Methods

- Dynamic programming for sequence and structure
comparison and searching
- Pairwise comparison
- Variable gap penalty
- Local
*versus*global alignment - Similarity
*versus*distance scores - Multiple comparisons

- Optimization of the objective function by MODELLER

- Equations used in the derivation of the molecular pdf

- Flowchart of comparative modeling by MODELLER
- Loop modeling method

Ben Webb 2008-02-01