinder might give<br></blockquote><blockquote =
type=3D"cite">indications on druggability (I extrapolate from the =
methodology I just<br></blockquote><blockquote type=3D"cite">read very =
quickly, so maybe I'm wrong here ;) ).<br></blockquote><blockquote =
type=3D"cite"><br></blockquote><blockquote type=3D"cite">Regarding =
question 3, I think ligsite csc can help =
there<br></blockquote><blockquote type=3D"cite">(<a =
href=3D"http://projects.biotec.tu-dresden.de/pocket/">http://projects.biot=
ec.tu-dresden.de/pocket/</a>), or else hpocket, =
which<br></blockquote><blockquote type=3D"cite">is part of the fpocket =
webserver :<br></blockquote><blockquote type=3D"cite"><a =
href=3D"http://bioserv.rpbs.univ-paris-diderot.fr/fpocket/">http://bioserv=
.rpbs.univ-paris-diderot.fr/fpocket/</a><br></blockquote><blockquote =
type=3D"cite"><br></blockquote><blockquote type=3D"cite">I hope that =
this gives you at least a direction, there are really =
lots<br></blockquote><blockquote type=3D"cite">of methods and it is =
indeed not easy to know which one to use ;)<br></blockquote><blockquote =
type=3D"cite"><br></blockquote><blockquote type=3D"cite">Ah, I nearly =
forgot, metapocket2.0 is a sort of consensus =
pocket<br></blockquote><blockquote type=3D"cite">prediction method that =
makes use of LIGSITEcsc, PASS, Q-SiteFinder,<br></blockquote><blockquote =
type=3D"cite">SURFNET, Fpocket, GHECOM and ConCavity. This has again =
advantages and<br></blockquote><blockquote type=3D"cite">disadvantages, =
but well, at least you know that it exists =
;)<br></blockquote><blockquote type=3D"cite"><br></blockquote><blockquote =
type=3D"cite">Good luck.<br></blockquote><blockquote =
type=3D"cite"><br></blockquote><blockquote type=3D"cite">Peter =
Schmidtke<br></blockquote><blockquote =
type=3D"cite"><br></blockquote><blockquote =
type=3D"cite"><br></blockquote><blockquote =
type=3D"cite"><br></blockquote><blockquote =
type=3D"cite"><br></blockquote><blockquote type=3D"cite">On 12/11/2010 =
06:44 PM, Deepangi Pandit deepangi.pandit~!~gmail.com =
wrote:<br></blockquote><blockquote type=3D"cite"><blockquote =
type=3D"cite">Sent to CCL by: Deepangi Pandit =
[deepangi.pandit(!)gmail.com]<br></blockquote></blockquote><blockquote =
type=3D"cite"><blockquote type=3D"cite">Dear =
All:<br></blockquote></blockquote><blockquote type=3D"cite"><blockquote =
type=3D"cite">I tried to search literature and Internet to find a =
reliable method<br></blockquote></blockquote><blockquote =
type=3D"cite"><blockquote type=3D"cite">that I can use to identify =
protein-ligand binding site. I came =
across<br></blockquote></blockquote><blockquote type=3D"cite"><blockquote =
type=3D"cite">number of papers but I am unable to evaluate the methods =
before I<br></blockquote></blockquote><blockquote =
type=3D"cite"><blockquote type=3D"cite">start using them. I was also =
unable to find a review which =
compares<br></blockquote></blockquote><blockquote =
type=3D"cite"><blockquote type=3D"cite">the methods. It seems method can =
be broadly classified as =
"Geometry<br></blockquote></blockquote><blockquote =
type=3D"cite"><blockquote type=3D"cite">based" and "Energy Based". Could =
you please recommend from your =
own<br></blockquote></blockquote><blockquote type=3D"cite"><blockquote =
