BMB/Bi/Ch 170 Course information

Description
Syllabus
Lecture notes
Course Policies

Problem sets, final project, and data for problems

Set 1 - Protein Stability
Supplement
Answers
Set 2 - Protein Crystallography
prob2.zip: files for work outside of lab
Set 3 - Membrane proteins
prob3.zip: files for work outside of lab
Set 4 - Protein/Nucleic Acid interactions, Viruses, and Cytoskeletal proteins

prob4.zip: files for work outside of lab

BMB/Bi/Ch 170, Final project ideas
Instructions to Authors for the final project
Example final projects

Molecular Modeling programs: manuals and other information

PyMol
Downloading and installing Pymol
PyMOL wiki
Swiss PDB Viewer
Downloading and installing SPDBV
Known bugs, glitches, and gotchas in Swiss PDB Viewer 3.5
Basic Tutorial For Swiss PDB Viewer
Hot Keys in Swiss PDB Viewer
Other Features in Swiss PDB Viewer
Short Manual For Swiss PDB Viewer
Coot/WinCoot
Downloading and installing Coot or WinCoot
Coot home page
Coot Manual
WinCoot home page
O manuals
O Manual
O for Morons
Bi/Ch 170 O tutorial
Index to Bi/Ch 170 O tutorial
Animation
Making movies using SPDBV, miniproc, povinterp.mpc, and mpeg_encode (David Mathog)
SPDBV animation (Simon Andrews)
pdb2mgif low resolution animated gif from pdb
PovRay manual (read the animation section)
Linux/IRIX - General Information
Linux/IRIX - SAF specific software: Molecular modeling and display
Unix command basics
SAF - Software documentation

Class Miscellaneous

Note: only computers on the campus network have file access to the SAF machines
Drag and Drop access to your class directory: Windows Macintosh
scp or sftp access to your class directory: Windows Macintosh
Send a question via email to the TAs: bi170ta@saf.bio.caltech.edu

Reference lists

Ig superfamily
DNA/protein interactions
Basic Elements of Protein Structure, part 1
Basic Elements of Protein Structure, part 2
Protein Stability
Membrane Proteins
Chaperone references

Relevant Web pages

Atlas of protein sidechain conformations
Atlas of Side-Chain and Main-Chain Hydrogen Bonding
BioMolecular Engineering Research Center tools (Boston University)
Crystallography World Wide
Database of interacting proteins
DALI - query with a structure, search PDB database for similar 3D structures
Molscript official web site
The O WWW Home Page
NDB database
PDB database (search)
PDB database (download)
CATH - Protein Structure Classification
SCOP - Structural Classification of Proteins
Generate 3D model from protein sequence(Swiss Model)
Molecules R US (select and display models of PDB entries)
NIH molecular modeling home page
Tutorial on Fourier transforms
Video clips illustrating topics in crystallography
List of most popular molecular modeling and display programs
XRayView home page