| Lecture |
Title |
Handouts |
Recommended Reading |
| 1 |
Introduction |
PDF file
PowerPoint file
|
Review on Bioinformatics:
Ouzounis, 2003 |
| 2 |
Protein Building Blocks |
PDF file
PowerPoint file
|
Extended Genetic code?: pdf
The 21st amino acid codon: pdf
Do proteins fold sequentially? pdf
Summary picture of the 20 amino acids |
| 3 |
Protein Sequence Comparison |
PDF file
PowerPoint file
|
Original paper by Needleman and Wunsch, 1970
An overview of Sequence Alignment, Gene Myers
Statistics of multiple seq. alignment, Altshul
Original paper by Dayhoff, 1978: Substitution matrices
Original paper by Henikoff & Henikoff, 1992: BLOSUM matrices
|
| 4 |
Protein Secondary Structures |
PDF file
Powerpoint file |
Original Stride Paper: pdf
Secondary Structure Assignment based on tessalation pdf
Secondary Structure Assignment: a review pdf
Fitting lines in secondary structures pdf
Ramachandran Plot Explorer (download site) |
| 5 |
Protein Tertiary Structures |
PDF file
Powerpoint file |
Review on protein structures: pdf
My own review on protein structures: pdf
|
| 6 |
Protein Structure Comparison |
PDF file
Powerpoint file |
Review on protein structure comparison (Koehl, 2006)
Review (Koehl, 2001) on protein structure comparison
A polynomial approach to structure superposition
Comparisons of protein structure alignment methods
Original DALI paper
Original Structal paper (see methods) |
| 7 |
Protein Structure Classification |
PDF file
Powerpoint file |
W. Taylor paper on domain definition
Original SCOP paper
Original CATH paper
|
| 8 |
Protein Structure Energetics |
PDF file
Powerpoint file |
Recent review on Electrostatics calculation
Recent review on Poisson Boltzmann Equation
Statistical potentials |
| 9 |
Homology Modeling |
PDF file
Powerpoint file |
Current status of CASP
Homology modeling at CASP
Overview on 5 CASP experiments
review on Homology Modeling: Vriend, 2003
review on Homology Modeling: Honig, 2003 |
| 10 |
Ab initio structure prediction |
PDF file
Powerpoint file |
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
Review on Protein folding Pande, 2005 |
| 11 |
Molecular Simulations |
PDF file
Powerpoint file |
A thorough review on Molecular Dynamics
A recent review on Monte Carlo methods |