Lac repressor bending the DNA operon. More..
Announcement - Two Day Course:
Protein 3D Structure Visualization and Structural Bioinformatics

May 15-16, 2007, University of Massachusetts Medical School, Worcester MA.

taught by Eric Martz,
(of the University of Massachusetts, Amherst MA USA. Principal author of FirstGlance in Jmol, Protein Explorer, and related resources.)

Organizers: and
This is a free course sponsored by the Cooperative Centers for Translational Research on Human Immunology and BioDefense, and the New England Regional Center of Excellence/Biodefense and Emerging Infectious Diseases.
Drug resistant HIV protease, D25N mutation hydrogen bonding to substrate peptide Asn (2FNT). Prabu-Jeyabalan, Nalivaika, Romano and Schiffer, 2006. More..

Level: This course is designed for faculty, postdocs, research staff and graduate students in biochemical sciences. No prior experience with protein 3D visualization or bioinformatics is necessary.
Objectives: Participants will use highly user-friendly software for visual investigation of 3D molecular structures of proteins, nucleic acids, and their interactions with each other and with ligands, substrates, and drugs, and protein evolutionary conservation. Hands-on experience will be largely with molecules of each participant's choosing. Those who participate in the optional second day will learn how to create rotatable, zoomable slides of customized molecular views.

Major histocompat- ibility protein (MHC I 2VAA): evolutionary conservation and variability from ConSurf. More..
Day One:
    9:00 - 12:30; 1:30 - 5:00:
      9:00 - 9:30: Amphitheater I S2-102
      9:30 onwards: Rooms S2-307C and S2-307D

    Today, participants will get lots of hands-on experience with:
  • Visual exploration of the 3D structures of macromolecules, such as proteins bound to ligands or nucleic acids.
  • Where to find protein structures related to your research, how they are determined, and how much of the genome is (and is not) known.
  • Teaching protein 3D structure, ligand interactions, and structural bioinformatics (some slides ready-made).

  • Seeing noncovalent bonds between a ligand and protein, and measuring distances.
  • Finding amino acids or sequence numbers of interest.
  • Locating patches conserved in evolution, and regions of rapid mutation.
  • Visualizing specific oligomers, and their subunit interactions.
  • Finding gaps in protein chains and evaluating the quality of a molecular model.
Day Two:
    Potassium channel (1R3J) showing membrane surface planes (from OPM).
    10:00 - 11:00: Amphitheater I S2-102
  • Seminar by Yorgo Modis (Research Website. Molecular Biophysics and Biochemistry, Yale University). The Structural Basis of Flaviviral Membrane Fusion.

    11:00 - 12:30, 1:30 - 5:00   Prerequisite: Attendence at Day One.   Rooms S2-307C and S2-307D
    Today, participants will get lots of hands-on experience with:
  • Using Protein Explorer to create custom molecular views.
  • Saving MolSlides showing rotatable, zoomable, custom molecular views. (See Sample MolSlides.)

    For interested participants, these methods can be introduced (time permitting):
  • Animating (morphing) molecular conformational changes. (See sample animations.)
  • Introduction to homology (comparative) modeling.
  • Mutating molecular models with DeepView/Swiss-PDB-Viewer.

Software & Ease of Use: Participants will use powerful, state of the art, free, open-source software designed for ease of use. Most of the software works equally well on Microsoft Windows, Macintosh OS X (Intel or PPC), or linux, and requires no installation. Learning specialized scripting command language, such as needed for RasMol or PyMol, is not necessary. Most of the resources use the Jmol java applet.

Computers: Computers will be provided for those who cannot bring their own laptops. Participants should bring their own laptop computers if possible. Windows, Mac OSX, or linux laptops are suitable for Day One. For most of Day Two, only Windows laptops will work.

Contents in Detail: Please see the course Syllabus. Direct questions about course content to Eric Martz.