Topic outline

  • General

    Introduction to 3D-Structure Visualization and Homology Modeling using the Swiss-Model Workspace

    Lorenza Bordoli, SIB & Biozentrum University Basel


    Three-dimensional protein structures are key to a detailed understanding of the molecular basis of protein function. Combining sequence information with 3D structure gives insights for the development of effective rational strategies for experiments such as site directed mutagenesis, studies of disease related mutations, or the structure based design of specific inhibitors.

    The goal of this course is to expose the participants to 3-dimensional structures of proteins. Analysis and visualization softwares (DeepView) will be used to display, analyze, compare and interpret protein structures. The second part of the course is dedicated to protein structure prediction using the Swiss-Model expert system for homology modeling.

    • Part I

      Topics:

      • Theory: "3D Structures of proteins: recapitulation" [pdf]

      • Practice: "3D Structure Analysis and Visualization using DeepView":

        - DeepView website
        - Download/Installation: Please download DeepView on your local PC from the website.
        - Please follow Gale Rhodes's Basic Tutorial (Chapters 1-6) to learn the basics of the DeepView program.
        - Molecular coordinate files (in *.pdb format) can be downloaded from the PDB home page or directly imported within Deep View from the server (File Menu-> Import ...).

      • Part II

        Topics:

        • Theory: "Introduction to Homology Modeling"
        • Theory: "Recapitulation: Sequence alignments, Protein domain annotation"

        • Lecture [pdf]

      • Part III

        Topics:

        • Theory: "Homology Modeling using the Swiss-Model Workspace (Part I)":
          • Target sequence feature annotation
          • Template identification
          • Target-template alignment
          • Homology Modeling by template based fragment assembly
          • Model quality estimation

        • Lecture [pdf]

        • Practice: The Swiss-Model Workspace: please first create an account for your personal workspace.
        • DeepView website:
          • Download/Installation: Please download DeepView on your local PC from the website.
          • Download the PROSITE patterns ("prosite.dat" file) into your "spdbv/usrstuff" directory. The FTP site for download can be found [here]
        • Link to the exercises Part 1&2
      • Part IV

        Topics: