Goals:
This course will prepare students to understand and
incorporate 3D macromolecular structure into their research
and teaching.
The principles of protein structure will be
reviewed, including noncovalent bonds. Structural bioinformatics
and genomics will be introduced. Students will learn what
percentage of proteins have known 3D structures, and the
importance of crystallographic models compared to homology or
theoretical models.
In the computer laboratory, students will learn how to find 3D protein molecular models for proteins in their research, and how to use the FirstGlance in Jmol molecular visualization software (adopted by Nature) to investigate key structural features. | Protein structure will be related to function, evolutionary conservation and multiple-sequence alignments, and drug design. Specific oligomers will be constructed automatically by quaternary structure servers, and visualized. Students will learn how to prepare customized publication-quality molecular images, animations for Powerpoint slides, and online molecular scenes in the Proteopedia.Org wiki. Students will be challenged with molecular structure problems, and each student will prepare Powerpoint slides capturing examples of the skills they have learned. All the software is web browser-based, easy to use, works on Windows or Macintoshes, requires no installation, is free and open-source, and should be available for years to come. |
Day 1, Afternoon 13:00-16:10, Monday May 19.
Nanobiology Seminar Room 3F.
Bioinformatics Tools, by Katsumi Imada. |
Day 2, Morning 10:30-12:00, Tuesday May 20.
Nanobiology Seminar Room 3F.
Review of Protein Chemistry and Structure. Introduction to Structural Bioinformatics. |
![]() |
Day 2, Afternoon 13:00-17:50, Tuesday May 20.
Computer Lab, GSE Common 2F.
Proteopedia and FirstGlance in Jmol for exploring any macromolecule. Finding published molecules of interest. Begin Powerpoint Slides. |
After displaying many times, the molecule might not display. To correct this, please close/quit your browser, and then start a new browser session. This clears java memory, which is the problem. |
Day 3, Morning 10:30-12:00, Wednesday May 21.
Nanobiology Seminar Room 3F.
Introduction to Multiple Sequence Alignment (MSA) and Conservation ConSurf Server Structure of Atomic Coordinate ("PDB") Files |
Day 3, Afternoon, 13:00-17:50 Wednesday May 21.
Computer Lab, GSE Common 2F.
Evolutionary Conservation with ConSurf Authoring Molecular Scenes in Proteopedia Publication-Quality Images & Animations for Powerpoint |
Day 4, Morning 10:30-12:00, Thursday May 22.
Nanobiology Seminar Room 3F.
FirstGlance in Jmol -- Part III Salt Bridges & Cation-Pi Orbital Interactions Color by Undertainty ("Temperature") Gaps in the Model due to Disorder Intrinsically Unstructured Proteins |
Day 4, Afternoon 14:40-17:50, Thursday June 22.
Nanobiology Seminar Room 3F.
Mr. Suwa, Life Science Library |
Day 5, Morning 10:30-12:00, Tuesday May 27.
Nanobiology Seminar Room 3F.
Flagellar Assembly Structural Bioinformatics and Genomics. Homology (Comparative) Modeling Assessing Model Quality |
Day 5, Afternoon, 13:00-17:50 Tuesday May 27.
Computer Lab, GSE Common 2F.
Challenges Publication Quality Images and Animations with Polyview-3D Finishing Powerpoint Slides |
![]() |
Click on the above image for a larger view and explanation. |
Additional Resources.
Probably we will not have time in class to spend on these resources. Links are provided here in case you are interested to look at these later. |