MCB 501 Introduction to Computers
2008 lectures on
bioinformatics and computational biology resources
Slide Show
Objectives
The objective of these lectures and laboratories is to
provide students with a basic knowledge about some of the open computational
resources related to studies in the fields of
bioinformatics and
computational biology,
structural genomics,
and
protein structure and function prediction,
and to enable them to use some of these tools:
- Most of our attention will be given to
three sets of programs: Rasmol, VMD,
and the DeepView/Swiss-Model set.
- We will have a brief introduction to Modeller
and the Autodock/Autodoctools set.
- These are tools for viewing molecular structure and
dynamics,
for protein structure prediction through
comparative homology modeling, and for
predicting the fit of ligands to protein binding sites.
- Here is a VMD visualization of
a very large molecular dynamics calculation,
illustrating how these tools provide an indispensible contribution
to our understanding of biological function.
- here is an AutoDock Tools visualization of
an Autodock prediction of ligand binding, illustrating
the intelligent design of drugs.
One of the principle goals in structural genomics research is to know the
three dimensional structure and function of
the proteins derived from genes in the human genome,
and to use this information to engineer molecules that
will alter those functions in very specific ways
that are beneficial to human health.
One example is the design of drugs that
block HIV with no side effects.
These goals require molecular modeling.
A google search on "molecular modeling"
will yield other lists of useful resources.
Wednesday 17 September
- Discuss "Related External Links".
- View 2TUN using several viewers.
- Discuss and practice methods for viewing stereo images.
Raswin and its help file are already installed on your computer in C:\williams.
- Using windows explorer, run raswin.exe
- File -> Open C:\williams\crambin.pdb
- Display, Options, Settings, click to show atom, and the Manual.
- Command Line, select, background.
- zoom, Export as bitmap and paste into MS Word.
- Example of article using Rasmol images.
Friday 19 September
- View these Molecular Dynamics Movies:
from
http://www.ks.uiuc.edu/Gallery/Movies/.
These movies were made with VMD and are owned by the Theoretical and
Computational Biophysics Group, an NIH Resource for Macromolecular
Modeling and Bioinformatics, at the Beckman Institute, University of Illinois at Urbana-Champaign.
They demonstrate what can be achieved with molecular dynamics calculations
and the visualization of those results.
- Students will go through the VMD tutorial.
This tutorial is available at UIUC, here.
- If you are interested in more, VMD uses
the tcl/tk scripting language resources to extend and customize the program.
Wednesday 24 September
Friday 26 September
Exercises for Credit (Homework), 200 points total:
For the Wednesday 17 Sept. class:
- Point your browser to the PDB site, find an image of Crambin (any image)
and print it with a white background. Put your name on the page and
turn it in to Dr. Williams. .... 10/100 points
-
Practice viewing both convergent and divergent stereo images until you see a
3D image. Then print the files
crambin-stereo-1.pdf and
crambin-stereo-2.pdf, correctly label
each page as being either convergent (crossed eyes) or divergent (stare to infinity)
stereo, and turn them in to Dr. Williams. .... 10/100 points.
- Using Rasmol, construct and print a stereo image of 2TUNA.pdb
(pdb id: 2TUN) that has the following properties:
white background, at least three different "display" types
with residues 140-150 and 30-40 having
one type, 147 and 32 having another type,
and the rest having yet another different type.
Turn your printed page, with your name, in to Dr. Williams. .... 30/100 points.
- In preparation for the tutorials next Wednesday, download the
loop database from here,
unzip it, and put it into your _stuff_ subdirectory.
When you are done, you should have a "_loopdb_" file in the "_stuff_" directory.
(You will also have a "loopdb" subdirectory in "_stuff_".)
You will use the same computer throughout this set of laboratory exercises.
For the Friday 19 Sept. class:
- Using VMD, indentify how many beta-sheets (which may include several beta strands)
and helices (alpha or otherwise, which may include only one turn or loop) you can find
in 1UBQ. Find the amino acid and residue number where each strand of helix or
beta sheet starts and ends. Put these findings on a piece of paper.
10/100 points.
- Using VMD, determine how many Lysines and Glycines are present in 1UBQ and
add these findings to your paper. 10/100
- Perform the "Saving your Work" exercise at the end of the
basic VMD tutorial, print the high resolution image you
created of 1UBQ (picture-yourname.dat.bmp)
and give it, with your name on it, to Dr. Williams.
30/100 points.
- Be sure your name is on your papers and hand them in to Dr. Williams.
For the Wednesday 24 September class:
- Perform the Deep View exercises at
this link
.... 50 points.
For the Friday 26 September class:
Example of a paper where Rasmol and
Homology molecular modeling (Modeller) were used
Ken Gable, Gongshe Han, Erin Monaghan, Dagmar Bacikova, Mukil Natarajan, Robert Williams, and Teresa M. Dunn,
"Mutations in the Yeast LCB1 and LCB2 Genes, Including Those Corresponding to the
Hereditary Sensory Neuropathy Type I Mutations, Dominantly Inactivate Serine Palmitoyltransferase",
J. Biol. Chem., Vol. 277, Issue 12, 10194-10200, March 22, 2002
Lists of free and open Bioinformatics, Proteomics, and Protein Structure Prediction software
Other Resources
Software and files that should already be installed on your in-class computer in
C:\williams
Robert Williams,
Room G58J, (301) 295-3568,
Send email to
bob@bob.usuhs.mil