- compbio-allhands@cgl.ucsf.edu - RBVI Mailing Lists

[Compbio-allhands] 1/15/15 Seminar with Edward Marcotte
by Flowers, Nicole 09 Jan '15

09 Jan '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 Edward Marcotte University of Texas at Austin Evolution, the proteome, and disease January 15, 2015 J. Webber, 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 BMI, BP, & 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

1 0

[Compbio-allhands] Fwd: postdoc opening
by Jacobson, Matt 08 Jan '15

08 Jan '15

Begin forwarded message: From: "Jansen, Johanna" <johanna.jansen(a)novartis.com<mailto:johanna.jansen@novartis.com>> Subject: postdoc opening Date: January 8, 2015 4:55:49 PM PST To: "'Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>'" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>>, "shoichet(a)cgl.ucsf.edu<mailto:shoichet@cgl.ucsf.edu>" <shoichet(a)cgl.ucsf.edu<mailto:shoichet@cgl.ucsf.edu>> Dear Matt & Brian, It was good seeing you at the event today. Below is the summary of the postdoc position that is opening in our group. I will be the mentor and Heinz Moser will be co-mentor. I would appreciate it if you could advertise this at UCSF and I’ll be happy to speak with any interested graduate students to provide further information. Thanks ! Hanneke New in silico descriptors for correlations with biological endpoints and drug design principles: The Computer-Aided Drug Discovery (CADD) group has a strong focus on utilizing the vast Novartis knowledgebase to extract relationships between properties of molecules and their biological activity, and on developing approaches to make predictions based on those relationships using properties calculated from chemical structure (in silico descriptors). We work closely with experimentalists to design the compound sets for measurements of biological and physical properties in an effort to drive drug discovery and determine which molecular properties we can calculate that are predictive of the experimental properties. Two molecular properties that are not well described by the in silico descriptors commonly used in drug discovery are conformational flexibility and hydrogen-bonding strength. These properties play an important role in many biological activities, including various aspects of permeability (entry into mammalian cells, entry into gram-negative pathogens, blood-brain-barrier penetration, and passage across epithelial barriers). In order to better guide chemistry designs in drug discovery, we need better in silico descriptors to capture flexibility and hydrogen bonding strength. Our platform brings together computational, medicinal, and analytical chemistry, with the scientists that measure the relevant physicochemical and biological properties. This environment of experts, software, instruments, and data is particularly suited to develop new approaches for predicting these properties, including creating experimental datasets, and developing and evaluating new in silico descriptors. Applications of such descriptors include selection efforts (archive enhancement, library design, screening set design) as well as prospective chemistry designs during optimization. Qualifications: PhD degree holders, and PhD students within one year of completing of their degrees are eligible to apply. For more information, contact Hanneke Jansen at Johanna.Jansen(a)novartis.com<mailto:Johanna.Jansen@novartis.com>. To download the cover letter template and apply, please visit http://postdoc.nibr.com/ 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>

1 0

[Compbio-allhands] Murcko talk at noon
by Jacobson, Matt 08 Jan '15

08 Jan '15

A reminder that Mark Murcko is giving the Kollman lecture today at noon, on free energy calculations in drug discovery. Hope to see a good turnout -- Matt Sent from my iPhone

1 0

[Compbio-allhands] Fwd: Bioinformatics/biostats positions at Roche Sequencing
by Andrej Sali 05 Jan '15

05 Jan '15

-- 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 > Begin forwarded message: > > From: "Chaivorapol, Christina" <christina.chaivorapol(a)roche.com> > Date: January 5, 2015 at 10:59:48 AM PST > Subject: Bioinformatics/biostats positions at Roche Sequencing > To: Andrej Sali <sali(a)salilab.org> > > Hi Andrej, > > Happy new year! I hope things are well with you. I'm not sure if you heard, but I moved to Roche Sequencing to build a bioinformatics group that will focus on developing diagnostics based on NGS technology. I am currently looking to fill a few positions in my group and hope you will be able to forward this to people in your lab and/or at UCSF who might be interested in these jobs. > > Attached are the job postings for the positions in my group. If anyone is interested, please have them apply to the position of interest at the following links: > > Principal Scientist <http://www.roche.com/careers/jobs/jobsearch/job.htm?id=E-3017264312&locale=…> > Senior Biostatistican <http://www.roche.com/careers/jobs/jobsearch/job.htm?id=E-3017264212&locale=…> > > Thanks, > Christina > -- > Christina Chaivorapol, Ph.D. > Research Leader, Bioinformatics > > Roche Sequencing > Bioinformatics > 4300 Hacienda Dr. > Pleasanton, CA 94588 > Email: christina.chaivorapol(a)roche.com <mailto:christina.chaivorapol@roche.com> > Phone: +1 925-474-7343 > Fax: +1 925-730-8988 > > Confidentiality Note: This message is intended only for the use of the named recipient(s) and may contain confidential and/or proprietary information. If you are not the intended recipient, please contact the sender and delete this message. Any unauthorized use of the information contained in this message is prohibited. >

1 0

[Compbio-allhands] CheMBL: The Organization of Drug Discovery Data Workshop, January 30, 2015, 1:30pm, Byers Hall 212
by Hilary Mahon 18 Dec '14