type=3D"cite">experience which method gives reasonable results. Also, =
feel free to<br></blockquote></blockquote><blockquote =
type=3D"cite"><blockquote type=3D"cite">share pros and cons of the =
method.<br></blockquote></blockquote><blockquote type=3D"cite"><blockquote=
 type=3D"cite"><br></blockquote></blockquote><blockquote =
type=3D"cite"><blockquote type=3D"cite">Thank =
you.<br></blockquote></blockquote><blockquote type=3D"cite"><blockquote =
type=3D"cite">Deepa<br></blockquote></blockquote><blockquote =
type=3D"cite"><blockquote =
type=3D"cite"><br></blockquote></blockquote><blockquote =
type=3D"cite"><blockquote type=3D"cite">List of methods I came =
across<br></blockquote></blockquote><blockquote type=3D"cite"><blockquote =
type=3D"cite"><br></blockquote></blockquote><blockquote =
type=3D"cite"><blockquote type=3D"cite">Q-Site =
Finder<br></blockquote></blockquote><blockquote type=3D"cite"><blockquote =
type=3D"cite"><a =
href=3D"http://www.bioinformatics.leeds.ac.uk/qsitefinder">http://www.bioi=
nformatics.leeds.ac.uk/qsitefinder</a><br></blockquote></blockquote><block=
quote type=3D"cite"><blockquote =
type=3D"cite"><br></blockquote></blockquote><blockquote =
type=3D"cite"><blockquote type=3D"cite">Surface triplet =
propensities<br></blockquote></blockquote><blockquote =
type=3D"cite"><blockquote type=3D"cite"><a =
href=3D"http://opus.bch.ed.ac.uk/stp">http://opus.bch.ed.ac.uk/stp</a><br>=
</blockquote></blockquote><blockquote type=3D"cite"><blockquote =
type=3D"cite"><br></blockquote></blockquote><blockquote =
type=3D"cite"><blockquote =
type=3D"cite">Screen<br></blockquote></blockquote><blockquote =
type=3D"cite"><blockquote type=3D"cite"><a =
href=3D"http://interface.bioc.columbia.edu/screen">http://interface.bioc.c=
olumbia.edu/screen</a>&gt;<br></blockquote></blockquote><blockquote =
type=3D"cite"><blockquote =
type=3D"cite"><br></blockquote></blockquote><blockquote =
type=3D"cite"><blockquote =
type=3D"cite"><br></blockquote></blockquote><blockquote =
type=3D"cite"><br></blockquote><blockquote =
type=3D"cite"><br></blockquote><blockquote =
type=3D"cite"><br></blockquote><blockquote type=3D"cite">-=3D This is =
automatically added to each message by the mailing script =
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te><blockquote type=3D"cite">Conferences: <a =
href=3D"http://server.ccl.net/chemistry/announcements/conferences/">http:/=
/server.ccl.net/chemistry/announcements/conferences/</a><br></blockquote><=
blockquote type=3D"cite"><br></blockquote><blockquote type=3D"cite">Search=
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type=3D"cite"><br></blockquote><blockquote type=3D"cite">If your mail =
bounces from CCL with 5.7.1 error, check:<br></blockquote><blockquote =
type=3D"cite">&nbsp; &nbsp; &nbsp;<a =
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type=3D"cite"><br></blockquote><blockquote =
type=3D"cite"><br></blockquote></div></blockquote></div><br><div>
<div><div>Peter =
Schmidtke</div><div><br></div><div>-----------------</div><div>PhD =
Student</div><div>Department of Physical Chemistry</div><div>School of =
Pharmacy</div><div>University of Barcelona</div><div>Barcelona, =
Spain</div></div>
</div>
<br></body></html>=

