Table of Contents
1) METALLOPROTEIN MODELING & COMPUTATIONAL CHEMISTRY
2) Some exciting & rapidly developing areas...
3) Isopotential maps...
4) Brownian Dynamics calculations...
5) Protein docking...
6) Comparison of Docking and Brownian Dynamics
7) MOLECULAR MECHANICS is the workhorse of Computational Biochemsitry
8) The Molecular Mechanics description of a structure consists of...
9) Molecular Mechanics Force Field Or Potential Functions
10) What about the ellipsis, …?
11) Force fields may be classified by...
12) A Survey & Comparison of some Force Field Functions
13) Some Bond Stretch Functions:
14) Model bond as spring...
15) Harmonic is simplest function, but...
16) However, only fit to bottom of “well” is important.
17) Similarly, Bond Angle Functions
18) Torsion Angle Functions
19) Torsion Angle Functions...
20) Some other torsion potentials...
21) NON-BONDING INTERACTIONS
22) Other combination rules...
23) Hill potentials
24) Buffered-14-7 potential (Halgren, 1992)
25) Soft versus Hard potentials
26) Electrostatic interactions
27) Monopole models...
28) Multipole models...
29) MM2 dipole-dipole potential:
30) Fixes for Coulombic Potentials
31) Solvent screening...
32) Each force field has added functions...
33) To get this potential
34) By evaluating it,
35) Example...
36) Such maps help explain the Ramachandran plots
37) MM offers a method of minimizing the energy toward the optimum geometry
38) Example… the Lysyl-aspartate dipeptide
39) Molecular Dynamics
40) The MD Process…
41) Process...EQUILIBRATION
42) The result is ...
43) Frame-by-frame examination...
44) A variety of trajectories from this data
45) Issues for Metals and Metalloproteins
46) Appropriate Experimental data is limited
47) Three general MM approaches…(see Hay, 1993)
48) Three general MM approaches…Pros and Cons:
49) Are charges needed?
50) What’s been done?
51) Read more about it…
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Author: John E. Wampler
Email: wampler@bmb.uga.edu
Home Page: http://bmbiris.bmb.uga.edu/wampler/ibsw00
For References See:
http://bmbiris.bmb.uga.edu/wampler/ibsw00/ref.html
AND
http://bmbiris.bmb.uga.edu/wampler/ibsw00/morerefs.html
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