Protein Architecture
Protein Structure
Chapter 2: "
In Vivo, In Vitro, In Silicio"
Page 1
: Genomes
Page 2
: Questions
Page 3
: Stabilizing interactions
Page 4
: Accessible surface area
Page 5
: Packing
Page 6
: Polypeptide conformations
Page 7
: Structural databases
Assignment:
Chapter 2 of Lesk's "Introduction to Protein Architecture"
Exercise 2.2
Problem 2.2
Problem 2.6
Weblem 2.1
Swiss PROT: (
http://www.expasy.org/srs5/
)
Weblem 2.2
PIR/PROSITE: (
http://www-nbrf.georgetown.edu/pirwww/search/patmatch.html
)
Weblem 2.7 - Also, determine what fraction of all of the atoms in pepsin are completely burried (A.S.A. = 0.0)
Protein Data Bank: (
http://www.rcsb.org/pdb/
)
A.S.A. Calculator: (
http://www.bork.embl-heidelberg.de/ASC/scr1-form.html
)
Weblem 2.8
Hydrophobicity index (
http://bioinformatics.weizmann.ac.il/hydroph/hydroph.html
)
Transmembrane Helices in Proteins Server (TMHMM)
(
http://www.cbs.dtu.dk/services/TMHMM/
)