Unit 5: Predicting Protein Structure and Function: The Holy Grail of Bioinformatics

Featured Software: PSI-BLAST

Suggested Reading

Gibas Ch. 7 (pairwise comparison, dynamic programming) pp. 172-179
Gibas Ch. 8 (profiles and motifs) pp. 205-214
Gibas Ch. 9 (protein structure basics) pp. 215-229
Gibas Ch. 9 (software) pp. 229-241
Gibas Ch. 9 (classification and alignment) pp. 241-250
Article on PSI-BLAST (Altschul 1997)
About protein structure prediction (short review)

Discussion

Protein motifs, patterns and classification.
Protein structure prediction from sequence data.
Modeling how-to page.

Exercises

Protein structure viewers, structure databases and analytical resources.
Structural prediction problems.

Unit Problem

What can you learn about protein structure from position specific iterative local alignment? An analysis of PSI-BLAST article by Altschul, 1997.