--Apple-Mail-2-330577573--


From owner-chemistry@ccl.net Sun Dec 12 12:10:00 2010
From: "Igor Filippov igor.v.filippov]=[gmail.com" <owner-chemistry]*[server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian Linux
Message-Id: <-43349-101212111758-4384-BcdEKFoDuHzNaMyqVsNQCg]*[server.ccl.net>
X-Original-From: Igor Filippov <igor.v.filippov _ gmail.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset="UTF-8"
Date: Sun, 12 Dec 2010 11:17:45 -0500
Mime-Version: 1.0


Sent to CCL by: Igor Filippov [igor.v.filippov|gmail.com]
The list of supported Linux/Unix versions:
http://gaussian.com/g09_plat.htm

For Linux the choice boils down to SUSE EL (9,10,11) or RHEL 5.
I would certainly recommend RHEL. Re: SUSE - remember that Novel just
got bought off and the future of SUSE seems to be uncertain.
Fedora is great if you know what you're doing, otherwise stay with the
Enterprise Linux versions. RHEL 4 is really quite old at this point, so
RHEL 5 is an obvious choice for me.

RHEL 5.2, 5.3, 5.4, and 5.5 is basically the same system with the more
recent patches installed so it doesn't really make sense to talk about
installing 5.2 vs. for example 5.5.

Regards,
Igor

On Sun, 2010-12-12 at 06:20 -0500, eurisco1%pochta.ru wrote:
> Dear Shirin Seifert,
>  
> I suggest you to install the OS that you know better or is known by
> the expert who works in your Department or Lab.
> Personally,  I would suggest to install OpenSuse (SuSE Linux 11.1
> 11.2). It is free and well behaved on different platforms.
> 
> Sincerely,
> Ol Ga
>  
>  
>  
>  
> From: Shirin Seifert shirin.seifert : gmail.com 
> Sent: Sunday, December 12, 2010 9:07 AM
> To: Ga, Ol 
> Subject: CCL:G: Gaussian Linux
>  
> Dear CCL'ers
> 
> Which of these Os'es do you recommend to install for Gaussian 09
> (64bit) ?  (The CPUs are Intel (R) Xeon(R))
> Thanks for your recommendations in advance:
> 1- SuSE Linux 9.3, 10.3, 11.1, 11.2;
> 2- Fedora 
> 3- Red Hat Enterprise Linux 5.2
> 4- Red Hat Enterprise Linux 4.7, 5.3, 5.4, 5.5;
> 5- SuSE Linux Enterprise Server 
> 9 and 10
> 
> Regards,
> SS
>


From owner-chemistry@ccl.net Sun Dec 12 12:45:00 2010
From: "Juan C. Drosos jdrosos{:}gmail.com" <owner-chemistry__server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian Linux
Message-Id: <-43350-101212115535-22424-QDHOPfQqNbsLbmWP3h0Bvw__server.ccl.net>
X-Original-From: "Juan C. Drosos" <jdrosos###gmail.com>
Content-Transfer-Encoding: 8bit
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Date: Sun, 12 Dec 2010 11:55:29 -0500
MIME-Version: 1.0


Sent to CCL by: "Juan C. Drosos" [jdrosos!A!gmail.com]
Dear Shirin
It depends on your hardware.
for xeon processors multicore and modern chipsets 5500 and up on
multiprocessor machines the best performance and stability combination
of your list is opensuse 11.x, better for the 2 or 3 =x.
On the other hand the latest redhat EL 6.0 looks very strong and updated.
We have observed an improve in velocity, changing from centos 5.5
x86_64 = Redhat 5.5 x86_64 to Opensuse 11.2 or 11.3, of about 40% to
50%.
of course the  best choice is to install and test performance and make
conclusions from your own experience.

Best Regards

Juan Drosos
Grupo de Quimica Cuantica y Teorica
Grupo de Quimica Bioorganica
Facultad de Ciencias Exactas y Naturales
Universidad de Cartagena.

On Sun, Dec 12, 2010 at 1:07 AM, Shirin Seifert shirin.seifert :
gmail.com <owner-chemistry_._ccl.net> wrote:
> Dear CCL'ers
>
> Which of these Os'es do you recommend to install for Gaussian 09 (64bit) ?
> (The CPUs are Intel (R) Xeon(R))
>  Thanks for your recommendations in advance:
> 1- SuSE Linux 9.3, 10.3, 11.1, 11.2;
> 2- Fedora
> 3- Red Hat Enterprise Linux 5.2
> 4- Red Hat Enterprise Linux 4.7, 5.3, 5.4, 5.5;
> 5- SuSE Linux Enterprise Server
> 9 and 10
>
> Regards,
> SS
>


From owner-chemistry@ccl.net Sun Dec 12 13:19:00 2010
From: "dipankar roy theodip- -gmail.com" <owner-chemistry#%#server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian Linux
Message-Id: <-43351-101212104738-6197-1NZwHioIRXlSkqcjZVBJMQ#%#server.ccl.net>
X-Original-From: dipankar roy <theodip ~ gmail.com>
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Date: Sun, 12 Dec 2010 10:47:31 -0500
MIME-Version: 1.0


