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

May 28, 2008, Osaka University (Japan)
Nanobiology 3F, 9:00 - 17:00. Host: Professor Keiichi Namba.

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

To register, please contact Kana Moriya
The bacterial flagellar hook: a molecular universal joint. 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.
Language: The course will be taught in English.
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. Participants will learn how to create publication-quality molecular images, rotating molecules in Powerpoint slides, and custom on-line rotating molecular scenes in Jmol.

Potassium channel (1R3J) showing membrane surface planes (from OPM).
Participants will gain hands-on computer experience with:
  • Visual exploration of the 3D structures of macromolecules, such as proteins bound to ligands or nucleic acids.
  • Finding protein structures related to your research, how they are determined, and how much of the genome (and is not) known.
  • Resources for teaching protein 3D structure, ligand interactions, and structural bioinformatics (some slides ready-made).

  • Seeing noncovalent bonds between a ligand and protein, and measuring interatomic 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.
  • Evaluating the quality of a molecular model, and finding gaps in protein chain models.

  • Creating static publication-quality molecular images for papers or slides.
  • Creating rotating or animated molecular views ready to paste into Powerpoint slides or websites.
  • Creating customized, rotatable/zoomable molecular scenes and molecular structure tutorials online in Jmol at Proteopedia.Org.

Major histocompat- ibility protein (MHC I 2VAA): evolutionary conservation and variability from ConSurf. More..
Software & Ease of Use: Participants will use powerful, state of the art, free, open-source software designed for ease of use. This 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: Participants should bring their own laptop computers if possible (Windows, Mac OSX, or linux). A limited number of Windows laptops will be available for participants who cannot bring their own laptops. Network connections will be required: please bring a network cable.

What is Not Covered: Crystallography and model building. Changing molecular models (mutation, energy minimization). Building protein molecular models from sequences alone (as by homology modeling). Making animations of conformational changes. Professor Martz will be available the day after the course to help with these or other methods not covered in the first day.

Contents in Detail: For the complete agenda, please see the course Syllabus. Direct questions or applications to Professor Keiichi Namba