From owner-chemistry@ccl.net Sat Feb 22 00:34:00 2014 From: "Rajarshi Guha guhar~~mail.nih.gov" To: CCL Subject: CCL: Oncologic chemo drug side effect prediction Message-Id: <-49787-140222002424-14076-o6Y1whVmStzdq48kZPZMlA^^server.ccl.net> X-Original-From: Rajarshi Guha Content-Type: multipart/alternative; boundary=001a11c1da06ac4dbb04f2f7dfae Date: Sat, 22 Feb 2014 00:18:50 -0500 MIME-Version: 1.0 Sent to CCL by: Rajarshi Guha [guhar:mail.nih.gov] --001a11c1da06ac4dbb04f2f7dfae Content-Type: text/plain; charset=ISO-8859-1 This is fundamentally an off-target prediction problem (or alternatively, partitioning polypharmacological behavior between intended- and side-effects). A somewhat older overview is http://genomebiology.com/2009/10/9/238 whereas more methodologically oriented papers include Schieber et al 2009 http://pubs.acs.org/doi/abs/10.1021/ci800344p Pauwels et al 2011 http://www.biomedcentral.com/1471-2105/12/169 Yamanishi et al 2012 http://pubs.acs.org/doi/full/10.1021/ci2005548 Lounkine et al 2012 http://www.nature.com/nature/journal/v486/n7403/full/nature11159.html On Fri, Feb 21, 2014 at 5:50 PM, Jim Kress ccl_nospam-*-kressworks.com < owner-chemistry(0)ccl.net> wrote: > Is there a published overview of computational tools or methods that can > be used for the prediction of chemo drug side effects? If so, would > someone please provide me with a reference? > > > > Thanks. > > > > Jim Kress > > > -- Rajarshi Guha | http://blog.rguha.net NIH Center for Advancing Translational Science --001a11c1da06ac4dbb04f2f7dfae Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
This is fundamentally an off-target prediction problem (or= alternatively, partitioning polypharmacological behavior between intended-= and side-effects). A somewhat older overview is=A0

http://genomebiology.com/200= 9/10/9/238

whereas more methodologically oriented papers inc= lude

Schieber et al 2009 =A0http://pubs.acs.org/doi/abs/10.1021/ci8= 00344p
Pauwels et al 2011=A0http://www.biomedcentral.com/1471-2105/12/169
<= div>Yamanishi et al 2012 http://pubs.acs.org/doi/full/10.1021/ci2005548
Lounkine et al 2012 http://www.nature.com/nature/journal/= v486/n7403/full/nature11159.html





On Fri, Feb 21, 2014 at 5:50 PM, Jim Kress ccl_nospam-*-kressworks.com <owner-chemistry(0)ccl.net>= ; wrote:

Is there a published overview of c= omputational tools or methods that can be used for the prediction of chemo = drug side effects?=A0 If so, would someone please provide me with a referen= ce?

=A0

Thanks.<= span class=3D"HOEnZb"><= /p>

=A0

Jim Kress

=A0




--
Rajarshi Guha |=A0http://blog.rguha.net
NIH Center for Advancing Translational Science
--001a11c1da06ac4dbb04f2f7dfae-- From owner-chemistry@ccl.net Sat Feb 22 01:54:00 2014 From: "Mohammed Khaled Tumbi khaledtumbi^_^gmail.com" To: CCL Subject: CCL: Oncologic chemo drug side effect prediction Message-Id: <-49788-140222014706-30645-3QStjJbQOz83MthAqNW8yg:+:server.ccl.net> X-Original-From: Mohammed Khaled Tumbi Content-Type: multipart/alternative; boundary=f46d0444e81fe8cdea04f2f91a1f Date: Sat, 22 Feb 2014 12:16:39 +0530 MIME-Version: 1.0 Sent to CCL by: Mohammed Khaled Tumbi [khaledtumbi() gmail.com] --f46d0444e81fe8cdea04f2f91a1f Content-Type: text/plain; charset=ISO-8859-1 Dear Jim: Side and or adverse effects of a Drug/Lead molecule can be predicted by quantifying it's potential to interact with unexpected proteins (so called off-targets). This potential can be determined by plethora of methodology like: *1) Binding site similarity approach or protein based*: In which we the proteins with similar binding site (like almost same chemical environment) are searched throughout the human proteome. Than, interaction of the said molecule with these short-listed targets can be established using computational (reverse docking, MD, etc.) and *in vitro* binding assays. *Case Study 1: **" **Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors" : **This is consider as one of the benchmark study in off-target identification. (--Personal View--) * *Case study 2:* You can find a case study of Nelfinavir here . (http://goo.gl/dXrwsb). *2)* *Ligand Based approaches*: In this case, similarity of molecule under consideration is determined with available drug molecules. Targets of most hits will be explored in the same manner as in above case. Selected *3) Chemogenomic approaches: * In this case both of the above methodologies are exploited at a time. Selected Literature : 1) * http://goo.gl/YjMtEc ** (* * ***recommended)* 2) http://goo.gl/4jRXe7 3) http://goo.gl/gzdVar *Personal Experience: * It is very useful if all the methods are exploited, we in our lab able to fish some of the important off-target of an anti-cancer molecule under clinical trial (Unpublished-Data). *=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=* *Tumbi Mohammed Khaled Abdul Waheed ,* Research Scholar, Department Of Pharmacoinformatics, NIPER, S.A.S. Nagar, Mohali, Punjab, India. Mob. +91 78145 24855 www.niper.ac.in My Blog: http://pin4matics.wordpress.com On Sat, Feb 22, 2014 at 10:10 AM, RICHARD WOOD rwoodphd,+,msn.com < owner-chemistry ~ ccl.net> wrote: > i was asked once why I wanted to compute this type of thing. > > Richard > > ------------------------------ > From: owner-chemistry{}ccl.net > To: rwoodphd{}msn.com > Subject: CCL: Oncologic chemo drug side effect prediction > Date: Fri, 21 Feb 2014 17:50:29 -0500 > > > Is there a published overview of computational tools or methods that can > be used for the prediction of chemo drug side effects? If so, would > someone please provide me with a reference? > > > > Thanks. > > > > Jim Kress > > > --f46d0444e81fe8cdea04f2f91a1f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Jim:
Side and or adverse effects of a Drug/Lead molecule c= an be predicted by quantifying it's potential to interact with unexpected= proteins (so called off-targets).
This po= tential can be determined by plethora of methodology like:

