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    Opportunity: COMPUTATIONAL BIOLOGIST Postoctoral Fellow -- SCOP/ASTRAL (#73669) @ Lawrence Berkeley National Laboratory -- Berkeley, CA (US)
    Submitted by Jeff Todd; posted on Tuesday, November 27, 2012



    This position is a postdoctoral research appointment responsible for several computational projects related to the SCOP and ASTRAL databases. The incumbent will help design and build the next generation of SCOP and ASTRAL. These resources provide carefully curated standards that are widely used by biologists to explore remote homologs of proteins of interest, and by computational biologists as a "gold standard" for benchmarking prediction algorithms. SCOP and ASTRAL are a critical resource for such studies: together, they have thousands of citations and tens of thousands of users. However, neither database has changed its basic design since early releases – more than 15 years ago in the case of SCOP.

    Both databases must be redesigned to account for aspects of protein evolution that were not appreciated at the project's inception, such as metamorphic proteins and homologous proteins that have evolved different folds. To address bottlenecks in the curation process, machine learning-based algorithms must be developed in order to automatically and reliably classify newly solved structures in the SCOP hierarchy.

    Work will be done in close collaboration with the SCOP curators, Alexey Murzin's group at the MRC Laboratory of Molecular Biology in Cambridge, UK, and with Steven Brenner's computational biology lab at University of California, Berkeley. The redesigned and integrated databases will provide a revitalized foundation for future studies of protein structure and evolution.


    • Evaluate and develop novel algorithms for detection of evolutionary relationships between proteins
    • Help restructure the SCOP hierarchy to reflect recent changes in understanding of protein evolution
    • Publish scientific papers and present findings at meetings
    • Participate in group meetings and seminars
    • Maintain an accurate and detailed electronic notebook documenting research activities and results


    • Demonstrated experience in developing and publishing novel computational biology algorithms
    • Experience using machine learning tools and algorithms
    • Experience working with macromolecular structure data
    • Familiarity with computational biology databases, including SCOP, ASTRAL, Pfam, PDB
    • Excellent communication skills
    • Ph.D. in computer science or computational biology-related discipline


    • Familiarity with modern open source databases and website development technology (e.g., MySQL, Java, and AJAX)
    • Familiarity with Linux


    This is a one-year term position with the opportunity for renewal dependent upon many factors, including job performance and budget.


    Berkeley, CA




    For full consideration, follow the link to the job posting and apply directly to Berkeley Lab. As part of the online application process, please complete a profile, including uploading attachments relevant to the opportunity. Be sure to reference where you found the position (Bioinformatics.Org).[...]73669


    Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce.

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