September 2012 - compbio-allhands@cgl.ucsf.edu

[Compbio-allhands] Seminar October 4, noon
by Jacobson, Matt 28 Sep '12

28 Sep '12

David Shaw will give a seminar at noon on Thursday, October 4, in Genentech Hall auditorium, entitled "Millisecond-long molecular dynamics simulations of proteins" http://www.deshawresearch.com/ Hope to see you there (No BBC seminar was scheduled for this date, so we are using that time slot for this somewhat impromptu seminar. I've included all the listservs that I have access to on this email, but feel free to forward.) -- Matt 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] BBC Journal Club, Tuesday, October 2- 10:45AM, GH Aud
by Bass, Karche 26 Sep '12

26 Sep '12

BMI ~ BP ~ CCB Tuesday, October 2nd 10:45 am, GH Auditorium Kyle Barlow, BMI Schaub, M. A., Boyle, A. P., Kundaje, A., Batzoglou, S. & Snyder, M. Linking disease associations with regulatory information in the human genome. Genome Res. 22, 1748-1759 (2012). Noah Younger, CCB Illing PT et al. Immune self-reactivity triggered by drug-modified HLA-peptide repertoire. Nature. 2012; 486:554-558. bioinformatics ~ biophysics ~ chemistry and chemical biology Karché K. Bass Karché K. Bass | Administrative Analyst Asst. to John D. Gross, Charles Craik, Susan Miller, Thomas James Department of Pharmaceutical Chemistry Administration; Box 2280 | University of California, San Francisco 600 16th Street, Suite 512 (5th Floor) | San Francisco, CA •: 415-502-0943 | 7: | •: Karche.Bass(a)ucsf.edu<mailto:Karche.Bass@ucsf.edu>

1 0

[Compbio-allhands] Fwd: CADD position at BMS
by Jacobson, Matt 25 Sep '12

25 Sep '12

Begin forwarded message: From: "Johnson, Stephen" <stephen.johnson(a)bms.com<mailto:stephen.johnson@bms.com>> Subject: CADD position at BMS Date: September 25, 2012 2:30:27 PM PDT To: "Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Dear Professor Jacobson, Debbie Loughney and I were discussing our visit to UCSF earlier this year as we just recently opened a new position within the CADD group at BMS. In short, the scientist that fills the position will be expected to help us expand and extend our toolset for addressing off-target liabilities including both ADMET and selectivity issues. The scientist will be active in the development of new methodology and its application in discovery projects. As such, we’re hoping to find someone with reasonable programming skills, in addition to being a top-tier CADD scientist. I wonder if you might have any current or former students/postdocs that you think may be a good fit for the position? Anyone that is interested can view the position profile and apply here: https://bms.taleo.net/careersection/jobdetail.ftl?job=45378&lang=en&sns_id=… They are also welcome to email directly in addition to applying through the website. Regards, Steve ================= Stephen Johnson Sr. Principal Scientist, CADD Head, Molecular Analytics Bristol-Myers Squibb, Co. stephen.johnson(a)bms.com<mailto:stephen.johnson@bms.com> ________________________________ This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited. 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] 9/27/12 Seminar with Sheng Zhong
by Nicole Takesono Flowers 21 Sep '12

21 Sep '12

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 Sheng Zhong University of Illinois Comparative Epigenomics: a case study of human, mouse and pig pluripotent stem cells. September 27, 2012 Bo Huang, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, and the Center for Systems and Synthetic Biology. 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

1 0

[Compbio-allhands] Fwd: Postdoctoral opening
by Jacobson, Matt 20 Sep '12

20 Sep '12

As some of you know, I think very highly of Gilson's work Begin forwarded message: From: "Michael K. Gilson" <mgilson(a)ucsd.edu<mailto:mgilson@ucsd.edu>> Subject: Postdoctoral opening Date: September 20, 2012 1:56:32 PM PDT To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Dear Matt, I thought I would mention that there is a current opening for a postdoctoral position in my lab. It is posted here on the computational chemistry list: http://www.ccl.net/cca/jobs/joblist/mess0025099.shtml I would be grateful if you could pass this along to trainees who might be interested. Feel free to contact me if you would like any more information. All the best, Mike -- Michael K. Gilson, M.D., Ph.D. Professor, Skaggs School of Pharmacy and Pharmaceutical Sciences Director, UCSD Drug Discovery Institute U. C. San Diego 9500 Gilman Drive Pharmaceutical Sciences Building, Room 3224 La Jolla, CA 92093-0736 Voice: 858-822-0622 Fax: 858-822-7726 http://gilson.ucsd.edu http://www.bindingdb.org http://drugdiscovery.ucsd.edu 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] Fwd: Faculty position in medicinal/pharmaceutical chemistry preferrably with computational research emphasis
by Brian Shoichet 19 Sep '12

