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

[Compbio-allhands] Fwd: Hiring computational chemist at Denali Therapeutics
by Brian Shoichet 20 Jun '16

20 Jun '16

FYI Brian Shoichet, Professor Dept. of Pharmaceutical Chemistry, UCSF by courtesy: Faculty of Pharmacy & OICR, UofT sent from my phone. ---------- Forwarded message ---------- From: "JW Feng" <feng(a)dnli.com> Date: Jun 20, 2016 7:46 PM Subject: Hiring computational chemist at Denali Therapeutics To: <shoichet(a)cgl.ucsf.edu> Cc: Hi Brian, This is JW Feng at Denali Therapeutics, a neuroscience startup in South San Francisco. We met while I was a computational chemist at Genentech. I joined Denali a year ago to lead the data science group and we are looking for an outstanding computational chemist to join our growing team. As you may know, Denali raised a historic biotech series A funding at $217 million. We have a world class team of scientists to discover drugs to treat neurodegenerative diseases. It would be great if you can recommend students or postdocs that would be interested in the job. Online job description: http://www.denalitherapeutics.com/careers?gh_jid=235936 Best, JW ___________________ JW Feng, Ph.D. Denali Therapeutics Inc. 201 Gateway Blvd. South San Francisco, CA 94080 | (650) 270-0628

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[Compbio-allhands] Fwd: Postdoc opening at Stanford
by Jacobson, Matt 10 Jun '16

10 Jun '16

- Matt Begin forwarded message: From: Ron Dror <rondror(a)stanford.edu<mailto:rondror@stanford.edu>> Subject: Postdoc opening at Stanford Date: June 10, 2016 at 1:15:01 AM PDT Dear colleagues, I have an opening for a postdoc to lead one or more projects in my group at Stanford. If you can recommend a promising candidate, please let me know. I’d welcome applications from outstanding researchers with backgrounds in molecular simulation (either methods development or biological applications), molecular modeling, protein design, or related areas. A description of the position is below. Best, Ron Applications are invited for postdoctoral research positions in Prof. Ron Dror’s lab at Stanford University. Successful applicants will use a variety of computational techniques to address key scientific questions in biochemistry and to enable advances in drug discovery, particularly for G-protein-coupled receptors (GPCRs), which represent the largest class of drug targets. This work will be carried out in close collaboration with world-class experimentalists. Candidates must have an outstanding record of research and academic performance, strong communication skills, and an ability to work independently and collaborate effectively. Experience with molecular dynamics simulation, enhanced sampling methods, programming, protein design, or molecular modeling of membrane proteins is desirable, but candidates are not expected to have experience in all of these areas. Dr. Dror’s lab focuses on computational approaches to studying the spatial organization and dynamics of biomolecules and cells. Our work spans fields ranging from biophysics and computational chemistry to high-performance computing, image processing, and machine learning. We have access to substantial computational and experimental facilities and are based in an interdisciplinary biosciences building immediately adjacent to Stanford’s medical, science, and engineering schools. Stanford, one of the world’s top universities, is located on a beautiful campus in the San Francisco Bay Area. Stanford has long been a magnet for talent in computing and the biosciences, and is considered the birthplace and spiritual center of Silicon Valley, an unparalleled center of technological and scientific innovation. Stanford University is an equal opportunity employer. To apply, please send the following to drorlabopenings(a)gmail.com<mailto:drorlabopenings@gmail.com>: a CV, a cover letter explaining your interest in the position, contact information for three referees, and a document you wrote that has not been edited by anyone else (for example, a report, an early draft of a manuscript, or an email to a colleague about a scientific topic). -- Ron Dror Associate Professor of Computer Science and, by courtesy, Molecular and Cellular Physiology and Structural Biology Stanford University http://drorlab.stanford.edu/

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[Compbio-allhands] Fwd: Postdoc opening at Stanford
by Andrej Sali 10 Jun '16

