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


Monday, May 14, 2012, 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, molecular tutorials,
coauthor of Proteopedia.Org, and coauthor of the ConSurf Server.


To register, please contact Kana Moriya
Please Bring a Laptop Computer (details).
 
The bacterial flagellar hook: a molecular universal joint. More..

Level: This course is designed for faculty, postdocs, research staff and graduate students in biological/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. We will touch on the challenges of crystallography, uncertainty in electron density maps, and the nature of 3D structure data ("PDB files"). Participants will learn how to create interactive, on-line customized molecular structure scenes useful in teaching, research, and journal supplementary materials; as well as publication-quality molecular images, and rotating molecules in Powerpoint slides.

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.
  • Obtaining homology models with an automated server (Swiss-Model) when a crystallographic structure is not available.

  • 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 and sharing customized, rotatable/zoomable online 3D molecular structure-function explanations in the Proteopedia.Org wiki.

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 MacBook (or older Windows) laptops will be available for participants who cannot bring their own laptops. Network connections will be required: please bring a network cable. Wireless network may be available also. Bring your power adaptor: electrical power outlets will be available.

What is Not Covered: Crystallography and model building. Changing molecular models (mutation, energy minimization). Making animations (morphs) of conformational changes. Professor Martz will be available for private appointments on Tuesday May 15 to help with specific projects and methods not covered in the workshop.

Contents in Detail: For the detailed agenda, please see the course Syllabus.

Direct questions or applications to Professor Keiichi Namba: