Chemistry 115/215: Modeling Biological Macromolecules

Course information

Instructor

Prof. Lynn Ten Eyck

lteneyck at sdsc .dot. edu

Chemistry Research Building 202 (534-5141)

Teaching Assistant

David Minh

dminh at ucsd .dot. edu

Urey Hall 4217 (534-2916)

Office hours by appointment

Spring 2005, Tuesday and Thursday 2-3:50, San Diego Supercomputer Center 279

Lecture notes, Spring 2005

• 3/29/2005 Lecture 1a: Course Introduction
• 3/29/2005 Lecture 1b: UNIX Essentials
• 3/31/2005 Lecture 2: Overview of Molecular Modeling
• 4/05/2005 Lecture 3: More modeling basics
• 4/07/2005 Lecture 4: Structural Alignment
  • Paper mentioned: The cAMP binding domain: an ancient signaling module.
    Berman HM, Ten Eyck LF, Goodsell DS, Haste NM, Kornev A, Taylor SS.
• 4/12/2005 Lecture 5: Homology Modeling (Prof. Gribskov)
  • Link to Critical Assessment of Techniqes for Protein Structure Prediction (CASP) 6
• 4/14/2005 Lecture 6
  • Link to Biology Workbench
  • Getting started on your project, Molecular Mechanics, Computer Arithmetic, Energy scales
• 4/19,4/21,4/26 Lectures 7,8,&9: Molecular Mechanics and Molecular Dyanamics (Jessica Swanson)
• 5/10/2005 DeepView homology modeling
  Recommended reading: PNAS Chemical Theory and Computation Special Feature: Molecular dynamics and protein function.
  M. Karplus and J. Kuriyan
• 5/19/2005 Electrostatics (Jessica Swanson)
• Protein-Ligand Interactions/Data Analysis (Donald Hamelberg) (PDF) (Powerpoint)
  • 5/24/2005 Protein-Ligand
    • For the tutorial, download GROMACS input files. Save the file and enter gunzip mdp.tar.gz to decompress it. Then use tar -xvf mdp.tar to separate it into different files.
    • You may want to use this Python script to modify DRGFIN.GRO for use in trp.gro. First, save the file. You can execute it by typing python chNum.py (filename), where (filename) is the location of your DRGFIN.GRO file.
  • 5/26/2005 Analysis
    • To run the analysis, you will need a longer trajectory to analyze. The trajectory .trr and the .gro file are in /users/u2/che115/FKGtraj/. You can make a symbolic link to the copy them to the trajectories using: ln -s /users/u2/che115/FKGtraj/md2.trr . and ln -s /users/u2/che115/FKGtraj/md.gro .. Alternatively, you can copy the trajectories to your own directory. Do the same for all the files that you need.
    • To visualize the principal components using VMD, try IED

Archive notes

• Molecular Mechanics and Dynamics Simulations
• Lecture 4: Electrostatics of Macromolecules
• Lecture 6: Structural Databases (Prof. Bourne)
• Lecture 7: Brownian Dynamics Simulations
• Lecture 8: Calculating Binding Energetics
• Lecture 3a: Math for Computer Modeling
• Lecture 3b: Macromolecular Energy Functions
• Lecture 3c: Scale of Energy Functions
• Lecture 10: NMR Refinement/Analysis (Prof. Komives)
• Lecture 11: pH-Dependent Properties of Macromolecules
• Lecture 12: Critical Evaluation of Theoretical Papers
• Lecture 13: Molecular Docking with DOT
• Lecture 14: Graphics Processing
• Lecture 15: More on Molecular Docking
• Lecture 16: X-ray Structure Validation
• In class project time.
• Lecture 19: Writing a Theoretical Paper
• Lecture 20: Special Topics (drug design, force fields, future of modeling)

Computer Notes

Setting up your account to run VMD, SPDBV, Chimera, ect. using the vi editor (you can use another editor)

• Login to your account and open a LINUX terminal. (Right click on the screen and select "Open Terminal" using KDE.)
• Edit your login script .cshrc by entering "vi .cshrc"
• Pressing Shift+G will take you to the end of the script. Press i to change to insert mode.
• Type or copy "source /misc/model/che115/class_setup"
• Press ESC to leave insert mode and type ":wq" to write the file and quit vi.
• Next time you restart the terminal (by logging in and out, or opening a new terminal), the programs should be set up. Alternatively, you can type "source .cshrc". Take a look at the class_setup file to see what is in it. I will continue to change this file so that you don't have to follow special setup instructions for every piece of software.