April 2016 - compbio-allhands@cgl.ucsf.edu

[Compbio-allhands] 4/14/16 Seminar with Ian Wilson- NOTE LOCATION
by Flowers, Nicole 08 Apr '16

08 Apr '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall N114 NO SIMULCAST. URL for live capture will be sent out on 4/13/16. HARC Center Speaker: Ian Wilson Scripps Broad neutralization of viral pathogens April 14, 2016 B. Stroud, 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, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: job opportunity in Seattle area
by Jacobson, Matthew 05 Apr '16

05 Apr '16

- Matt Begin forwarded message: From: Jaline Gerardin <gerardin(a)gmail.com<mailto:gerardin@gmail.com>> Subject: job opportunity in Seattle area Date: April 5, 2016 at 9:17:13 PM PDT To: Matthew Jacobson <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Hi Matt, We have an interesting position open at the interface of software and research. Could you forward to compbio-allhands? thanks, Jaline -------------------------------------------------------------------------------------------------- Open position at Institute for Disease Modeling, Bellevue WA: The IDM Research Software Engineer will work on an elite team of software developers along with testers and researchers at IDM tasked with developing software tools for all stages of the disease modeling pipeline. This pipeline includes designing and querying large data for climate, demographic, and transportation data for input to the disease modeling software; specifying and commissioning simulation jobs on a high performance computing cluster; detailed simulation of disease transmission dynamics; data reduction and analysis of simulation output; and workstation and web based data visualization tools. This position focuses on building tools and applications to support the different disease teams. Full job posting: http://iv.avature.net/careers/JobDetail/Bellevue-Wa-Washington-United-State… Institute for Disease Modeling: www.idmod.org<http://www.idmod.org/>

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[Compbio-allhands] Fwd: Hands-On Computer Aided Drug Design Workshop @ UCSF, San Francisco - Friday Apr. 15
by Jacobson, Matthew 05 Apr '16

05 Apr '16

I don’t recall whether this has been distributed on this list previously If you want to learn MOE ... - Matt Begin forwarded message: From: Audrey Bonin <abonin(a)chemcomp.com<mailto:abonin@chemcomp.com>> Subject: Hands-On Computer Aided Drug Design Workshop @ UCSF, San Francisco - Friday Apr. 15 Date: April 5, 2016 at 11:33:07 AM PDT To: Audrey Bonin <abonin(a)chemcomp.com<mailto:abonin@chemcomp.com>> Dear Friends and Colleagues , I would like to invite you to our hands-on computer-aided drug design workshops which will take place at UCSF - April 15th, 2016. The workshops are open to the public and all interested parties are welcome to attend - no prior software experience is required to participate. Please find course information and related details below. The workshop is free but pre-registration is required since places are limited, to register please visit : http://www.chemcomp.com/Workshops-North_America.htm Lunch, and refreshments will be provided during the workshops, please bring your own laptop to the workshop*. Date: CCG Workshops - Friday April 15, 2016 Location: UCSF - Smith Cardiovascular Research Bldg (CVRI), 555 Mission Bay Blvd S., first floor seminar room. ================================================================ 08:30-09:00 Morning break* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -- - - - 09:00-12:00 Structure-Based Drug Design and Ligand Modification Molecular Surfaces and Maps / Ligand Interactions / Conformational Searching / Ligand Optimization / Ligand Selectivity / Protein Alignments and Superposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -- - - - 12:00-13:00 Lunch* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -- - - - 13:00-17:00 Antibody Modeling and Protein Engineering in MOE Protein-Protein Interactions / Protein Properties / Developability / Hot Spot Analysis / Antibody Modeling / Molecular Surfaces / Protein-protein docking ================================================================ *Continental breakfast and lunch will be provided. ================================================================ -- Course title: Structure-Based Drug Design and Ligand Modification Course description: The course covers MOE applications for interactive structure based design. Examples include active site visualization, protein-ligand contact analysis and ligand modification/optimization in the receptor pocket. Conformational searching and analysis of the ligand to assess ligand flexibility will be discussed. A protocol for aligning and superposing protein complexes in the context of protein selectivity will be studied. Course title: Antibody Modeling and Protein Engineering in MOE Course description: The course covers approaches for structure-based biologics design and includes protein-protein interactions analysis, in silico protein engineering, affinity modeling and antibody homology modeling. The interaction of a co-crystallized antibody-antigen complex will be evaluated by generating and examining the molecular surface topology and visualizing protein-protein interactions in 3D and 2D. The application of protein engineering tools for homology modeling and conducting property optimization of an antibody-antigen complex in the context developability will be studied.All the steps necessary for producing and assessing antibody homology models will be described. Methods for evaluating the structure of protein and antibody models will be discussed. *If you don't have access to MOE, please communicate with me prior to the workshop, I will set up a demo key for you so you can follow along on your personal laptop. Regards, Audrey Bonin, M. Sc. Chemistry Academic Services Manager Chemical Computing Group T. +1 514 393-1055<tel:%2B1%20514%20393-1055> abonin(a)chemcomp.com<mailto:abonin@chemcomp.com> | www.chemcomp.com<http://www.chemcomp.com/> Follow us on Twitter! @CCG_MOE

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[Compbio-allhands] Fwd: Editorial
by Brian Shoichet 03 Apr '16

03 Apr '16

---------- Forwarded message ---------- From: Patrick Walters <wpwalters(a)gmail.com> Date: Sun, Apr 3, 2016 at 8:29 AM Subject: Re: Editorial To: Brian Shoichet <shoichet(a)cgl.ucsf.edu> W e're looking for someone with MD expertise (see below). I think this could be a huge opportunity for someone of that phenotype. Please let me know if you know of anyone who would be interested in joining our band. Best, Pat ------- Relay Therapeutics is seeking a highly motivated computational chemist to join our rapidly growing team. This individual will utilize cutting edge computational methods, in conjunction with information generated by a variety of biophysical techniques, to design novel therapeutics targeted to allosteric sites. In this role, the ideal candidate will work as part of a multidisciplinary team to integrate computational and experimental insights and drive drug discovery. *Responsibilities* - Carry out analyses that combine computational and experimental data to develop testable hypotheses that drive drug discovery programs - Collaborate with scientists throughout the company to maximize the impact of computational efforts on projects - Work collaboratively with external computational groups to develop and refine new computational methods - Ensure effective communication of computational results across departments and teams - Develop new approaches to streamline and enhance computational workflows *Preferred Qualifications* - Ph.D. in Computational Chemistry, Computational Biology, Biophysics, or a related discipline - 1 to 5 years of industrial or postdoctoral experience - Demonstrated expertise applying wide variety of modern computational chemistry methods - Demonstrated expertise in structure-based drug design - In depth knowledge of molecular dynamics and its application to drug discovery - Facility working in a Unix/Linux environment - Ability to program in at least 1 modern scripting language (e.g. Python) - Strong interpersonal and communications skills - Ability to conduct independent research >>>> >>>> -- Brian Shoichet, Professor http://bkslab.org/ <http://www.uoft.bkslab.org/> 415-514-4126 University of California, San Francisco Dept. of Pharmaceutical Chemistry By Courtesy: University of Toronto, Faculty of Pharmacy Ontario Institute for Cancer Research

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[Compbio-allhands] 4/7/16 Seminar with Ronen Marmorstein
by Flowers, Nicole 01 Apr '16

01 Apr '16

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 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Ronen Marmorstein University of Pennsylvania Molecular mechanisms of post-translational and co-translational protein acetylation April 7, 2016 D. Fujimori, 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, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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