Begin forwarded message:

From: Ram Samudrala <ram@compbio.washington.edu> Subject: recruitment letter... Date: February 21, 2013 4:31:36 PM PST To: sali@salilab.org Reply-To: ram@compbio.washington.edu

Hi Andrej, I hope you are well. I am wondering if you could forward this email around to your local CompBio groups? Thanks.

--Ram

Postdoctoral opportunity in Translational Research Project at the Samudrala Group in University of Washington, Seattle

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The Samudrala group at the University of Washington in Seattle is seeking to recruit 2-3 postdoctoral fellows to work on the Computational Analysis of Noval Drug Opportunities (CANDO) drug discovery project funded by a 2012 NIH Director's Pioneer Award (http://cando.compbio.washington.edu). The project goals are to screen all human ingestible compounds against all proteins (primarily solved protein structures) computationally to identify new uses for existing drug compounds. Computational hits/leads are verified in vitro quickly followed by clinical studies (since all compounds studied initially are FDA approved drugs) for more than 30 indications with the aid of numerous collaborations.

The project has just begin its 3rd year, and an initial version of the compound-protein matrix covering several thousand drugs (mostly FDA approved drugs) vs. ~40,000 protein structures has been completed. Bench studies are underway for two of the initial indications we are going after (beta thalessemia major and multi-drug resistant tuberculosis) and numerous other bench studies are soon to follow. This is based on the multitargeting idea of how one compound (or more) interacts with multiple proteins (all structures and homologues) in a given system to produce a desired outcome (which is how it happens in nature). More importantly, anything we find can be directly evaluated by quick clinical study to demonstrate efficacy since everything we'll initially focus on would've made it clinical trials or through phase 2 testing at least.

We are looking for individuals with the passion and skill set to help us complete and deploy the pipeline for maximal benefit. Particularly we are interested in a pipeline developer who would ideally be an expert on machine learning techniques that will help integrate the chem- and bioinformatic data with docking simulations, i.e., create a more robust and automated pipeline that is adaptable to individual indications and genotypes. We are also interested in a docking code developer that will help implement the third version of the fragment-based docking with dynamics protocol we have developed and integrate the pipeline and docking methodology as a systems-based drug discovery product. Another role which is part of the developer job description is to work on a web application that can handle personalisation and integrate it with our in-house cando database API. This will finally give one-stop-shop-software to find putative drugs for a particular indication of interest done using all the proteins of the related organisms. So the final output of our methodology is a drug-disease network which is linked back to protein-compounds network, i.e. an atomistic description of all existing and new drug prediction we are making.

Gaurav Chopra, one of my postdocs and the overall project manager of CANDO, will be attending CASP10 and is the person who you'd closely work with should you accept this position. So please talk to him and if you're interested in this position, and if you feel the project is a good fit for you, send us both your CV and a brief statement of interest to gaurav@compbio.washington.edu and ram@compbio.washington.edu

--

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--20cf306f722a5dcabe04d6442e13 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

<font color=3D"#000000"><font><font face=3D"arial,helvetica,sans-serif">Hi = George,</font></font></font><div><font color=3D"#000000"><font><font face= =3D"arial,helvetica,sans-serif"><br></font></font></font></div><div><font c= olor=3D"#000000"><font><font face=3D"arial,helvetica,sans-serif">Here is th= e email we sent out for CASP when I met people there. Please change as need= ed and spread the word for recruiting two postdocs!</font></font></font></d= iv>

<div><font color=3D"#000000"><font><font face=3D"arial,helvetica,sans-serif= "><br></font></font></font></div><div><font color=3D"#000000"><font><font f= ace=3D"arial,helvetica,sans-serif">Thanks,</font></font></font></div><div><= font color=3D"#000000"><font><font face=3D"arial,helvetica,sans-serif">Gaur= av</font></font></font></div>

<div><font color=3D"#000000"><font><font face=3D"arial,helvetica,sans-serif= "><br></font></font></font></div><div><font class=3D"Apple-style-span" face= =3D"arial, helvetica, sans-serif">--</font></div><div><font class=3D"Apple-= style-span" face=3D"arial, helvetica, sans-serif"><span class=3D"Apple-styl= e-span" style=3D"border-collapse:collapse;color:rgb(34,34,34);font-family:a= rial,sans-serif;font-size:13px"><br>

