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

[Compbio-allhands] Fwd: Post Doctorant positions_BiMoDyM_France
by Andrej Sali 25 Jun '12

25 Jun '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: Luba Tchertanov <luba.tchertanov(a)lbpa.ens-cachan.fr> > Subject: Post Doctorant positions_BiMoDyM_France > Date: June 25, 2012 3:16:39 AM PDT > To: kuriyan(a)berkeley.edu, Mark Sansom <mark.sansom(a)bioch.ox.ac.uk>, jmccammon(a)ucsd.edu, ruthnu(a)helix.nih.gov, roux(a)uchicago.edu, rebecca.wade(a)eml-r.villa-bosch.de, Frank Noe <frank.noe(a)fu-berlin.de>, shoshana.wodak(a)sickkids.ca, "Bahar, Ivet" <bahar(a)pitt.edu>, sali(a)salilab.org, "Ronald M. Levy" <ronlevy(a)lutece.rutgers.edu>, jonuchic(a)ucsd.edu, modesto.orozco(a)irbbarcelona.org, klebe(a)mailer.uni-marburg.de, igor.pivkin(a)usi.ch, mzoppe(a)ifc.cnr.it, Woody.Sherman(a)schrodinger.com, Ruben Abagyan <ruben(a)ucsd.edu>, maculan(a)cos.ufrj.br, okeskin(a)ku.edu.tr, marc_vidal(a)dfci.harvard.edu, "Prof. Haim J. Wolfson" <wolfson(a)tau.ac.il>, pascal.hersen(a)univ-paris-diderot.fr, Fabian Theis <fabian.theis(a)helmholtz-muenchen.de>, jaxelrod(a)stanford.edu, stas(a)princeton.edu, kandt(a)bit.uni-bonn.de, Jaroslaw Polanski <jaroslaw.polanski(a)us.edu.pl>, okamoto(a)phys.nagoya-u.ac.jp, denispt(a)pasteur.fr, yamato(a)phys.nagoya-u.ac.jp, akimura(a)tb.phys.nagoya-u.ac.jp, caflisch(a)bioc.uzh.ch, philippe.derreumaux(a)ibpc.fr, Chantal Prevost <chantal(a)ibpc.fr>, cragnolini(a)ibpc.fr, phuong.nguyen(a)ibpc.fr, francesco.oteri(a)ibpc.fr, charles.robert(a)ibpc.fr, Sophie.Sacquin-Mora(a)ibpc.fr, heidi.koldsoe(a)bioch.ox.ac.uk, michal.linial(a)huji.ac.il, taly(a)ibpc.fr, Viet Duc <frauman05(a)yahoo.de>, Elena.Papaleo(a)bio.ku.dk, Fabian Theis <fabian.theis(a)helmholtz-muenchen.de>, Sara Nichols <sara.nichols(a)gmail.com>, gregor.lichetner(a)fu-berlin.de, "Coulon, Antoine (NIH/NIDDK) [F]" <antoine.coulon(a)nih.gov>, johannes.schoeneberg(a)fu.berlin.de, alexander.ullrich(a)fu-berlin.de, mickael.lelimousin(a)bioch.ox.ac.uk, matthieu.chavent(a)bioch.ox.ac.uk > > Dears Colleagues, > > Two post doctoral research positions are available at the Bioinformatics, Molecular Dynamics and Modeling (BiMoDyM) team (http://tinyurl.com/tchertanov) Molecular Oncology and Pharmacology, LBPA, ENS de Cachan (http://www.ens-cachan.fr/) France. > The required profiles of candidats are descibed in the attached documents. > Thank you very much for larger distribution of this information. > > Sincerely your, > Luba Tchertanov > > ********************* > Dr. Luba Tchertanov > Directeur de Recherche, CNRS > > Membre du Comité de Pilotage du LabEx LERMIT > Coordinateur ENSC-UFRJ > Collége Universitaire Franco-Brésilien Santos Dumont > > Resp. BiMoDyM > LBPA-CNRS, ENS de Cachan, > 61 avenue du Président Wilson > 94235 CACHAN CEDEX, FRANCE > > Tel: +33 (0)1 4740 7662 > Cell: +33 (0)6 6115 9611 > Fax: +33(0)1 4740 7671 > e-mail: Luba.Tchertanov(a)lbpa.ens-cachan.fr > > >

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[Compbio-allhands] Fwd: postdoctoral and PhD positions
by Andrej Sali 25 Jun '12