Sent to CCL by: dipankar roy [theodip[a]gmail.com]
Hi,
For individual machines and running a cluster SUSE 11.2 is fine (it is
free too, but you may need to use a third party cluster management)

-Dipankar Roy

On Sun, Dec 12, 2010 at 1:07 AM, Shirin Seifert shirin.seifert :
gmail.com <owner-chemistry.#%#.ccl.net> wrote:
> Dear CCL'ers
>
> Which of these Os'es do you recommend to install for Gaussian 09 (64bit) ?
> (The CPUs are Intel (R) Xeon(R))
>  Thanks for your recommendations in advance:
> 1- SuSE Linux 9.3, 10.3, 11.1, 11.2;
> 2- Fedora
> 3- Red Hat Enterprise Linux 5.2
> 4- Red Hat Enterprise Linux 4.7, 5.3, 5.4, 5.5;
> 5- SuSE Linux Enterprise Server
> 9 and 10
>
> Regards,
> SS
>



-- 
-----------------------------------
Dr. Dipankar Roy
Research Associate
Hunter College (CUNY)
695 Park Avenue
New York, USA
NY-10065
-----------------------------------


From owner-chemistry@ccl.net Sun Dec 12 13:54:00 2010
From: "Ya-Huei Huang walilelale*o*gmail.com" <owner-chemistry###server.ccl.net>
To: CCL
Subject: CCL: The help from HELANAL program.
Message-Id: <-43352-101212092346-9431-+NLNov7xMQRw+RrYm/TwKA###server.ccl.net>
X-Original-From: "Ya-Huei  Huang" <walilelale]-[gmail.com>
Date: Sun, 12 Dec 2010 09:23:39 -0500


Sent to CCL by: "Ya-Huei  Huang" [walilelale,,gmail.com]
Dear CCLers,
 
I used HELANAL to analyze the helix from MD. 
It can give me bending angles between residues instead of the kinked angle as HELANAL's paper wrote.

Although the MC-HELAN program have helped me to calculate the kinked angle of the helix from MD, I still want to check it. Later I found the ProKink program and ProKink program can evaluate the angle.
Due to the failure of evaluation about the pre- and post-proline helix axis, I can not use ProKink to calculate the kinked angle out.
 
Fortunately, I found the reply between CCLers and Mireille Krier on internet.  
http://www.ccl.net/chemistry/resources/messages/2005/06/19.002-dir/index.html
Anyone can give me some suggestions?
 
Many thanks in advance to any help. :)
Thanks for reading.
Ya-Huei, Huang :)


From owner-chemistry@ccl.net Sun Dec 12 14:29:00 2010
From: "i.nick||mail.ru" <owner-chemistry*|*server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian Linux
Message-Id: <-43353-101212133751-26087-ixPLuTfP7E5FHLWRJsTFxQ*|*server.ccl.net>
X-Original-From: i.nick|a|mail.ru
Content-Transfer-Encoding: quoted-printable
Content-Type: text/html; charset=iso-8859-1
Date: Sun, 12 Dec 2010 21:37:27 +0300
MIME-Version: 1.0


Sent to CCL by: i.nick^mail.ru
<html><head><title>Re: CCL:G: Gaussian Linux</title>
<META http-equiv=3DContent-Type content=3D"text/html; charset=3Diso-8859-1">
</head>
<body>
<span style=3D" font-family:'Courier New'; font-size: 9pt;">I recommend you=
 to use virtual machine (like VirtualBox from Oracle) under any OS you know=
 enough (as for me it Windows))) , install any Linux there (I use ubuntu 10=
.10 as it seems more user friendly) and perform all your calculations under=
 this "guest" os. You may also create share &nbsp;folder the way it would b=
e visible under both systems. Also it prevents you from some problems in pa=
re Linux/Gaussview ;-)&nbsp;<br>
<br>
</span><table>
<tr>
<td width=3D10 bgcolor=3D #0000ff><br>
</td>
<td width=3D756><span style=3D" font-family:'courier new'; font-size: 9pt;"=
>Dear CCL'ers<br>
<br>
Which of these Os'es do you recommend to install for Gaussian 09 (64bit) ? =
&nbsp;(The CPUs are Intel (R) Xeon(R))<br>
&nbsp;Thanks for your recommendations in advance:<br>
1-&nbsp;<span style=3D" font-size: 8pt;">SuSE Linux 9.3, 10.3, 11.1, 11.2;<=
br>
2- Fedora&nbsp;<br>
3- Red Hat Enterprise Linux 5.2<br>
4- Red Hat Enterprise Linux 4.7, 5.3, 5.4, 5.5;<br>
5- SuSE Linux Enterprise Server&nbsp;<br>
9 and 10<br>
<br>
Regards,<br>
SS</td>
</tr>
</table>
<br><br>
<br>
<br>
<span style=3D" font-family:'arial'; color: #c0c0c0;"><i>--&nbsp;<br>
&#1057; &#1091;&#1074;&#1072;&#1078;&#1077;&#1085;&#1080;&#1077;&#1084;,<br>
&nbsp;i &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbs=
p; &nbsp; &nbsp; &nbsp;<a style=3D" font-style: normal;" href=3D"mailto:i.n=
ick###mail.ru">mailto:i.nick###mail.ru</a></body>