Postdoctoral opportunity in Translational Research Project at the Samudrala= Group in University of Washington, Seattle<br><br>--<br><br>The Samudrala = group at the University of Washington in Seattle is<br>seeking to recruit 2= -3 postdoctoral fellows to work on the<br>

Computational Analysis of Noval Drug Opportunities (CANDO) drug<br>discover= y project funded by a 2012 NIH Director's Pioneer Award<br>(<a href=3D"= http://cando.compbio.washington.edu/" target=3D"_blank" style=3D"color:rgb(= 17,85,204)">http://cando.compbio.washington.edu</a>). The project goals are= to screen<br>

all human ingestible compounds against all proteins (primarily solved<br>pr= otein structures) computationally to identify new uses for existing<br>drug= compounds. Computational hits/leads are verified in vitro quickly<br> followed by clinical studies (since all compounds studied initially<br> are FDA approved drugs) for more than 30 indications with the aid of<br>num= erous collaborations.<br><br>The project has just begin its 3rd year, and a= n initial version of the<br>compound-protein matrix covering several thousa= nd drugs (mostly FDA<br>

approved drugs) vs. ~40,000 protein structures has been<br>completed. Bench= studies are underway for two of the initial<br>indications we are going af= ter (beta thalessemia major and multi-drug<br>resistant tuberculosis) and n= umerous other bench studies are soon to<br>

follow. =A0This is based on the multitargeting idea of how one compound<br>= (or more) interacts with multiple proteins (all structures and<br>homologue= s) in a given system to produce a desired outcome (which is<br>how it happe= ns in nature). More importantly, anything we find can be<br>

directly evaluated by quick clinical study to demonstrate efficacy<br>since= everything we'll initially focus on would've made it clinical<br>t= rials or through phase 2 testing at least.<br><br>We are looking for indivi= duals with the passion and skill set to help<br>

us complete and deploy the pipeline for maximal benefit. Particularly<br>we= are interested in a pipeline developer who would ideally be an<br>expert o= n machine learning techniques that will help integrate the<br>chem- and bio= informatic data with docking simulations, i.e., create a<br>

more robust and automated pipeline that is adaptable to individual<br>indic= ations and genotypes. We are also interested in a docking code<br>developer= that will help implement the third version of the<br>fragment-based dockin= g with dynamics protocol we have developed and<br>

integrate the pipeline and docking methodology as a systems-based drug<br>d= iscovery product. Another role which is part of the developer job<br>descri= ption is to work on a web application that can handle<br>personalisation an= d integrate it with our in-house cando database<br>

API. This will finally give one-stop-shop-software to find putative<br>drug= s for a particular indication of interest done using all the<br>proteins of= the related organisms. So the final output of our<br>methodology is a drug= -disease network which is linked back to<br>

protein-compounds network, i.e. an atomistic description of all<br>existing= and new drug prediction we are making.<br><br>Gaurav Chopra, one of my pos= tdocs and the overall project manager of<br>CANDO, will be attending CASP10= and is the person who you'd closely<br>

work with should you accept this position. So please talk to him and<br>if = you're interested in this position, and if you feel the project is<br>a= good fit for you, send us both your CV and a brief statement of<br>interes= t to=A0<a href=3D"mailto:gaurav@compbio.washington.edu" style=3D"color:rgb(= 17,85,204)">gaurav@compbio.washington.edu</a>=A0and<br>

<a href=3D"mailto:ram@compbio.washington.edu" style=3D"color:rgb(17,85,204)= ">ram@compbio.washington.edu</a></span></font></div><div></div><div><font c= lass=3D"Apple-style-span" color=3D"#222222" face=3D"arial, sans-serif"><spa= n class=3D"Apple-style-span" style=3D"border-collapse:collapse"><br>

</span></font></div><div><font class=3D"Apple-style-span" face=3D"arial, he= lvetica, sans-serif">--</font></div>

<p></p>

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--20cf306f722a5dcabe04d6442e13--

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary@salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali@salilab.org; Web http://salilab.org