25 Jun '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: Michael Nilges <michael.nilges(a)pasteur.fr> > Subject: postdoctoral and PhD positions > Date: June 25, 2012 5:03:38 AM PDT > To: Alexandre Bonvin <a.m.j.j.bonvin(a)uu.nl>, Andrej Sali <sali(a)salilab.org>, annick.dejaegere(a)igbmc.fr, Axel Brunger <brunger(a)stanford.edu>, carol.robinson(a)chem.ox.ac.uk, Catherine Etchebest <catherine.etchebest(a)univ-paris-diderot.fr>, Cheryl Arrowsmith <carrow(a)uhnres.utoronto.ca>, Christian Griesinger <cigr(a)nmr.mpibpc.mpg.de>, Christoph Mueller <christoph.mueller(a)embl.de>, "David A. Agard" <agard(a)msg.ucsf.edu>, DavidBaker <dabaker(a)u.washington.edu>, David Perahia <david.perahia(a)ens-cachan.fr>, Dmitri Svergun <svergun(a)embl-hamburg.de>, Edward Egelman <egelman(a)virginia.edu>, Ernest Laue <e.d.laue(a)bioc.cam.ac.uk>, "G. Klebe" <Klebe(a)staff.uni-marburg.de>, Gerald Kneller <gerald.kneller(a)cnrs-orleans.fr>, Gerhard Wagner <gerhard_wagner(a)hms.harvard.edu>, Gilles Labesse <Gilles.Labesse(a)cbs.cnrs.fr>, Helmut Grubmueller <hgrubmu(a)gwdg.de>, Hoch Jeffrey <hoch(a)uchc.edu>, Ivano Bertini <bertini(a)cerm.unifi.it>, Jody Puglisi <puglisi(a)stanford.edu>, Julie Forman-Kay <forman(a)sickkids.ca>, Juri Rappsilber <juri.rappsilber(a)ed.ac.uk>, Konrad Hinsen <research(a)khinsen.fastmail.net>, liliane.mouawad(a)curie.u-psud.fr, Lewis Kay <kay(a)pound.med.utoronto.ca>, Luba Tchertanov <luba.tchertanov(a)lbpa.ens-cachan.fr>, Marc Baaden <baaden(a)smplinux.de>, Marc Baldus <maba(a)mpibpc.mpg.de>, Marius Clore <mariusc(a)intra.niddk.nih.gov>, Martin Beck <martin.beck(a)embl.de>, Michael Levitt <michael.levitt(a)stanford.edu>, Michael Sattler <sattler(a)helmholtz-muenchen.de>, michel kochoyan <michel(a)cbs.cnrs.fr>, Michele Vendruscolo <mv245(a)cam.ac.uk>, Oliver Lange <oliver.lange(a)tum.de>, Roland STOTE <rstote(a)igbmc.fr>, Aebersold Rudolf <aebersold(a)imsb.biol.ethz.ch>, Rebecca Wade <rebecca.wade(a)h-its.org>, ZINN Sophie 140275 <Sophie.ZINN(a)cea.fr>, Tom Simonson <Thomas.Simonson(a)polytechnique.fr>, William.Degrado(a)ucsf.edu, Wolfgang Baumeister <baumeist(a)biochem.mpg.de> > > Dear collegues, > > I would be very grateful indeed if you could transmit the information on the available positions to interested candidates. > > Best regards > > Michael > > Applications are invited for Postdoctoral and PhD positions funded by the ERC project BayCellS, to work on the development of innovative molecular modeling concepts for cellular structural biology. The successful candidates will join the Structural Bioinformatics Unit in the Department of Structural Biology and Chemistry at the Pasteur Institute in Paris, France. > > To characterize 3D structures of the large and often flexible macromolecular complexes that govern cellular processes, high resolution structure determination is the exception, and multiple sources of structural data at multiple resolutions are employed. Integrating these data into one consistent picture poses particular difficulties: data are much more sparse than in high resolution methods; data sets from heterogeneous sources are of highly different and unknown quality and may be mutually inconsistent; data are in general averaged over large ensembles and long measurement times. The project is to develop a consistent framework for this highly complex data integration problem, principally based on Bayesian probability theory. Appropriate models for the major data types used in hybrid approaches (electron microscopy, cross-linking/ mass spectrometry, various spectroscopy techniques, SAXS, ...) will be developed, as well as representations to include structural knowledge for individual components of the complexes. The new methods will be applied to a series of problems with increasing complexity. The ideal candidate has a strong background in mathematics/ statistics, theoretical biophysics or molecular modeling applied to macromolecular structure determination; experience in programming (Python, C); and an interest in Bayesian probability theory. > > Contact: Michael Nilges, Department of Structural Biology and Chemistry, Structural Bioinformatis Unit; michael.nilges(a)pasteur.fr > > > > > > > > ================ > Prof. Michael Nilges > Structural Bioinformatics Unit, Head > Department of Structural Biology and Chemistry, Head > Institut Pasteur, CNRS URA 2185 > 25-28 rue du docteur Roux, F-75015 Paris, France. > Tel: +33 1 45 68 82 30; Fax: +33 1 45 68 87 19 > secrétariat: +33 1 44 38 91 09 > > >