10 Jun '16

> Begin forwarded message: > > From: Ron Dror <rondror(a)stanford.edu> > Subject: Postdoc opening at Stanford > Date: June 10, 2016 at 1:17:03 AM PDT > To: "Lennart.Nilsson(a)ki.se" <Lennart.Nilsson(a)ki.se>, "bojan.zagrovic(a)univie.ac.at" <bojan.zagrovic(a)univie.ac.at>, "hgrubmu(a)gwdg.de" <hgrubmu(a)gwdg.de>, "c.de.graaf(a)vu.nl" <c.de.graaf(a)vu.nl>, "gerhard.hummer(a)biophys.mpg.de" <gerhard.hummer(a)biophys.mpg.de>, "schlick(a)nyu.edu" <schlick(a)nyu.edu>, "p.carloni(a)grs-sim.de" <p.carloni(a)grs-sim.de>, "ursula.roethlisberger(a)epfl.ch" <ursula.roethlisberger(a)epfl.ch>, "Michael.Grabe(a)ucsf.edu" <Michael.Grabe(a)ucsf.edu>, "sali(a)salilab.org" <sali(a)salilab.org>, "peter(a)kolblab.org" <peter(a)kolblab.org>, Koby Levy <Koby.Levy(a)weizmann.ac.il> > Cc: Ron Dror <ron.dror(a)stanford.edu> > > Dear colleagues, > > I have an opening for a postdoc to lead one or more projects in my group at Stanford. If you can recommend a promising candidate, please let me know. I’d welcome applications from outstanding researchers with backgrounds in molecular simulation (either methods development or biological applications), molecular modeling, protein design, or related areas. A description of the position is below. > > Best, > Ron > > > Applications are invited for postdoctoral research positions in Prof. Ron Dror’s lab at Stanford University. Successful applicants will use a variety of computational techniques to address key scientific questions in biochemistry and to enable advances in drug discovery, particularly for G-protein-coupled receptors (GPCRs), which represent the largest class of drug targets. This work will be carried out in close collaboration with world-class experimentalists. > > Candidates must have an outstanding record of research and academic performance, strong communication skills, and an ability to work independently and collaborate effectively. Experience with molecular dynamics simulation, enhanced sampling methods, programming, protein design, or molecular modeling of membrane proteins is desirable, but candidates are not expected to have experience in all of these areas. > > Dr. Dror’s lab focuses on computational approaches to studying the spatial organization and dynamics of biomolecules and cells. Our work spans fields ranging from biophysics and computational chemistry to high-performance computing, image processing, and machine learning. We have access to substantial computational and experimental facilities and are based in an interdisciplinary biosciences building immediately adjacent to Stanford’s medical, science, and engineering schools. > > Stanford, one of the world’s top universities, is located on a beautiful campus in the San Francisco Bay Area. Stanford has long been a magnet for talent in computing and the biosciences, and is considered the birthplace and spiritual center of Silicon Valley, an unparalleled center of technological and scientific innovation. > > Stanford University is an equal opportunity employer. > > To apply, please send the following to drorlabopenings(a)gmail.com <mailto:drorlabopenings@gmail.com>: a CV, a cover letter explaining your interest in the position, contact information for three referees, and a document you wrote that has not been edited by anyone else (for example, a report, an early draft of a manuscript, or an email to a colleague about a scientific topic). > > -- > > Ron Dror > Associate Professor of Computer Science and, by courtesy, Molecular and Cellular Physiology and Structural Biology > Stanford University > http://drorlab.stanford.edu/ <http://drorlab.stanford.edu/>

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[Compbio-allhands] Fwd: An announcement from COMP Together
by Magdalena Korczynska 02 Jun '16

