April 2014 - compbio-allhands@cgl.ucsf.edu

[Compbio-allhands] 5/1/14 Seminar with Dorothee Kern
by Flowers, Nicole 25 Apr '14

25 Apr '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus Library 220 Dorothee Kern Brandeis The evolution of kinase dynamics over 1 billion years reveals Gleevec’s selectivity May 1, 2014 J. Fraser, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] a fellow position at iHuman institute, ShanghaiTech, and UCSF
by Andrej Sali 24 Apr '14

24 Apr '14

We seek a research fellow or assistant professor applicant to engage in an integrative structural biology study of a cellular signaling pathway (e.g., GPCR signaling cascades). The candidate will contribute to the collaboration between the Sali research group at University of California, San Francisco, USA (http://salilab.org) and the Stevens research group at iHuman Institute of ShanghaiTech University, Shanghai, China (http://www.shanghaitech.edu.cn/en/en_iHuman_Overview.asp). The goal will be to develop a spatiotemporal model of the selected system, based on data from a variety of experimental techniques, such as X-ray crystallography, NMR spectroscopy, mass spectrometry, super resolution optical microscopy, and others, generated at iHuman. The prerequisites include a background in computational structural biology, experience with designing and coding computational algorithms, statistical mechanics, and statistics, as well as willingness to learn about integrative structural biology methods and applications in the Sali laboratory. The fellow will spend considerable time initially at UCSF, transitioning into a tenure track faculty position at iHuman. The position will be funded for 5 years at a very competitive international faculty startup level. Please email your cover letter, including a cv and names of at least 3 referees, to Andrej Sali (sali(a)salilab.org) or Ray Stevens (stevens(a)shangaitech.edu.cn). -- 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(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] 4/24/14 Seminar with Alexander Hoffmann
by Flowers, Nicole 18 Apr '14

18 Apr '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Alexander Hoffmann UCSD Network Dynamics as a basis for Specificity April 24, 2014 Hana El Samad, Hosts BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd:
by Jacobson, Matt 15 Apr '14

15 Apr '14

-- Matt Sent from my iPhone Begin forwarded message: From: Olaf Wiest <Olaf.G.Wiest.1(a)nd.edu<mailto:Olaf.G.Wiest.1@nd.edu>> Date: April 15, 2014 at 7:32:14 AM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Dear Matt I would like to alert you and your students to an opening of one (possibly two) postdoctoral positions in the Computer Aided Molecular Design (CAMD) core facility here at the University of Notre Dame. If you know of suitable candidates from your group or other, please encourage them to apply. I attach the position description, which will also be posted on ccl.net<http://ccl.net> in the next few days. If you have any question, please do not hesitate to contact me at any time. With the best wishes Olaf Wiest Postdoctoral position in the CAMD core at the University of Notre Dame Applications are invited for a postdoctoral position in the Computer Aided Molecular Design core facility at the University of Notre Dame. The successful candidate will work with researchers in the Warren Family Center for Drug Discovery, the Center for Rare and Neglected Diseases, and other researchers at the University of Notre Dame as well as their collaborators to design chemical probes molecules as well as new hit and lead compounds to a treatment of a variety of diseases. Current areas of interest include malaria and other infectious diseases, cancer, and neurodegenerative diseases. The initial appointment will be for one year with additional years, including a possibility to apply for a staff position, available upon mutual agreement. Requirements for the position include: - Ph.D in chemistry, biophysics or other relevant field - documented experience in virtual screening, molecular dynamics simulation of biomolecular systems and/or structure based drug design - ability to support multiple projects simultaneously - ability to work independently and in effective collaborations with medicinal chemists, biochemists and biologists - excellent verbal and written communication skills Previous experience with common programs (Schrödinger Suite, AMBER, G09 etc.), electronic structure calculations, library design, cheminformatics, good programming skills and other aspects of computer aided drug design as well as an understanding of the drug discovery process would be beneficial. To apply, send a CV, statement of research experience and contact addresses of three references to owiest(a)nd.edu<mailto:owiest@nd.edu>. For information on the CAMD core, see http://www3.nd.edu/~camd/.

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[Compbio-allhands] 4/17/14 Seminar with Rama Ranganathan
by Flowers, Nicole 11 Apr '14

11 Apr '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Rama Ranganathan UT Southwestern The evolutionary “design” of proteins April 17, 2014 S. Calhoun & D. Garrdio Ruiz, Hosts BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Postdoc opening
by Jacobson, Matt 09 Apr '14

09 Apr '14

I think I may have already sent out a description of this position, but this is much more detailed Begin forwarded message: From: "Xing, Li" <li.xing(a)pfizer.com<mailto:li.xing@pfizer.com>> Subject: Postdoc opening Date: April 9, 2014 6:15:26 AM PDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Hi Matt, I am writing to see if you can help me out here. Recently I was fortunate to get an internal Pfizer postdoctoral fellowship funded to investigate PPI targets by molecular dynamics simulations. Specifically, the goals are to expand the current understanding of the complex dynamic phenomena of many biological mechanisms, and to make traditionally difficult targets an increasingly fruitful drug discovery area. I am hoping you may be able to provide suggestions for candidates from your institution or elsewhere where there may be an overlapping interest or experience in this research area. Clearly experience in scientific scripting and programming is essential. The Postdoctoral fellowship is for 2 years with a possible extension to 3 years and is to be focused on generating publishable work (i.e. not constrained by Pfizer drug discovery activities) through internal studies as well as collaborations within and outside of Pfizer. This could be a great opportunity for people who want to gain industrial experience in a real drug discovery setting. I have attached a copy of the recruitment flyer. Online application can be submitted through the link from Pfizer careers website. http://pfizercareers.com/apply Job ID 994031 Any help or guidance that you can provide would be much appreciated. Thanks, Li Li Xing, Ph.D. Pfizer Worldwide Research and Development Cambridge, MA Tel: 617 665 5369 Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] 4/10/14 Seminar with David Baker
by Flowers, Nicole 04 Apr '14

04 Apr '14

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Sytems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 David Baker University of Washington Design of protein structures, functions and assemblies April 10, 2014 J. Kung & J. Rettenmaier, Hosts BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] reminder: Tack Kuntz talking at noon
by Jacobson, Matt 03 Apr '14

03 Apr '14

From: "Flowers, Nicole" <Nicole.Flowers(a)UCSF.EDU<mailto:Nicole.Flowers@UCSF.EDU>> Date: March 31, 2014, 10:49:12 AM PDT To: <BBCFACULTY(a)LISTSRV.UCSF.EDU<mailto:BBCFACULTY@LISTSRV.UCSF.EDU>> Subject: PETER A. KOLLMAN LECTURESHIP - April 3, 2014 Reply-To: "Flowers, Nicole" <Nicole.Flowers(a)UCSF.EDU<mailto:Nicole.Flowers@UCSF.EDU>> THURSDAY, APRIL 3, 2014 AT 12:00 PM PETER A. KOLLMAN LECTURESHIP GENENTECH HALL BYERS AUDITORIUM - UCSF MISSION BAY CAMPUS SIMULCAST TO PARNASSUS CAMPUS LIBRARY 221 WEBCAST: Reception in Byers Hall 5th Floor Lounge at 3:30 Please see attached flyer. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546 ------------------------------------------------------------------------ Use the following link to unsubscribe from this mailing list: http://listsrv.ucsf.edu/cgi-bin/wa?SUBED1=BBCFACULTY&A=1 Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] Fwd: available postdoc position at Pfizer in Cambridge
by Jacobson, Matt 02 Apr '14

02 Apr '14

Begin forwarded message: From: Arjun Narayanan Subject: available postdoc position at Pfizer in Cambridge In our department one of my colleagues is looking for a postdoc candidate to use MD to better understand and predict PPI druggability. Do you know anyone who would be interested? Here is the posting info: Postdoctoral Fellow - Computational Chemistry United States-Massachusetts-Cambridge You can view and apply for this job on our careers website (www.pfizer.com/careers<http://www.pfizer.com/careers>) by searching for the job opening title Postdoctoral Fellow - Computational Chemistry as keywords, or by using the job opening ID 994031 I believe it is a 2 year position. I also believe, unlike some industrial postdocs, there is nothing preventing us from hiring the person at the end of the postdoc (though, of course, there are no guarantees that we will be able to, either). Arjun Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences Institute for Neurodegenerative Diseases Director, Graduate Group in Biophysics UCSF MC 2540 1700 4th St., Byers Hall, Room 408E San Francisco, CA 94158-2330 matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu> jacobsonlab.org<http://jacobsonlab.org>

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[Compbio-allhands] PETER A. KOLLMAN LECTURESHIP - April 3, 2014
by Flowers, Nicole 01 Apr '14

01 Apr '14

THURSDAY, APRIL 3, 2014 AT 12:00 PM PETER A. KOLLMAN LECTURESHIP GENENTECH HALL BYERS AUDITORIUM - UCSF MISSION BAY CAMPUS SIMULCAST TO PARNASSUS CAMPUS LIBRARY 221 WEBCAST: Reception in Byers Hall 5th Floor Lounge at 3:30 Please see attached flyer. Nicole Takesono Flowers CCB Graduate Program Assistant AMBER Software Administrator UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94158-2517 Phone: (415) 502-6518 Fax: (415) 514-1546

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compbio-allhands April 2014