Topic outline

  • General

    Protein Bioinformatics: Sequence-Structure-Function

    25-28 January 2016, Basel

    Trainers: Amos Bairoch, Alessandro Barbato, Marie-Claude Blatter, Martino Bertoni, Lorenza Bordoli, Geoffrey Fucile, Elisabeth Gasteiger, Pascale Gaudet, Jürgen Haas, Ivo Pedruzzi, Torsten Schwede, Christian Sigrist, Gabriel Studer, Christian von Mering
    Venue: University of Basel, Biozentrum
    ECTS: 1.0 (given a passed exam)
    Fee: 200 CHF for academics (social dinner included). Others, please contact us.
    Application deadline:        
    January 15, 2016
    Application status: Closed


    Sequence-structure-function relationships of proteins are central to a comprehensive understanding of cellular biology. However, many proteins lack direct and detailed information regarding structure, function, and complex formation. This knowledge gap can be overcome through clearly defined relationships between proteins and the integration of existing data.

    Participants will be introduced to primarily web-based tools, designed for life scientists without substantial computational training, for integration and inference of protein structure and function data. The lectures and workshops will be led by the SIB developers of these methods, with specific emphasis on translating this training to the participants' own research questions culminating in a "bring your own protein(s)" workshop.


    This course is intended for a wide audience covering Master and PhD students, post-docs, and senior researchers in all areas of life science.

    Learning objectives

    At the end of this course, participants are expected to be able to:

    • identify proteins related by sequence and/or structure and integrate functional annotations from public databases
    • develop homology models of protein structure, assess their quality, and make inferences regarding function and regulation
    • integrate and interpret protein-protein interaction data
    • apply these methods to their own proteins of interest


    Participants should bring a laptop with wireless connectivity and make sure they have the permission to install software if necessary. Knowledge of UNIX is not necessary.


    The registration fees for academics are 200 CHF. This includes course content material, coffee breaks, and a social dinner. Participants from non-academic institutions should contact us before application

    Deadline for registration and free-of-charge cancellation is set to January 15, 2016. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to this and other general conditions.

    Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.


    University of Basel, Biozentrum, room 106 and Kaktuslounge

    Additional information

    Coordination: Geoffrey Fucile

    You are welcome to register to the SIB courses mailing-list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

    For more information, please contact

    • Monday January 25th

      Using sequence centered resources through the web and some of the tools used for annotation

      All the documents (slides and practicals) are online here:

      9:00-10:30 | Welcome address, SIB overview, and the ExPASy resource portal (Elisabeth Gasteiger)

      10:30-11:00 | Coffee break

      11:00-13:00 | Protein sequence databases, sequence annotation pipeline and UniProtKB/Swiss-Prot (Marie-Claude Blatter)

      13:00-14:00 | Lunch

      14:00-15:00 | Practicals (Elisabeth Gasteiger and Marie-Claude Blatter)

      15:00-15:30 | Coffee break

      15:30-17:00 | Practicals and discussion

      • Tuesday January 26th

        Protein structure: Going 3D!

        9:00-10:30 | Introduction to protein structure analysis (Geoffrey Fucile)

        10:30-11:00 | Coffee break

        11:00-12:30 | Protein Structure Visualization with Swiss PDB Viewer / DeepView (Lorenza Bordoli)

        12:30-13:45 | Lunch

        13:45-15:15 | Homology modeling (Torsten Schwede)

        15:15-15:45 | Coffee break

        15:45-17:45 | Practicals

        • Wednesday January 27th

          Using sequence centered resources through the web and some of the tools used for annotation

          9:00-10:30 | Protein sequence standardization resources (Pascale Gaudet)

          10:30-11:00 | Coffee break

          11:00-12:30 | InterPro, GO, PROSITE-HAMAP (Christian Sigrist & Ivo Pedruzzi)

          12:30-14:00 | Lunch

          14:00-15:30 | neXtprot (Amos Bairoch)

          15:30-16:00 | Coffee break

          16:00-17:00 | Practicals

          ~19:00 | Social Dinner!

          • Thursday January 28th

            Protein-Protein Interactions

            9:00-10:30 | STRING (Christian von Mering)

            10:30-11:00 | Coffee break

            11:00-12:30 | STRING Practicals

            12:30-14:00 | Lunch

            14:00-15:30 | "Bring your own protein" workshop! (and course exam for those participating)

            15:30-16:00 | Coffee break

            16:00-17:00 | "Bring your own protein" workshop!