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

[Compbio-allhands] Fwd: reminder, seminar by Chia-en Chang
by Jacobson, Matt 01 Jun '12

01 Jun '12

Just a reminder about this seminar, 1pm, BH212 Begin forwarded message: I'm hosting Chia-en Chang on Friday June 1. She will give a seminar at 1 pm in BH212; title and abstract below. Chia-en did her graduate work with Mike Gilson and postdoc with Andy McCammon, and has been at UC Riverside for about 4 years now. The mining minima work she will be discussing is some of the most impressive free energy calculations I've seen. http://chem.ucr.edu/chang If you'd like to meet with her, Lili is helping to coordinate her schedule. Title: Insights from Free Energy Calculations: Protein Conformational Equilibrium, Driving Forces and Ligand Binding Processes Abstract: To accurately calculate ligand-protein binding affinity is still challenging in computational chemistry. In this presentation, we used a free energy calculation method, the mining minima algorithm (M2), to compute the binding affinities of various types of inhibitors to p38α MAP kinase. This end-point approach uses an empirical force field and implicit solvent models to find stable conformations in the free and bound states of a system and then compute the binding free energy of each species. Here we selected 30 different p38α inhibitors that can bind to either DFG-in or DFG-out conformations. Notably, some analogs do not have ligand-p38 co-crystal structures. Our computed absolutely binding free energies yield excellent agreement with experimental data and reveal the driving forces of binding. Our results also show the dynamic equilibrium in the DFG-in and DFG-out states and explain why the conformations can co-exist. In addition, I will introduce a novel method to study ligand binding processes in chemical host-guest system. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences 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] seminar on Friday
by Jacobson, Matt 30 May '12

30 May '12

I'm hosting Chia-en Chang on Friday June 1. She will give a seminar at 1 pm in BH212; title and abstract below. Chia-en did her graduate work with Mike Gilson and postdoc with Andy McCammon, and has been at UC Riverside for about 4 years now. The mining minima work she will be discussing is some of the most impressive free energy calculations I've seen. http://chem.ucr.edu/chang If you'd like to meet with her, Lili is helping to coordinate her schedule. Title: Insights from Free Energy Calculations: Protein Conformational Equilibrium, Driving Forces and Ligand Binding Processes Abstract: To accurately calculate ligand-protein binding affinity is still challenging in computational chemistry. In this presentation, we used a free energy calculation method, the mining minima algorithm (M2), to compute the binding affinities of various types of inhibitors to p38α MAP kinase. This end-point approach uses an empirical force field and implicit solvent models to find stable conformations in the free and bound states of a system and then compute the binding free energy of each species. Here we selected 30 different p38α inhibitors that can bind to either DFG-in or DFG-out conformations. Notably, some analogs do not have ligand-p38 co-crystal structures. Our computed absolutely binding free energies yield excellent agreement with experimental data and reveal the driving forces of binding. Our results also show the dynamic equilibrium in the DFG-in and DFG-out states and explain why the conformations can co-exist. In addition, I will introduce a novel method to study ligand binding processes in chemical host-guest system. Matthew P. Jacobson Professor, Department of Pharmaceutical Chemistry Department of Bioengineering and Therapeutic Sciences California Institute for Quantitative Biosciences 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] QBC Journal Club, Tuesday, June 5- 10:45AM, GH Aud
by Nicole Takesono Flowers 30 May '12

30 May '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, June 5 10:45 am, GH Auditorium Jessica Thomaston, CCB Experimental adaptation of an influenza H5 HA confers respiratoryrndroplet transmission to a reassortant H5 HA/H1N1 virus in ferrets. Imai, Masaki et al. Nature. Available online May 2012. bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics 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: Faculty positions
by Andrej Sali 25 May '12

25 May '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry University of California at 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: pettitt <mpettitt(a)utmb.edu> > Subject: Faculty positions > Date: May 25, 2012 12:58:39 PM PDT > To: sali(a)salilab.org > > Dear Andrej, > > To expand our programs in structural biology at the University of Texas Medical Branch in Galveston, we are beginning searches to fill three senior-level faculty positions in the Sealy Center for Structural Biology and Molecular Biophysics. We currently seek individuals whose connection to structural biology is through cryo EM, x-ray or NMR (nominally one position each) and who wish to take advantage of a rich collaborative environment. This is part of a large investment by the university in structural biology and ten related hires are expected over the next 5 years. The first individual(s) hired will have a significant role in selecting the remaining senior and junior individuals hired into the program. > > We have facilities with excellent instrumentation and fully staffed with high quality individuals. Ours is a research resource supported by the University so there are no core charges for Center faculty to use our facilities. That and our location on the outskirts of Houston with proximity to the Texas Medical Center are attractive features. > > If you know of anyone that may have interest, we would be delighted to hear about it. Further information about the position(s) can be found attached. As well, additional information about the Sealy Center for Structural Biology may found on the web at http://www.scsb.utmb.edu/ > Thank you in advance for any help that you can provide in identifying suitable senior-level candidates for these positions. > > Sincerely, > Monte > > B. Montgomery Pettitt > Robert A. Welch Professor of Chemistry > in Pharmacology and Toxicology > Professor of Biochemistry and Molecular Biology > Director, Sealy Center for Structural Biology > and Molecular Biophysics > University of Texas Medical Branch > mpettitt(a)utmb.edu

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[Compbio-allhands] 5/31/12 Seminar with Ira Mellman
by Nicole Takesono Flowers 25 May '12

25 May '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 Jim Ferrell Stanford University Dissecting the Mitotic Trigger May 31, 2012 W. Lim, 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

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[Compbio-allhands] Fwd: Request for assistance - Associate Scientist opportunity with Genentech - Absorption process & PK/PD Formulation
by Jacobson, Matt 23 May '12

23 May '12

-- Matt Sent from my iPhone Begin forwarded message: From: Keith Terry <terry.keith(a)gene.com<mailto:terry.keith@gene.com>> Date: May 23, 2012 11:00:23 AM PDT To: <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Subject: Request for assistance - Associate Scientist opportunity with Genentech - Absorption process & PK/PD Formulation Hi Matthew, My name is Keith Terry and I am an internal recruiter with Genentech in South San Francisco. I am reaching out to you today to ask for your assistance. I am supporting Genentech’s Early Research and Development (gRED) department in the area of formulation development small molecules. We have an outstanding opportunity for a passionate and innovative Ph.D. to join our group. I thought that you might know of a dynamic scientist (either a recent graduate or currently in post doc) that would be interested in the attached job. Potential candidates DO NOT need previous pharmaceutical industry experience. A well published Ph.D. who has recently graduated from a highly regarded program would be perfect. To summarize what we are looking for: • Ph.D. level candidates with strong scientific knowledge in Pharmaceutical Sciences and a proven record of publications. • In-depth knowledge absorption process, PK/PD and application of such knowledge in science-based formulation approaches and drug delivery design. • Good communication and problem-solving skills and be a team player. • Must have a Ph.D in Pharmaceutics, Chemistry, or related fields with minimum of 0-5 years-experience in the Pharmaceutical Industry. Please feel free to pass the attached flier along to individuals that you feel would be qualified and potentially interested. You are welcome to post the flier on your department’s job board. If you have any questions at all regarding this opportunity or would like to learn more about Genentech, please feel to call me directly. Thanks so much for your assistance. Cheers, Keith Keith Terry Talent Acquisition Specialist Genentech, A Member of the Roche Group 650-467-1557<tel:650-467-1557> terry.keith(a)gene.com<mailto:terry.keith@gene.com> Why is Genentech such a great place to work? Check out this video! Our People<http://www.youtube.com/watch?v=DMalKJ0_8-A> (click to view)

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[Compbio-allhands] QBC Journal Club, Tuesday, May 29- 10:45AM, GH Aud
by Nicole Takesono Flowers 23 May '12

23 May '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, May 29 10:45 am, GH Auditorium Yu Jack Yue, iPQB Evolution of Human-Specific Neural SRGAP2 Genes by Incomplete Segmental Duplication. Megan Y. Dennis, et al. Cell 149, 4, 912-922. 2012 Diego Garrido Ruiz, iPQB Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing. Hopf, Thomas A., Colwell, Lucy J.,Sheridan, Robert, Rost, Burkhard, Sander, Chris, Marks, Debora S. Cell, Available online May 2012. bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics 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: Genentech postdoc position: request for candidates
by Andrej Sali 22 May '12

22 May '12

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry University of California at 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: "Isidro (Dan) Zarraga" <zarraga.isidro(a)gene.com> > Subject: Genentech postdoc position: request for candidates > Date: May 22, 2012 2:31:30 PM PDT > To: sali(a)salilab.org > Cc: hilary(a)salilab.org > > Dear Prof. Sali, > > Please find attached a description of a Genentech postdoc opportunity. Kindly circulate to those who might be interested. We would like to fill the position soon so those interested are encouraged to send their resumes as soon as possible. Thank you very much. > > Sincerely, > > Dan E. Zarraga, PhD > Late Stage Pharmaceutical Development > Genentech Bldg 56 Rm 2119 > South San Francisco CA 94030 > Tell: 650 2257617

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[Compbio-allhands] 5/24/12 Seminar with Ira Mellman
by Nicole Takesono Flowers 18 May '12

18 May '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 Ira Mellman Genentech Next Generation Approaches to Basic Cell Biology & Drug Discovery May 24, 2012 Justin Rettenmeier, 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

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[Compbio-allhands] QBC Journal Club, Tuesday, May 22- 10:45AM, GH Aud
by Nicole Takesono Flowers 16 May '12

16 May '12

BMI ~ BP ~ CCB ~ PSPG Tuesday, May 22 10:45 am, GH Auditorium Andrew Van Benschoten, iPQB Sexual Deprivation Increases Ethanol Intake in Drosophila. Shohat-Ophir et al. Science, 2012 Mar 16; 335 (6074): 1351-5. Naomi Yonis, CCB Atg7 Modulates p53 Activity to Regulate Cell Cycle and Survival During Metabolic Stress. Lee, I.H. et al. Science ,336, 225 (2012). bioinformatics ~ biophysics ~ chemistry and chemical biology ~ pharmaceutical sciences and pharmacogenomics 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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