19 Sep '12

FYI ---------- Forwarded message ---------- From: Peter Oelschlaeger <poelschlaeger(a)westernu.edu> Date: Wed, Sep 19, 2012 at 11:53 AM Subject: Faculty position in medicinal/pharmaceutical chemistry preferrably with computational research emphasis To: Peter Oelschlaeger <poelschlaeger(a)westernu.edu> Dear Professors,**** ** ** I would like to let you know about a faculty position in medicinal/pharmaceutical chemistry (preferably with a computational research emphasis) that the Department of Pharmaceutical Sciences in the College of Pharmacy at Western University of Health Sciences is offering.*** * ** ** Could you please inform any postdocs or colleagues that might be interested in applying?**** A posting with job description and instructions on how to apply has been posted on Science Careers:**** http://scjobs.sciencemag.org/jobs/153661-91602/**** ** ** Thank you very much for your help,**** ** ** Peter**** ** ** ************************************************************* *Peter Oelschlaeger, PhD* *Assistant Professor* *Department of Pharmaceutical Sciences* *College of Pharmacy* *Western University of Health Sciences* *309 E. Second St., Pomona, CA 91766* *Phone: 909-469-8232 (office), 909-469-8234 (lab)* *Fax: 909-469-5600* *Email: poelschlaeger(a)westernu.edu* *http://www.westernu.edu/stp/bios.php?bio=poelschlaeger* ** ** ** ** -- Brian Shoichet Professor University of California, San Francisco Dept. of Pharmaceutical Chemistry phone: 415-514-4126; fax: 415-514-4260 http://shoichetlab.compbio.ucsf.edu

1 0

[Compbio-allhands] Informal Seminar: David Minh, "Molecular Docking: Foundations in Statistical Mechanics"; Friday, 10:30am, GH S204
by David Sivak 19 Sep '12

19 Sep '12

Informal Seminar: Friday, September 21, 10:30am, Genentech S204 Molecular Docking: Foundations in Statistical Mechanics David Minh (mccammon.ucsd.edu/~dminh/) I will describe implicit ligand theory, a new formalism for noncovalent binding free energies that separates the calculation into two simulation stages: (i) sampling receptor configurations and (ii) calculating the binding PMF - the affinity of a ligand to a rigid receptor - for each receptor snapshot. Molecular docking may be interpreted as applying a dominant state approximation to each stage. Implicit ligand theory provides a pathway for the improvement of scoring functions. Recommended reading: http://arxiv.org/abs/1208.4885 -- David Sivak Systems Biology Fellow University of California, San Francisco david.sivak(a)gmail.com davidsivak.com 510-541-9006

1 0

[Compbio-allhands] Fwd: A postdoc to work with Peter Minary in Computer Science at Oxford University
by Andrej Sali 17 Sep '12

17 Sep '12

Begin forwarded message: > From: "Michael Levitt" <michael.levitt(a)stanford.edu> > Subject: A postdoc to work with Peter Minary in Computer Science at Oxford University > Date: September 17, 2012 1:20:07 PM PDT > To: "'Michael Levitt'" <michael.levitt(a)stanford.edu> > > Dear Colleague and Friend, > > I am writing to ask for your help in identifying suitable candidates for a postdoctoral fellow to collaborate with Dr. Peter Minary. Peter has moved from Stanford to an independent position in Computer Science at Oxford and I can recommend him to any person who would like to become an expert at the most amazing methods for sampling macromolecular conformations. > > Searching Pubmed (http://www.ncbi.nlm.nih.gov/pubmed?term=minary%20p) shows Peter recent publications. His program remarkable program MOSAICS is athttp://csb.stanford.edu/minary/MOSAICS.html/ . > > This position has been advertised in Nature and Science. I append the Science add here (http://www.2020science.net/news/fellowship-computational-biology ). > > So many thanks and with all best regards, > Michael > -- 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: Subject: Postdoc opportunities at Princeton
by Andrej Sali 17 Sep '12