18 Dec '14

For more information, please see attached. --- Hilary Mahon Assistant to Dr. Sali University of California, San Francisco MC 2552 Byers Hall Room 503 1700 4th Street San Francisco, CA 94158-2330 Phone +1 (415) 514 4228 Fax +1 (415) 514 4231 Email hilary(a)salilab.org

1 0

[Compbio-allhands] Seminar - Tom Blundell/University of Cambridge - Thursday, January 15, 2015 - 10:30am - Genentech Auditorium
by Hilary Mahon 16 Dec '14

16 Dec '14

Please see attached for more information. --- Andrej Sali

1 0

[Compbio-allhands] Fwd: NIST Structure Biology Position
by Andrej Sali 26 Nov '14

26 Nov '14

> Begin forwarded message: > > From: "Marino, John P." <john.marino(a)nist.gov> > To: "sali(a)salilab.org" <sali(a)salilab.org> > Subject: FW: NIST Structure Biology Position > Date: November 25, 2014 at 12:06:33 PM PST > > Dear Andrej, > > I am writing to request your help in identifying outstanding candidates for an Assistant Professor equivalent position in our group at the National Institute of Standards and Technology (NIST) (http://jobs.sciencecareers.org/job/344641/faculty-equivalent-structural-bio…) We are looking for motivated scientists who could establish independent research teams focused on developing new experimental techniques and/or modeling methods to advance protein structure determination. We are particularly interested in applicants whose research will focus on novel ways to combine high resolution structural data (X-ray and NMR) with small angle scattering (SAS) techniques to address important problems in biology and biotechnology. > > This is a federally position with 100% salary support. Base research funds are also provided by NIST, as well as access to state-of-the-art equipment, including high field NMRs (two 600s and a 900 MHz instrument), HDX-MS, X-ray crystallography and SAS facilities (in-house SAXS and internal access to the NIST Center for Neutron Research). Group members can, and are encouraged to, to apply for external funding to expand their program. Moreover, as we are situated in a joint Institute with the University of Maryland, adjunct appointments within UM departments are also possible. > > Our group is currently undergoing a significant expansion and provides an exciting and stimulating environment for cutting edge, collaborative research. We would greatly appreciate it if you could recommend suitable candidates to us and don't hesitate to contact us if there are any questions. > > Note that as this is a federal position, US citizenship is required. > > Best Regards, > John > _______________________________________ > John P. Marino, Ph.D. > Leader, Biomolecular Structure & Function Group > National Institute of Standards and Technology > 9600 Gudelsky Drive, Rockville, MD 20850 > 240-314-6160 [Tel]; 240-314-6255 [Fax] > john.marino(a)nist.gov > -- 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

1 0

[Compbio-allhands] Fwd: faculty opening
by Jacobson, Matt 23 Nov '14

23 Nov '14

-- Matt Sent from my iPad Begin forwarded message: From: Emil Alexov <ealexov(a)g.clemson.edu<mailto:ealexov@g.clemson.edu>> Date: November 23, 2014 at 9:58:52 AM PST Cc: Konstantin Kornev <KKORNEV(a)clemson.edu<mailto:KKORNEV@clemson.edu>>, Igor Luzinov <luzinov(a)clemson.edu<mailto:luzinov@clemson.edu>> Subject: faculty opening Colleagues, With this email, I simply would like to bring to your attention a recent ad for a faculty position at Clemson University (including computational/theoretical approaches to bio-materials). See the ad attached. Please, forward the announcement to any interested party. I apologize for multiple copies of this email that you may receive. Thanks, Emil http://www.compbio.clemson.edu

1 0

[Compbio-allhands] Fwd: New position and I'm hiring - any mobile job candiates?
by Andrej Sali 19 Nov '14

19 Nov '14

> Begin forwarded message: > > From: Heidi Imker <hjimker(a)gmail.com> > Date: November 18, 2014 at 8:11:26 PM PST > Subject: New position and I'm hiring - any mobile job candiates? > To: Andrej Sali <sali(a)salilab.org> > > Hi Andrej, > > Hope things going really well in San Francisco! I have a great new position as the director of a campus-wide program for managing and stewarding research data (Research Data Service <http://researchdataservice.illinois.edu/>). I started in May and after getting up to speed, we're ready to to hire. > I’m casting a wide net for 3 new job positions that we’re filling in the data realm. With your group’s expertise and field knowledge, you might know of some great people who are ready to move on to new a position. We’re hiring two data curators (wide open job description - many different skill-sets could be of use) and a data repository developer. Salary will be in the $60K range but our house prices average about $140K. CU is an “easy” place to live. :) > > http://goo.gl/YsBHom <http://goo.gl/YsBHom> (curators) > > http://goo.gl/4vumxA <http://goo.gl/4vumxA> (developer) > > Please pass on to anyone you know who might be interested, and your help is greatly appreciated in getting the word out. > > Do mail back if you get a chance, too – hope to hear things are going great! > > Heidi >

1 0

[Compbio-allhands] 2015 USHUPO conference
by Andrej Sali 16 Nov '14

16 Nov '14

-- 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

1 0