Course
Syllabus and Overview
Physics
323/623: Computational Biophysics Lab
Time: Wed
Instructors: Drs. Jacquelyn S. Fetrow and Freddie R.
Salsbury, Jr.
Office: Olin 301A and Olin 301B
Email: salsbufr@wfu.edu, fetrowjs@wfu.edu
Web
page: http://www.wfu.edu/~fetrowjs/Teaching.htm
Office
Hours: TBA
Textbook: Molecular Modeling, Principles and
Applications (Leach), Prentice Hall; this comprehensive textbook will provide
theory and background on the methods that we will be using in this course. You
will not be required to know the chapters that we do not cover; we will also
use the lecture textbook, Molecular Biophysics (Duane), for supplemental
reading during the semester
Research-based learning: The best way to learn to use computational biophysics methods is to
apply those methods in a research-based format and we will follow this learning
approach in this course. We will teach
methods and theory, but you will apply the methods and theory to a problem for
which we do not yet know the “right answer;” however, it is a problem in which
we are interested.
This semester, we have chosen the
protein peroxiredoxin (Prx) for analysis.
Each of you will be assigned a different Prx structure. This structure will be the one that you use
and analyze during each of the laboratory exercises. Your grade will be partially dependent on your
knowledge of your structure, your observations and analysis of the results you
obtain for your structure, and your critical comparison of your data to the
results produced by other students on their own Prx structures.
Background reading for Prxs: The following journal articles will provide critical background
reading for the Prx protein family. All
are available on PubMed and all are required reading.
Grading:
Labs (8 exercises, 50
points each) 400
points (480 gr)
Quiz 50
points
Class participation,
observations, and creativity 100
points
Paper (4 drafts, 50
points each; final paper 100 points) 300
points
Total: 850
points
Graduate credit: Students registered for any of the graduate course numbers and receiving
graduate credit will be held to higher expectations than students receiving
undergraduate credit. Graduate students will be expected to answer lab and exam
questions in more detail. Often, there
will be an additional, more difficult question that graduate students must answer
in addition to the other questions.
Graduate students are expected to participate in class more often and to
offer more insightful observations.
Software/hardware required: Laptop computer, loaded with
SSH, Hummingbird Exceed (X-windowing software), NAMD (DEAC cluster), VMD (DEAC
cluster), MEAD (DEAC cluster), MatLab (laptop); printer access; Blackboard
Tentative Schedule
|
Date |
Topic |
|
Quizzes and Papers |
Laboratory Assignment Due Date (due by the beginning of lab on due date) |
Leader |
|
Wed Aug
25 |
Lab 1: Load
software; conformational analysis using physical models |
Leach, Sections 1.1-1.9, 9.1-9.3, 10.1-10.2; Duane,
Sections 4.1-4.4, 5.1-5.4 (Leach, 4.10)* |
|
|
JSF |
|
Wed Sep
1 |
Lab 2: Introduction
to protein structure web sites |
Section 9.11, Appendix 10.2, Leach; Prx journal articles (Duane, Section 5.6) |
Quiz
(amino acids and nucleotides) |
Lab 1
due |
JSF |
|
Wed Sep
8 |
Lab 3: Introduction
to DEAC cluster, Linux operating system; editing and queueing |
Prx
journal articles for assigned structure |
Paper,
chapter 1, Prx seq, struct, funct |
Lab 2
due |
FRS |
|
Wed
Sep15 |
Lab 4:
Dynamics in explicit solvent |
Sections
4.1-4.16, 5.1-5.7, 6.4-6.9, Leach |
|
Lab 3
due |
JSF,
FRS |
|
Wed Sep
22 |
Lab 4:
Dynamics in explicit solvent |
Sections
4.14, 7.1-7.9, Leach |
|
|
JSF,
FRS |
|
Wed Sep
29 |
Lab 5: Molecular
visualization using VMD |
Duane,
Section 5.6 |
|
Lab 4
due |
JSF |
|
Wed Oct
6 |
Lab 5
(cont): Molecular visualization using VMD |
Duane,
Section 5.6 |
Paper,
chapter 1 draft 2; chapter 2 (methods)
draft 1 |
|
JSF |
|
Wed Oct
13 |
Review
of simulation strategy and methods |
Sections
5.1-5.7, 6.4-6.9, 7.1-7.9 Leach |
|
Lab 5
due |
JSF/
FRS |
|
Wed Oct
20 |
Lab 6:
NAMD trajectory analysis (CHARMM and VMD) |
Sections
6.6, 7.1-7.9, Leach |
|
|
JSF |
|
Wed Oct
27 |
Lab 6:
NAMD trajectory analysis (CHARMM and VMD) |
Sections
6.6, 7.1-7.9, Leach |
|
|
JSF |
|
Wed Nov
3 |
Lab 6: NAMD
trajectory analysis (comparison between student results) |
Sections
6.6, 7.1-7.9, Leach |
Paper, chapter
1, draft 3; chapter 2 (methods and results) draft 2 |
|
JSF |
|
Wed Nov
10 |
Lab 7:
Electrostatic calculations: MEAD |
|
|
Lab 6
due |
FRS |
|
Wed Nov
17 |
Lab 7:
Analysis of electrostatic calculations; comparison between student
computational results; final discussion of research paper |
Section
4.9, Leach |
Paper, chapter
2 (complete, draft 3); chapter 3 (methods) draft 1; chapter 4 (interpretation
of MD results in terms of function, draft 1) |
|
FRS |
|
Wed Dec
1 |
Lab 7:
Analysis of electrostatic calculations; comparison between student
computational results; final discussion of research paper |
|
|
|
FRS/
JSF |
|
Thurs
Dec 2 |
|
|
|
Lab 7
due |
|
|
Mon Dec
6 |
|
|
Final
paper due (including final chapters on electrostatics and critical analysis) |
|
|
*Reading material in parentheses is
not required reading, but is provided for further reference and is recommended
reading prior to coming to lab.