17 Sep '12

Sent from my iPhone Begin forwarded message: > From: "Everett L. Morgan" <lmorgan(a)Princeton.EDU> > Date: September 17, 2012 1:07:08 PM PDT > To: "Everett L. Morgan" <lmorgan(a)Princeton.EDU> > Cc: William Bialek <wbialek(a)Princeton.EDU>, "Curtis G. Callan Jr." <ccallan(a)Princeton.EDU>, "Wingreen, Ned S." <wingreen(a)Princeton.EDU>, "Chase P. Broedersz" <cbroeder(a)Princeton.EDU>, "Ben Machta (ben.machta(a)gmail.com)" <ben.machta(a)gmail.com>, "Rava A. da Silveira (rava(a)ens.fr)" <rava(a)ens.fr> > Subject: Subject: Postdoc opportunities at Princeton > > Dear colleagues, > > We are searching for young theorists with interests at the interface of physics and biology, and hope that you will bring this opportunity to the attention of likely candidates. As described in the attached advertisement (also available at http://www.princeton.edu/physics/about/employment/biophysics/index.xml) problems of current interest in our group cover a wide range of topics, and we always welcome people who will bring new questions of their own devising. Our community is very interactive, with multiple opportunities for collaboration, both among theorists and with many friendly local experimentalists. > > Many thanks for your help, > > Bill, Chase, Curt, Ben, Rava, and Ned > > William Bialek > John Archibald Wheeler/Battelle Professor in Physics > > Chase P. Broedersz > Lewis-Sigler Theory Fellow > > Curtis G. Callan, Jr. > James S. McDonnell Distinguished University Professor of Physics > > Benjamin Machta > Lewis-Sigler Theory Fellow > > Rava A. da Silveira > Princeton Global Scholar > > Ned S. Wingreen > Howard A. Prior Professor in the Life Sciences > > >

1 0

[Compbio-allhands] Fwd: AMMA: job and postdoc opportunities
by Andrej Sali 16 Sep '12

16 Sep '12

Begin forwarded message: > From: Elizabeth Yuriev <Elizabeth.Yuriev(a)monash.edu> > Subject: AMMA: job and postdoc opportunities > Date: September 16, 2012 6:01:13 PM PDT > To: Undisclosed recipients: ; > > 1. Postdoctoral Research Associate, University of Liverpool > > £31,020 - £31,948 pa > Faculty of Science and Engineering, School of Physical Sciences, Department of Chemistry > Location: Liverpool City Centre > Ref: R-580533/WWW > Closing date for receipt of applications: 5 October 2012 > Joining a team of five postdoctoral researchers to develop a lead candidate compound, you will form part of a joint collaborative programme between the Departments of Chemistry and Pharmacology in a programme funded by the Medical Research Council (MRC). You should have a MChem degree and a PhD (or about to be obtained) in molecular modelling or closely related area. > The project involves the rational design, via molecular modelling, of novel analgesic compounds and will focus on exploring the structure activity relationships of molecules, their isosteres and optimising pharmacokinetic properties. Crucial to the vision is the use of molecular modelling to lead laboratory synthesis and testing to achieve compounds that are fit for purpose. The post is available for 12 months in the first instance. > > http://www.liv.ac.uk/working/job_vacancies/research/R-580533.htm > > Dr Neil Berry > Department of Chemistry > University of Liverpool > Liverpool > L69 7ZD > Tel: +44(0)151 794 3877 > Fax: +44(0)151 794 3588 > http://www.liv.ac.uk/~ngberry > > > 2. Senior Software Developer, Lhasa Limited > > There is more than one post on offer. There is no set closing date at the moment – but applications to be made as soon as possible. > Anyone interested in the job should contact my colleague Menaz Tabassum, who is responsible for recruitment here at Lhasa. Menaz’s email address is:- > Menaz.tabassum(a)lhasalimited.org > > (please see attachment for details) > > > 3. Postdoc position on Computational Protein Design at LAAS-CNRS, Toulouse, France > > The Robotics and Interactions group at LAAS-CNRS (Toulouse, France) is seeking for a postdoctoral researcher to work in an interdisciplinary project on Computational Protein Design. The project, ProtiCAD, is funded by the French National Research Agency (ANR). It involves three research groups with expertise in computer science / robotics, computational biology and enzyme engineering, and a start-up company. The work will mainly involve the development of algorithms to efficiently explore very large state-spaces, which correspond to different sequences and conformations of a protein. > > Candidates should have strong background in search algorithms and combinatorial optimization methods, as well as excellent programming skills. > Research will be carried in close collaboration with people in the other laboratories; therefore, applicants should enjoy teamwork and have very good communication skills. > Good English level is mandatory and notions of French would be a plus. > Toulouse is a beautiful, dynamic and safe city situated in the South West of France, within only 1.5 hour drive from the Pyrenees and the Mediterranean Sea. Toulouse offers outstanding opportunities for culture, entertainment and outdoor activities. > The position is available from December 2012, for a duration of up to two years. > Applications, including a CV, a cover letter and contact information of at least two references, should be sent by email to Juan Cortés (juan.cortes(a)laas.fr) with subject: "ProtiCAD postdoc application". > > > > > > > > > > ************ > Dr Elizabeth Yuriev > Senior Lecturer > Faculty of Pharmacy and Pharmaceutical Sciences > Medicinal Chemistry and Drug Action > Monash Institute of Pharmaceutical Sciences > Monash University (Parkville Campus) > 381 Royal Parade, Parkville VIC 3052, Australia > Tel: Int +61 3 9903 9611, Fax: +61 3 9903 9143 > E-mail: elizabeth.yuriev(a)monash.edu > www.pharm.monash.edu.au > -- 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