From owner-chemistry@ccl.net Sun Jan 10 09:58:00 2010
From: "amirhossein taghavi taghavi.amirhossein_-_gmail.com" <owner-chemistry[-]server.ccl.net>
To: CCL
Subject: CCL: Books or Links where i can concepts of Homology modeling and Threading
Message-Id: <-41019-100109083132-29169-IAgnd2A2Q0yBfuQHGnanKQ[-]server.ccl.net>
X-Original-From: amirhossein taghavi <taghavi.amirhossein++gmail.com>
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Sent to CCL by: amirhossein taghavi [taghavi.amirhossein.[].gmail.com]

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Hi,
I think for HM and blast search Bioinformatics books could help;

Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins 2nd
Edition (Methods of Biochemical Analysis)
*by:* Andreas D. Baxevanis, B. F. Francis Ouellette

Structural Bioinformatics (Methods of Biochemical Analysis, V. 44)
*by:* Philip E. Bourne

for energy minimization you can either use MD packages like AMBER or CHARMM
or simply use servers which do both structural search and EM.

good lucks


On Fri, Jan 8, 2010 at 8:41 PM, rocky walden rocky.walden19:-:gmail.com <
owner-chemistry[]ccl.net> wrote:

> Dear People,
>   I am interested in learning Homology modeling techniques, how to predict
> secondary structure,loop prediction,energy minimizations of proteins, Blast
> search techniques,HHMM models etc.,
> I request all users please you can suggest me some really good books if
> posible form beginners to advanced.
>
> Your help is invaluable.
>
> Thanks
> Rocky
>

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Hi,<br>I think for HM and blast search Bioinformatics books could help;<br>=
<br>Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins=
 2nd Edition (Methods of Biochemical Analysis)
		<br>
		<strong>by:</strong>=A0Andreas D. Baxevanis, B. F. Francis Ouellette
		<br><br>Structural Bioinformatics (Methods of Biochemical Analysis, V. 44=
)
		<br>
		<strong>by:</strong>=A0Philip E.  Bourne<br><br>for energy minimization y=
ou can either use MD packages like AMBER or CHARMM or simply use servers wh=
ich do both structural search and EM.<br><br>good lucks<br><br><br><div cla=
ss=3D"gmail_quote">
On Fri, Jan 8, 2010 at 8:41 PM, rocky walden rocky.walden19:-:<a href=3D"ht=
tp://gmail.com">gmail.com</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner=
-chemistry[]ccl.net">owner-chemistry[]ccl.net</a>&gt;</span> wrote:<br><block=
quote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, 204, 2=
04); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear People,<br>=A0 I am interested in learning Homology modeling technique=
s, how to predict secondary structure,loop prediction,energy minimizations =
of proteins, Blast search techniques,HHMM models etc.,<br>I request all use=
rs please you can suggest me some really good books if posible form beginne=
rs to advanced.<br>

<br>Your help is invaluable.<br><br>Thanks<br>Rocky<br>
</blockquote></div><br>

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From owner-chemistry@ccl.net Sun Jan 10 18:41:01 2010
From: "Dave A Winkler dave.winkler- -csiro.au" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL: 'Send it' for 100108225657-10066 produced error - please send it
Message-Id: <-41020-100110181633-14198-v6xXTkHzr5CdUy2eDZ1Kiw^server.ccl.net>
X-Original-From: "Dave A Winkler" <dave.winkler(_)csiro.au>
Date: Sun, 10 Jan 2010 18:16:29 -0500


Sent to CCL by: "Dave A Winkler" [dave.winkler[-]csiro.au]
Send it' for 100108225657-10066 produced error - please send it


From owner-chemistry@ccl.net Sun Jan 10 19:15:00 2010
From: "Dave.Winkler(-)csiro.au" <owner-chemistry(_)server.ccl.net>
To: CCL
Subject: CCL: Criteria for selecting if ligand activities and structures are enough diverse for building a 3D-QSAR model
Message-Id: <-41021-100108225657-10066-S1sQQce0T8Zp8BRk/PXGFg(_)server.ccl.net>
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Sent to CCL by: [Dave.Winkler(0)csiro.au]

This is a hard question to answer.  The domain of applicability of your mod=
el is clearly dependent on the chemical diversity of your training set. You=
 can get good models with diverse sets, and with much lower diversity.  The=
 ability to predict outside of the domain is clearly different for each cas=
e.  A rule of thumb is that you need at least 1-2 log variation in your bio=
logical response variable, at least 15-20 molecules in your data set.  Thes=
e are the bare minimum for which models have been successfully built, but a=
re far from ideal.  A better set would have 40-100 molecules and 2-3 log va=
riation in response variable.=20