From owner-chemistry@ccl.net Sun Dec 12 15:04:00 2010
From: "Arun Kumar Subramanian aksub007,,gmail.com" <owner-chemistry/a\server.ccl.net>
To: CCL
Subject: CCL: Prediction & Identification of protein-ligand binding sites - CONTINUED.
Message-Id: <-43354-101212130414-25161-OY5BHCn8kkdRbyzhRUcRaA/a\server.ccl.net>
X-Original-From: Arun Kumar Subramanian <aksub007_+_gmail.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Sun, 12 Dec 2010 10:03:46 -0800
MIME-Version: 1.0


Sent to CCL by: Arun Kumar Subramanian [aksub007(!)gmail.com]
Hi all,

Once I have been spending time on a similar task, where I was
searching for drug binding site in a protein (for which we had the
apo- form crystal structure). We knew for sure that the drug was
binding, but didnt knew where it was binding. Upon reading a paper
that described the evaluation of drug binding sites on a wide variety
of crystal structures, I decided to do a few tests myself. My test set
included 5 protein structures of "Thioredoxin" motifs which had been
crystallized in both presence and absence of drug/peptide molecules.
What I found from those tests were:

1. The drug binding site prediction was right in most of the proteins
which looked like dimers/trimers with quite large gaps (where the drug
sat in).

2. The predictions were wrong when some amount of conformational
changes happened upon drug binding (even minor changes like loop
movements). This was obvious when I ran the prediction algorithm once
on the ligand unbound structure and once on the ligand bound protein
conformation (removing the ligand molecule manually). The top three
sites that it predicted in the latter were 100% bad (if I remember it
rightly).

3. The paper that I was using as a reference also pointed out a
possible bias, in which the algorithms detected bigger holes as the
first ranked site. In some cases, the bigger holes were not the real
binding site and hence the second rank sites turned out to be the drug
binding site in reality (this was observed atleast for 1 protein).

Based on these points, I guess one have to be more intutive and
careful in concluding things from running these algorithms with
default settings. On the other hand, treatment of protein flexibility
is always a pain in the neck at the moment. You dont want to go for
long time molecular dynamics (even if you opt for it, there is no
guarantee that you might achieve what you wanted).

Please forward your comments and experiences, if any.

Thanks.

ArunKumar. S.





