Molecular Biophysics III: Biomolecular Interactions and Dynamics

1
Molecular Biophysics III Biomolecular
Interactions and Dynamics

• Course Directors
• Judith Klein-Seetharaman jks33_at_pitt.edu
• Sanford Leuba leuba_at_pitt.edu
• Course TA
• Oznur Tastan oznur_at_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

• 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 dont understand
• Identify holes in somebody elses 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 lots of papers
Lectures by you key papers
Not all key papers given
Lectures by you
Methods summary
Audience of lectures by you
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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
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What do we want you to learn in this class? D.
Networking goals

• 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

Lectures by you
Seminar Series
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Course materials

• Supporting website http//www.cs.cmu.edu/afs/cs.c
  mu.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

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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)

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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

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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
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Expectations

• 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 dont like
  something, preferably immediately

• 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

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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 dont
  know so that we can tell the difference if you
  didnt get time to look at a question