I hope this helps - others may want to comment on these 'rules of thumb'

Prof. Dave Winkler
Senior Principal Research Scientist
Biomaterials & Regenerative Medicine
CSIRO Molecular & Health Technologies
Clayton 3168, Australia
________________________________________
> From: owner-chemistry+dave.winkler=3D=3Dcsiro.au ~ ccl.net [owner-chemistry+d=
ave.winkler=3D=3Dcsiro.au ~ ccl.net] On Behalf Of Gerard Pujadas gerard.pujad=
as(a)gmail.com [owner-chemistry ~ ccl.net]
Sent: Friday, 8 January 2010 10:41 PM
To: Winkler, Dave (CMHT, Clayton)
Subject: CCL: Criteria for selecting if ligand activities and structures ar=
e enough diverse for building a 3D-QSAR model

Dear CCL subscribers,

I wonder if there is any bibliographic reference (review, book chapter, etc=
.) where I can find which are the minimum requirements of ligand diversity =
in activity and structure for building predictive 3D-QSAR models. In other =
words, before starting to build a 3D-QSAR model (for instance, with Catalys=
t or Phase) for a set of related molecules (developed during the same SAR s=
tudy), I would like to know which criteria I have to use to know if I have =
enough diversity:

(a) in ligand activities
(b) in ligand structures

to derive predictive 3D-QSAR models.

Any help would be highly appreciated

With many thanks in advances for your help

Yours sincerely

Gerard

--
Gerard Pujadas
http://bioquimica.urv.cat/eng/fitxa.jsp?id=3D22
Nutrigenomics Research Group
Biochemistry and Biotechnology Department
Universitat Rovira i Virgili
Tarragona, Catalonia


From owner-chemistry@ccl.net Sun Jan 10 21:54:00 2010
From: "jaleel uc a jaleel.uc|gmail.com" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL: melting points of coordination compounds
Message-Id: <-41022-100110203552-14934-TlvjoS31L143hi97Y8/JiA,+,server.ccl.net>
X-Original-From: "jaleel uc a" <jaleel.uc(a)gmail.com>
Date: Sun, 10 Jan 2010 20:35:48 -0500


Sent to CCL by: "jaleel uc a" [jaleel.uc[A]gmail.com]
sir 
 
Please  suggest me a  database of  retrieving the properties of coordination compounds 

-- 
Dr U.C.A.Jaleel.
lecturer in cheminformatics 
Malabar christian college 
calicut


From owner-chemistry@ccl.net Sun Jan 10 22:28:00 2010
From: "Matthew Clark mclark:+:pharmatrope.com" <owner-chemistry!^!server.ccl.net>
To: CCL
Subject: CCL: Criteria for selecting if ligand activities and structures are enough diverse for building a 3D-QSAR model
Message-Id: <-41023-100110215517-26275-/skAWjy8bnoM1S8PLeKpsw!^!server.ccl.net>
X-Original-From: Matthew Clark <mclark(0)pharmatrope.com>
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Date: Sun, 10 Jan 2010 21:22:33 -0500
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Sent to CCL by: Matthew Clark [mclark:-:pharmatrope.com]

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While one to two log units may be the minimum, it is difficult to make
predictive models with low variance of the dependent variable.  The r2
is related to both the error of prediction and not the range, but the
*standard deviation* of the dependent variable in the training set.  So
it is important that not only the range be good, but that the standard
deviation is also large for the dependent variable. That is, that they
are evenly distributed across the range.

Matthew Clark


________________________________________________________________________



Matthew Clark, Ph. D.
CIO Pharmatrope Ltd
610 772 4652
mclark[-]pharmatrope.com

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While one to two log units may be the minimum, it is difficult to make predictive models with low variance of the dependent variable.&nbsp; The r2 is related to both the error of prediction and not the range, but the *standard deviation* of the dependent variable in the training set.&nbsp; So it is important that not only the range be good, but that the standard deviation is also large for the dependent variable. That is, that they are evenly distributed across the range.<BR>
<BR>
Matthew Clark<BR>
<BR>
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<FONT SIZE="4">Matthew Clark, Ph. D.</FONT><BR>
CIO <A HREF="http://pharmatrope.com">Pharmatrope Ltd</A><BR>
610 772 4652<BR>
<A HREF="mailto:mclark[-]Pharmatrope.com">mclark[-]pharmatrope.com</A>
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