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[Compbio-allhands] FW: Hiring a Computational Biologist
by Jacobson, Matt 22 Jun '12

22 Jun '12

Brian was a BMI graduate student … very good scientist From: brian tuch <brian.tuch(a)gmail.com<mailto:brian.tuch@gmail.com>> Date: Friday, June 22, 2012 1:30 PM To: "btuch(a)onyx.com<mailto:btuch@onyx.com>" <btuch(a)onyx.com<mailto:btuch@onyx.com>> Subject: Hiring a Computational Biologist Hi all, I am looking for the best industry-bound graduate students and postdocs you know to join my new genomics group at Onyx. Onyx is small, but rapidly growing oncology therapeutics company in South San Francisco. My group's goals are to understand why certain patients respond to our existing drugs and to identify new drug targets in patients that do not. A lot of interesting basic and clinical research is involved in these efforts and I expect we will be publishing many of our findings. We will be starting with copious clinical samples and a generous budget, but not much else; our genomics infrastructure must be built from the ground up. This is my group's first hire, so I'm hoping to find an adaptable, star computational scientist, someone you might have thought to hire when you first started your labs. The hire will rapidly gain knowledge of cancer biology and the pharmaceutical process here, so those are not requirements. The most important characteristics are analytical chops and enthusiasm. The job description and specific requirements are attached. Please feel free to circulate this message. Thank you for your assistance. Cheers, Brian

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[Compbio-allhands] Fwd: Open Position for Computer System Administrator
by Andrej Sali 14 Jun '12

14 Jun '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: "Montelione, Gaetano" <guy(a)cabm.rutgers.edu> > Subject: Open Position for Computer System Administrator > Date: June 14, 2012 7:49:06 AM PDT > To: "Tejero, Roberto" <Roberto.Tejero(a)uv.es>, Honig Barry <bh6(a)columbia.edu>, Burkhard Rost <rost(a)columbia.edu>, "Y. Janet Huang" <yphuang(a)cabm.rutgers.edu>, "Ronald M. Levy" <ronlevy(a)lutece.rutgers.edu>, "Gerstein, Mark(a)yale.edu" <Mark.Gerstein(a)yale.edu>, Andrej Sali <sali(a)salilab.org>, "David A. Case" <case(a)biomaps.rutgers.edu> > Cc: John Everett <everett.jk(a)gmail.com> > > Phil Kostenbader, our computer system administrator, has taken a new job and will > be leaving CABM shortly. > > So we are looking for a new full time computer system administrator. Person > should be familiar with Linux system administration, including: > > - experience with Linux cpu clusters > - web server administration / Apache experience > - LDAP authentication > - network and system security /firewall DMZ > > > We will prepare a formal ad soon -- but I will appreciate if you can > circulate this to anyone you know who might be interested. They > can contact me directly > > Guy Montelione

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[Compbio-allhands] Fwd: Postdoc position available -- interactive molecular graphics -- Uppsala, Sweden
by Tom Ferrin 12 Jun '12

12 Jun '12

-------- Original Message -------- Subject: Postdoc position available -- interactive molecular graphics -- Uppsala, Sweden Date: Fri, 8 Jun 2012 12:47:08 -0500 From: Samuel Flores <samuelfloresc(a)gmail.com> To: tef(a)cgl.ucsf.edu Hi Tom, I hope all is well with you. As a longtime user of Chimera, I am familiar with your work. I think you may be able to help me identify a brilliant almost- or recently-graduated PhD for an opening in my lab. I am looking for a rare skill set -- someone who can make a next-generation interactive 3D modeling tool based on my internal coordinate MMB code and a graphics library (Blender, Rasmol, etc). The tool will go far beyond existing viewers, allowing users to assemble macromolecules, flexibilize them where desired, and rearrange domains interactively, as well as performing a number of dynamics tasks supported by MMB. I am attaching the job announcement and hope you can distribute it widely by email and (if possible) on bulletin boards at UCSF. I will be in Palo Alto July 2nd and perhaps 3rd and would love to drop by and chat, so as to receive your advice on this project, if you have the time. Sam

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[Compbio-allhands] Fwd: Referred by Christine Humblet
by Andrej Sali 04 Jun '12

