| Lecture |
Title |
Handouts |
Recommended reading |
| 1 |
Introduction |
pdf ppt |
Review on bioinformatics: pdf
|
| 2 |
Protein Primary Structures |
pdf ppt |
Extended Genetic code?: pdf
The 21st amino acid codon: pdf
Do proteins fold sequentially? pdf
|
| 3 |
Protein Secondary Structures |
pdf ppt |
Original Stride Paper: pdf
Secondary Structure Assignment based on tessalation pdf
Secondary Structure Assignment: a review pdf
Fitting lines in secondary structures pdf
|
| 4 |
Protein Tertiary Structures |
pdf ppt |
Review on protein structures: pdf
My own review on protein structures: pdf
|
| 5 |
Protein Structure Comparison |
pdf ppt |
Review on protein structure comparison: pdf
Review (2001) on protein structure comparison: pdf
A polynomial approach to structure superposition: pdf
Comparisons of protein structure alignment methods: pdf
Original DALI paper: pdf
Original Structal paper (see methods): pdf |
| 6 |
Protein Structure Classification |
pdf ppt |
Domain identification: Taylor (1999)
Classifications: Original SCOP paper
Original CATH paper
|
| 7 |
Protein Structure Energetics |
pdf ppt |
My recent paper on Electrostatics calculation: PDF file
Preprint of a paper on statistical potentials
|
| 8 |
Protein Structure Prediction: Homology Modeling (1) |
pdf ppt |
Current Status of CASP , Moult, 2005
Homology Modeling at CASP , Venclovas, 2005
Overview of 5 CASP experiments , Venclovas, 2005
Review on Homology Modeling , Vriend 2003
Review on Homology Modeling , Honig 2003
|
| 9 |
Protein Structure Prediction: Homology Modeling (2) |
pdf ppt |
|
| 10 |
Ab initio Protein Structure Predictions |
pdf ppt |
Secondary Structure Prediction: PHD Rost, 1993
Secondary Structure Prediction: JPred Jones, 1993
Success on small proteins D. Baker, 2005
Review on Structure Prediction , Kretzinger, 2004
Protein folding Pande, 2005
|
| 11 |
Molecular simulations: Molecular Dynamics and Monte Carlo |
pdf ppt |
A thorough review of Molecular Dynamics van Gunsteren and Berendsen, 1990
A review of Monte Carlo methods Okamoto et al, 2000
|
| 12 |
Normal mode analysis |
pdf ppt |
A good overview of "standard" normal modes analysis of proteins Stern, Levitt, 1985
Tirion's paper on "geometric" NMA Tirion, 1996
A review on applications of NMA Bahar, 2005
Vijay Pande's paper on the limits of elastic modes Petrone and Pande, 2006
|
| 13 |
Geometry |
pdf ppt |
Overview of geometry for protein solvation Koehl, Edelsbrunner, 2005
|
| 13 |
Protein Sequence Design |
pdf ppt |