Molecular Biophysics III: Biomolecular Interactions and Dynamics

1. Molecular Biophysics III: Biomolecular Interactions and Dynamics Course Directors: Judith Klein-Seetharaman jks33@pitt.edu Sanford Leuba leuba@pitt.edu Course TA: Oznur Tastan oznur@cs.cmu.edu Contact details in the handout.

2. What do we want you to learn in this class? • A. Scholarly goals • B. Scientific skills goals • C. Presentation goals • D. Networking goals

3. What do we want you to learn in this class and how will we help you reach these goals? • Lectures and review sessions by course directors • Lectures prepared and given by you • Summary of method written by you • Tutorials on data acquisition and analysis • Hands-on wet lab demos • Homeworks: analysis of real experimental data • Integration with the Seminar Series Lectures by course directors Lectures by you Methods summary Data acq / analysis Demos Data analysis homeworks Seminar Series

4. What do we want you to learn in this class? A. Scholarly goals • Goal: Obtain a rough idea of the current state of understanding of some of the major questions in biomolecular interactions and dynamics • Goal: Know how knowledge was obtained. • Goal: Given any biological question, provide ideas on how to address this question using biophysical approaches • Goal: Be able to weigh different biophysical approaches against each other in terms of • Complementary information • Applicability • Limitations • Goal: Get a practical idea and hands-on experience of some of the major biophysical techniques Lectures by course directors Lectures by you and the others Data acq / analysis Demos Data analysis homeworks

5. What do we want you to learn in this class? B. Scientific skills goals Lectures by you: lots of papers • Goal: Be able to skim through papers to extract most relevant information fast • Goal: Be able to read a paper in depth to understand all the details • Goal: Be able to identify which papers that are not part of the starting set of papers are important to get and read • Goal: Be able to synthesize the most important information from a large pool of information • Goal: Be able to ask scientific questions • Identify what it is that you don’t understand • Identify holes in somebody else’s scientific reasoning or presentation • Place information you obtain into context and identify what would be logical next steps in addressing a given problem, or what would be the next open questions that arise from a scientific result Lectures by you: key papers Not all key papers given Lectures by you Methods summary Audience of lectures by you

6. What do we want you to learn in this class? C. Presentation goals • Goal: Prepare well-structured, logical and understandable presentations • Goal: Be able to ask and answer questions • Goal: Be able to write a readable overview summary of a set of scientific publications Lectures by you Lectures by you Seminar Series Methods summary

7. What do we want you to learn in this class? D. Networking goals Lectures by you • Goal: Promote interactions between students and faculty • Goal: Prepare you to become an active member of the Structural Biology and Molecular Biophysics Seminar Series • Be able to ask questions in the discussion immediately following the seminar • Discuss science with the seminar speakers Seminar Series

8. Course materials • Supporting website: http://www.cs.cmu.edu/afs/cs.cmu.edu/project/structure-9/Courses/MB3/S07/ • Use to view and download syllabus, lecture notes etc. • Use to view and download papers • Emailing Judith or Sanford: • Communications regarding presentations (all of the intermediate and the final versions) • Your methods summaries • Emailing and/or handing out to Oznur: • Your homeworks • Your exams • Blackboard website: https://courseweb.pitt.edu/ • Login using your Pitt id (or id provided to you by Oznur) • Check on your grades

9. Lectures prepared by you • Read the papers • Identify additional papers if needed • Make first draft of presentation that includes • Overview of the field • Present key findings • Where does the field stand now? • What are open questions? • Show first draft to Oznur if you have difficulties with the English • Show first or 2nd draft to either Sanford or Judith, go through iterations with them as needed • Show xth draft to the expert (student mentor)

10. Participation • Students not presenting still need to read at least the main paper, ideally more • You will be judged on your participation, i.e. asking questions

11. Grading scheme 30% • 3 exams • 1st exam • 2nd exam • Final exam • Lectures prepared and given by you • Summary of method overview written by you • Participating in asking questions and discussing lectures given by your colleagues • Homeworks 10% 10% 10% 20% 5% 20% 25%

12. Expectations From US • Enthusiasm • We will help you as much as we can with the preparation of these lectures • Feedback: We will respond to your feedback • We will NOT explain the basics of the different techniques in class, you need to read up on the background yourself From YOU • Enthusiasm • Attendance and active participation • Lectures prepared and given by you are to be seen as projects: we expect you to spend a major amount of time on their preparation • Summary of methods overview written by you • Feedback: Tell us if you like or don’t like something, preferably immediately

13. Mock exam • Will not be graded, this is just to get an idea of background knowledge and for you to get an idea of the types of things we hope you will know as a minimum after the course • Try to briefly answer as many as possible • If you do not know the answer pls write “don’t know” so that we can tell the difference if you didn’t get time to look at a question