02 Jun '16

June COMP Together. > Begin forwarded message: > > From: comp_together(a)acscomp.org > Subject: An announcement from COMP Together > Date: June 2, 2016 at 8:43:50 AM PDT > To: Magdalena Korczynska <mkucsf(a)gmail.com> > Reply-To: BinQing Wei <wei.binqing(a)gmail.com> > > The COMP Together champions in your area would like to announce the following event: > > Speaker: Max Kuhn, Pfizer > Ignacio Aliagas, Genentech > Title: Two talks on machine learning and applications in drug discovery > Date: 2016-06-28 > Time: 6:00 PM > Event ID: 34 > Sponsor: Gilead > > Location > Gilead > 333 Lakeside Drive > > Foster City CA 94404 > > Description and Notes > 6-7 pm networking over pizza & drinks > > 7-7:45pm 1st talk, Max Kuhn, Pfizer > > Title: Under the Hood of Cubist > Abstract: Cubist model rules are a relatively unknown machine learning model that has been extensively utilized in QSAR. The model is related to work published by Ross Quinlan in the early 90’s but had remained closed source until 2010. This talk will describe the model and its mechanics and an illustrative example will be shown to demonstrate the result. > > 7:45-8:15pm 2nd talk, Ignacio Aliagas, Genentech > > Title: The Importance of Being Earnest: Assessing Risk in Model Predictions > Abstract: QSAR models for the prediction of properties and DMPK end points can play a very important role to guide synthesis and advance compounds in the drug discovery paradigm. For prediction models to be used efficiently and with ease, integration with other modeling tools and software can facilitate their use. At the same time, it is critical to provide validation tools to quickly inform on the models’ domain of applicability within a given therapeutic project or chemical series. We describe a probabilistic approach to model prediction and how various QSAR models and validation tools are being delivered to drug discovery scientists at Genentech. > > 8:30pm End > > > If you would like to attend this COMP Together event, please visit the COMP website and register using the > http://app.acscomp.org/COMP_Together/meeting_signup.php?event_id=34. > > If you have any questions about this event, please contact BinQing Wei atwei.binqing(a)gmail.com. > > If you would like to update your COMP Together registration or unsubscribe, please visit http://app.acscomp.org/COMP_Together/reg_update/update_login.php

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[Compbio-allhands] Fwd: Job openings at Schrodinger
by Brian Shoichet 02 Jun '16

02 Jun '16

FYI Brian Shoichet, Professor Dept. of Pharmaceutical Chemistry, UCSF ---------- Forwarded message ---------- From: "Devleena Shivakumar" <devleena.shivakumar(a)schrodinger.com> Date: Jun 2, 2016 1:03 AM Subject: Job openings at Schrodinger To: "Brian Shoichet" <bshoichet(a)gmail.com> Cc: Hi Brian, We are looking to hire Applications Scientists in San Diego, Boston and Europe Job Description: Schrödinger, a technology leader specializing in software solutions for life science research and development, is searching for an Applications Scientist to be based in Boston. Applications Scientists work on applying Schrodinger's computational chemistry software to address challenging problems in drug discovery. The position also involves the development of new computational methods for drug discovery, scientific publications, and helping customers with using Schrodinger software. Responsibilities include drug discovery project support, engaging in scientific discussions with customers, giving presentations at conferences, demonstrating optimal use of the software, and providing customer training. Applications Scientists gain familiarity with our entire suite of structure-based and ligand-based software, including packages for docking, molecular simulations, homology modeling, pharmacophore modeling, cheminformatics, and quantum mechanics. A strong background in molecular modeling and computational chemistry with application to biological problems is highly desired. Exceptional communication skills, an outgoing personality, and a willingness to travel are required. Experience working on drug discovery projects is highly desirable. *Requirements:* - Ph.D. in computational chemistry or biophysics plus experience with pharmaceutical applications of molecular modeling software tools - Excellent interpersonal, communication, and organizational skills - Strong problem-solving ability - A broad knowledge of molecular modeling theory and applications - Ability to conduct independent research *Preferred:* - Post-doctoral research and/or relevant experience in the commercial sector - Biologics modeling and *in silico *protein engineering - Python programming experience If you know anyone looking to join my super amazing team, please have them contact me directly. Anyone from your group would be great! Best, Devleena -- Devleena Shivakumar, Ph.D. Senior Applications Scientist Schrödinger, Inc. http://www.schrodinger.com (201) 455-4980 (Phone) (212) 295-5801 (FAX) http://www.linkedin.com/in/devleena

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