HI 6327 Session 8
Overview:
- Lecture1: Thermodynamics, Ergodicity, Monte Carlo
(PDF file)
- Lecture2:
Continuum Electrostatics
(PDF file)
- Group
Project
Resources and Assignments:
Group
Project
Due @ session 11.
Your assignment as a group
is to complete a review paper discussing advantages and limitations of
five different molecular modeling methods listed below. You will first
elect a project leader who is responsible for the coordination of the
effort and for writing the introduction and conclusions sections (not
less than one and not more than two pages each), and for making the
individual sections consistent. The other five students will each
contribute a section on an individual method (not less than two and not
more than four pages each). In the following the four methods to be
discussed are given. You can gather information from textbooks and from
class
material and references therein, including online resources.
<>The
last lecture on ligand binding and docking methods will be presented in
class only one week before the due date, so the person responsible for
this method may wish to read chapters 22 and 23 in Bourne and
Weissig to get started early. Also, don't wait too long to get started
as this project will overlap with
your final term project that will be posted in session 10 and is
due at session 14!
Given below are two
scientific
papers for each method, one that is highlighting advantages and one
that is highlighting limitations. Focus on general methods and not on
individual program packages, and write in your own words (don't copy
text longer than half a sentence at a time from text sources). Please
send the paper as a PDF e-mail attachment before session 11 to
wriggers >>at<< biomachina.org.
Molecular Dynamics
Simulation
- Karplus and McCammon,
Ann. Rev. Biochem. 1983. 53:263-300.
- Clarage et al., Proc.
Natl. Acad. Sci. USA 1995. 92:3288-3292.
Normal Mode Analysis
- Levitt, Sander, and
Stern, J. Mol. Biol. 1985. 181:423-447.
- Tama and Sanejouand,
Protein Engineering 2001. 14:1-6.
Continuum Electrostatics
- Davis and McCammon,
Chem. Rev. 1990. 90:509-521.
- Warshel and Papazyan,
Current Opinion Struct. Biol. 1998. 8:211-217.
Free Energy Calculations
- Reyes and Kollman. J.
Mol. Biol. 2000. 297:1145-1158.
- Gallicchio et
al. J. Phys. Chem. B, 2005. 109:6722 -6731.
Ligand Binding and Docking
- Wodak and Janin, J. Mol.
Biol., 1978. 124:323-342.
- Halperin et al.,
Proteins Struct. Funct. Genet. 2002. 47:409-443.
Good luck!