1) Binding site similarity approach or protein based: In which= we the proteins with similar binding site (like almost same chemical=A0env= ironment) are searched throughout the human=A0proteome. Than, interaction o= f the said molecule with these=A0short-listed=A0targets can be=A0establishe= d=A0using computational (reverse docking, MD, etc.) and in vitro=A0b= inding assays.=A0
Case Study 1: "Drug Discovery = Using Chemical Systems Biology: Identification of the Protein-Ligand Bindin= g Network To Explain the Side Effects of CETP Inhibitors": = This is consider as one= of the=A0benchmark=A0study in off-target identification. (--Personal View-= -)=A0
Case study 2:=A0You can find a case study of Nelfinavir=A0= here= =A0.=A0(http://goo.gl/dXrwsb).
2) Liga= nd Based=A0approaches:= In this case, similarity of molecule under consideration is=A0determined= =A0with=A0available=A0drug=A0molecules.=A0Targets of most hits will be expl= ored in the same manner as in above case.
Selected


=
3) Chemog= enomic=A0approaches:=A0=A0In this case both of the above methodologies are exploited at a = time.=A0
Selected=A0
Literature
:=A0
=
1)=A0
http://goo.gl/YjMtEc (
*
recommended)
= Personal Experience:=A0=
It is very useful if all the methods are exploited, we in our = lab able to fish some of the important off-target of an anti-cancer molecul= e under clinical trial (Unpublished-Data). =A0


= =3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-= =3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D
Tumbi Mohammed Khaled Abdul Waheed,
Research Scholar,
Department Of Pharmacoinformatics,
NIPER, S.A.S. Na= gar, Mohali,
Punjab, India. Mob. +91 78145 24855
www.niper.ac.in My Blog: htt= p://pin4matics.wordpress.com
=A0


On Sat, Feb 22, 2014 at 10:10 AM, RICHAR= D WOOD rwoodphd,+,msn.com = <owner-chemistry ~ ccl.net> wrote:
i was asked once why I wanted to compute this type of= thing.

Richard

From: owner-chemistry{}ccl.net
To: rwoodphd{}msn.com
Subject: CCL: Oncologic chemo drug side effect prediction
Date: Fri, 21 = Feb 2014 17:50:29 -0500


Is there a published overview o= f computational tools or methods that can be used for the prediction of che= mo drug side effects?=A0 If so, would someone please provide me with a refe= rence?

=A0

Thanks.