On Sun, Dec 12, 2010 at 7:53 AM, Deepangi Pandit
deepangi.pandit++gmail.com <owner-chemistry/./ccl.net> wrote:
>
> Sent to CCL by: Deepangi Pandit [deepangi.pandit|,|gmail.com]
> Thank you Peter, for your detailed reply. I would just like to clarify
> my case based on your questions.
>
>> 1 : Do you want to apply this method on a database of proteins or just a few structures?
>
> I am looking at just a few structures to identify the putative drug
> binding site. I have PDB files of protein structures (of course,
> without the compound) and have experimental data which suggests the
> compound is binding but do not know where.
>
>> 2 : Do you want to identify putative drug binding sites or whatever binding site a method could find (general purpose pocket prediction)
>
> I am trying to identify the putative drug binding sites not general
> purpose pocket prediction
>
>
>> 3 : Do you want to find conserved pockets among homologs?
>
> This is not my primary goal.
>
> Best,
> Deepa
>
> On Sat, Dec 11, 2010 at 4:45 PM, Peter Schmidtke
> pschmidtke[-]mmb.pcb.ub.es <owner-chemistry|-|ccl.net> wrote:
>>
>> Sent to CCL by: Peter Schmidtke [pschmidtke[*]mmb.pcb.ub.es]
>> Dear Deepangi,
>>
>> protein-ligand binding site detection is a very active field and there
>> is a large variety of methods out there.
>> Since the publication of PocketPicker
>> (http://www.journal.chemistrycentral.com/content/1/1/7/abstract/) lots
>> of newer methods used the comparative table that was published with
>> PocketPicker (table 2). A very recent example is the paper by Andrea
>> Volkamer, where you have an update of this table with a few more recent
>> methods (http://pubs.acs.org/doi/full/10.1021/ci100241y).
>>
>> This comparison is definitely arguable, but at least it gives some hint
>> on general pocket prediction performance. In order to find the perfect
>> method for your purpose you should maybe clarify what is the
>> functionality your are seeking. There are lots of webservers out there,
>> methods you have to pay and also free methods.
>>
>> Some questions that could influence your choice :
>>
>> 1 : Do you want to apply this method on a database of proteins or just a
>> few structures?
>> 2 : Do you want to identify putative drug binding sites or whatever
>> binding site a method could find (general purpose pocket prediction)
>> 3 : Do you want to find conserved pockets among homologs?
>>
>> Concerning question 1, if you just need a method for a few structures
>> you can go for slower programs (mostly energy based algorithms) like
>> SiteMap from Schrödinger (but you need a license) Q-SiteFinder or
>> PocketPicker or Vice (I think it's sold by Tripos) There are surely more
>> than that.
>> If you need to process a large number of structures, considering
>> geometry based methods might become an interesting choice. Choices could
>> be Ligsite, fpocket, PASS, SiteFinder (included in MOE by CCG) ...
>>
>> Regarding question 2. Pocket prediction is not equal drug binding site
>> prediction. Recent druggability prediction methods have been published
>> and some scores are available ready for use in SiteMap (I don't know if
>> you still have to calculate it or if they finally included it into the
>> SiteMap distribution) and fpocket. I suspect also QSiteFinder might give
>> indications on druggability (I extrapolate from the methodology I just
>> read very quickly, so maybe I'm wrong here ;) ).
>>
>> Regarding question 3, I think ligsite csc can help there
>> (http://projects.biotec.tu-dresden.de/pocket/), or else hpocket, which
>> is part of the fpocket webserver :
>> http://bioserv.rpbs.univ-paris-diderot.fr/fpocket/
>>
>> I hope that this gives you at least a direction, there are really lots
>> of methods and it is indeed not easy to know which one to use ;)
>>
>> Ah, I nearly forgot, metapocket2.0 is a sort of consensus pocket
>> prediction method that makes use of LIGSITEcsc, PASS, Q-SiteFinder,
>> SURFNET, Fpocket, GHECOM and ConCavity. This has again advantages and
>> disadvantages, but well, at least you know that it exists ;)
>>
>> Good luck.
>>
>> Peter Schmidtke
>>
>>
>>
>>
>> On 12/11/2010 06:44 PM, Deepangi Pandit deepangi.pandit~!~gmail.com wrote:
>>> Sent to CCL by: Deepangi Pandit [deepangi.pandit(!)gmail.com]
>>> Dear All:
>>> I tried to search literature and Internet to find a reliable method
>>> that I can use to identify protein-ligand binding site. I came across
>>> number of papers but I am unable to evaluate the methods before I
>>> start using them. I was also unable to find a review which compares
>>> the methods. It seems method can be broadly classified as "Geometry
>>> based" and "Energy Based". Could you please recommend from your own
>>> experience which method gives reasonable results. Also, feel free to
>>> share pros and cons of the method.
>>>
>>> Thank you.
>>> Deepa
>>>
>>> List of methods I came across
>>>
>>> Q-Site Finder
>>> http://www.bioinformatics.leeds.ac.uk/qsitefinder
>>>
>>> Surface triplet propensities
>>> http://opus.bch.ed.ac.uk/stp
>>>
>>> Screen
>>> http://interface.bioc.columbia.edu/screen>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt>
>
>