04 Jun '12

Hi Andrej, If you decide to post these positions to your email list please have the students and postdocs contact me at the information below. Jared Jared Kaleck Account Executive Klein Hersh International 215-830-9211 Ext. 116 jkaleck(a)kleinhersh.com www.kleinhersh.com Begin forwarded message: > From: Jared Kaleck <JKaleck(a)kleinhersh.com> > Subject: RE: Referred by Christine Humblet > Date: June 4, 2012 11:26:00 AM PDT > To: Andrej Sali <sali(a)salilab.org> > > > > Eli Lilly – Indianapolis, IN > Principal Research Scientist/Senior Research Scientist > Computational Chemistry > The Discovery Chemistry Research and Technology Division at Eli Lilly Company is looking to further enhance the scientific talent base of the organization by identifying individuals with high potential and emerging track record of delivering drug discovery innovation. > > Ideal Individuals to Compliment Lilly’s Scientific Team > · Talented Ph.D. Computational Chemistry with broad expertise in Computer-Aided Design approaches. > · Creative thinking and problem solving skills – ability to bring new ways of applying or pioneering computational approaches and/or new initiatives to facilitate and enhance drug discovery projects. > · Proven/emerging scientific leadership abilities – must include leadership work with outside partners and/or scientists from academia. > · Ability to influence scientific direction across research sites, discovery functions and teams. A proven desire to make an impact on projects through cross-functional teamwork. > · Strong background in medicinal chemistry and lead generation/lead optimization approaches. > · Organizational development and mentoring skills. > · Excellence in communication and networking skills. > · Demonstrated abilities to multi-task. > · Entrepreneurial and innovative approach to science; good judgment, risk taking and intuition. > · Programming skills (Perl, Python, Pipelining) preferred. > > > > NOVARTIS – Cambridge, MA > Computational Chemical-Biology Research Investigator (Ph.D) > > Job Description: > > A position is available for a highly motivated scientist in the in silico Lead Discovery group of the Center for Proteomic Chemistry platform. This is an exciting opportunity to perform cutting-edge computational research at our Cambridge USA site. The position will be responsible for the development of robust computational hypothesis with a variety of drug discovery project teams for the purposes of lead discovery. You will apply state of the art computational approaches to elucidate the biological profile of small molecules regarding their targets, off-targets and phenotypic outcome via an in-depth understanding of biological networks, systems biology, bioinformatics and cheminformatics > > Minimum requirements: > > The ideal candidates will possess the following qualifications: > > · Ph.D. degree in computational biology, systems biology, bioinformatics, cheminformatics or a related field. > · Experience with 'omics analysis (transcriptomics, proteomics, metabolomics, chemogenomics). > · Ability to computationally navigate molecular pathways and networks and form hypotheses about compounds, targets, phenotype, and disease associations > · Familiarity with compound databases, such as ChEMBL or PubChem, and public bioinformatics databases. > · Understanding of up-to-date biological screening paradigms like reporter assays, mRNA signatures, assays for transcription, translation, stability, and post-translational modifications and high content screens. > · A solid understanding of quantitative data analysis, data mining and pattern recognition methods. > · Ability to work independently and collaborate in multidisciplinary teams locally and globally. > · Strong analytical and problem-solving skills and scientific creativity are essential. > · Excellent oral and written communication skills and organizational skills are required. > · Familiarity with life sciences software (R, Spotfire, Pipeline Pilot, Knime, Cytoscape, GeneGo) is desirable, as is a working knowledge of Relational Databases and SQL. > > > > NOVARTIS – Cambridge, MA > Computational Chemistry or Biology Research Investigator (Ph.D) > > Job Description: A position is available for a highly-motivated scientist to join a dynamic group in the Center for Proteomic Chemistry/Lead Finding Platform. This is an exciting opportunity to perform cutting-edge research at our Cambridge site. > First, you will be responsible for the analysis and development of HTS screening hits to leads. You will apply state of the art chemometric or bioinformatics approaches for the elucidation of the biological profile of small molecules regarding their targets, off-targets and phenotypic outcome. Second, you will provide support, maintenance and further development of key infrastructure related to virtual screening databases and methods, and an internally developed computational services framework. > > Minimum requirements: The ideal candidate will possess the following qualifications: > • Ph.D. degree in computational biology, bioinformatics, cheminformatics or a related field. > • Databases: MySQL, SQL Server and Oracle > • Languages: C, C#, Perl, Python, Web Applications and Tools: HTML, ASP.net, > • Experience with 'omics data and molecular pathway/network analysis to enhance target knowledge. > • Familiarity with compound information databases such as ChEMBL or PubChem. > • Understanding of up-to-date biological screening paradigms like reporter assays, mRNA signatures, assays for transcription, translation, stability, and post-translational modifications and high content screens. > • A solid understanding of basic statistics and quantitative data analysis, data mining and pattern recognition methods. > • Familiarly with PipelipePilot and Knime – a big plus > • Ability to both work independently and collaborate in multidisciplinary teams. > • Strong analytical and problem-solving skills and scientific creativity are essential. > • Excellent oral and written communication skills and organizational skills > > > > > > > > Jared Kaleck > Account Executive > Klein Hersh International > 215-830-9211 Ext. 116 > jkaleck(a)kleinhersh.com > www.kleinhersh.com >

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[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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