=A0

Jim Kress

=A0

=

--f46d0444e81fe8cdea04f2f91a1f-- From owner-chemistry@ccl.net Sat Feb 22 15:43:00 2014 From: "Jim Kress ccl_nospam=-=kressworks.com" To: CCL Subject: CCL: Oncologic chemo drug side effect prediction Message-Id: <-49789-140222130947-27099-r6xiknkCUhEj704ol+uRNA_+_server.ccl.net> X-Original-From: "Jim Kress" Date: Sat, 22 Feb 2014 13:09:46 -0500 Sent to CCL by: "Jim Kress" [ccl_nospam!^!kressworks.com] Too bad they didn't ask the person in excruciating pain who was experiencing the dry heaves just after their most recent chemo treatment. Perhaps then, they would have understood. Jim > "RICHARD WOOD rwoodphd,+,msn.com" wrote: > > Sent to CCL by: RICHARD WOOD [rwoodphd|*|msn.com] > --_3104aaff-b15f-4e5d-95df-83b5baf93e89_ > Content-Type: text/plain; charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > i was asked once why I wanted to compute this type of thing. > > Richard > > > From: owner-chemistry-.-ccl.net > To: rwoodphd-.-msn.com > Subject: CCL: Oncologic chemo drug side effect prediction > Date: Fri=2C 21 Feb 2014 17:50:29 -0500 > > Is there a published overview of computational tools or methods that can be= > used for the prediction of chemo drug side effects? If so=2C would someon= > e please provide me with a reference? Thanks. Jim Kress = > > --_3104aaff-b15f-4e5d-95df-83b5baf93e89_ > Content-Type: text/html; charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > > > >
i was asked once why I wanted to= > compute this type of thing.

Richard

From:=3B owner-ch= > emistry-.-ccl.net
To:=3B rwoodphd-.-msn.com
Subject:=3B CCL:=3B = > Oncologic chemo drug side effect prediction
Date:=3B Fri=2C 21 Feb 20= > 14 17:=3B50:=3B29 -0500

Is there a = > published overview of computational tools or methods that can be used for t= > he prediction of chemo drug side effects? =3B If so=2C would someone pl= > ease provide me with a reference?

 =3B

class=3DecxMsoNormal>Thanks.

 =3B

ss=3DecxMsoNormal>Jim Kress

 =3B

= >
> = > > --_3104aaff-b15f-4e5d-95df-83b5baf93e89_-- > > From owner-chemistry@ccl.net Sat Feb 22 16:51:00 2014 From: "Reza Shojaei shojaei81**gmail.com" To: CCL Subject: CCL: Electrochromism Message-Id: <-49790-140222164959-20990-2t+iDqin8OgH0ZX0HMBKAQ*|*server.ccl.net> X-Original-From: "Reza Shojaei" Date: Sat, 22 Feb 2014 16:49:58 -0500 Sent to CCL by: "Reza Shojaei" [shojaei81]*[gmail.com] Dear CCL users, Does someone have computational experience on electrochromism? which softwares can be used to calculate the optical properties of electrochromic materials? From owner-chemistry@ccl.net Sat Feb 22 17:25:00 2014 From: "Robert Molt r.molt.chemical.physics{=}gmail.com" To: CCL Subject: CCL: Electrochromism Message-Id: <-49791-140222170808-32221-GEzJXpDSCY/dFNXFoxBv+A/a\server.ccl.net> X-Original-From: Robert Molt Content-Transfer-Encoding: 7bit Content-Type: multipart/alternative; boundary=Apple-Mail-A27D0A94-D500-4B86-BBF2-A6D814A18B40 Date: Sat, 22 Feb 2014 17:07:54 -0500 Mime-Version: 1.0 (1.0) Sent to CCL by: Robert Molt [r.molt.chemical.physics/./gmail.com] --Apple-Mail-A27D0A94-D500-4B86-BBF2-A6D814A18B40 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: quoted-printable Which optical properties? In bulk? Dr. Robert Molt Jr. r.molt.chemical.physics(~)gmail.com Nigel Richards Research Group Department of Chemistry & Chemical Biology Indiana University-Purdue University Indianapolis LD 326 402 N. Blackford St. Indianapolis, IN 46202 > On Feb 22, 2014, at 4:49 PM, "Reza Shojaei shojaei81**gmail.com" wrote: >=20 >=20 > Sent to CCL by: "Reza Shojaei" [shojaei81]*[gmail.com] > Dear CCL users, >=20 > Does someone have computational experience on electrochromism? which softw= ares can be used to calculate the optical properties of electrochromic mater= ials? >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script =3D= ->=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20>=20>=20>=20>=20 >=20 --Apple-Mail-A27D0A94-D500-4B86-BBF2-A6D814A18B40 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Which optical properties? In bulk?
=
Dr. Robe= rt Molt Jr.
r.molt.chemical.physics(~)gmail.com
Nigel Ri= chards Research Group
Department of Chemistry & Chemical Biology=
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackfor= d St.
Indianapolis, IN 46202


On Feb 22, 2014, at 4:49 PM, "Reza Shojaei shojaei81**gmail.com" <o= wner-chemistry(~)ccl.net> wrote:


Sent to CCL by: "Reza  Shojaei" [shojaei81= ]*[gmail.com]
Dear CCL user= s,

Does someone have computational experien= ce on electrochromism? which softwares can be used to calculate the optical p= roperties of electrochromic materials?



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