Molecular Biophysics & Biochemistry 447b3 / 747b3 Bioinformatics
Molecular Biology Information: Macromolecular Structure
Molecular Biology Information: Protein Structure Details
Sperm Whale Myoglobin
Structure Comparison: Alignment Rigid-Body Movements Superposition Significance
Structural Alignment of Two Globins
Immunoglobulin Alignment (Harder)
Some Similarities are Readily Apparent others are more Subtle
Automatically Comparing Protein Structures
RMS Superposition (1)
RMS Superposition (2): Distance Between an Atom in 2 Structures
RMS Superposition (3): RMS Distance Between Aligned Atoms in 2 Structures
RMS Superposition (4): Rigid-Body Rotation and Translation of One Structure (B)
RMS Superposition (5): Optimal Movement of One Structure to Minimize the RMS
Alignment (1) Make a Similarity Matrix (Like Dot Plot)
Structural Alignment (1b) Make a Similarity Matrix (Generalized Similarity Matrix)
Structural Alignment (1c*) Similarity Matrix for Structural Alignment
Alignment (2): Dynamic Programming, Start Computing the Sum Matrix
Alignment (3):Dynamic Programming, Keep Going
Alignment (4): Dynamic Programming, Sum Matrix All Done
Alignment (5): Traceback
In Structural Alignment, Not Yet Done (Step 6*)
Structural Alignment (7*), Iterate Until Convergence
Score S at End Just Like SW Score, but also have final RMS
Scores from Structural Alignment Distributed Just Like Ones from Sequence Alignment (E.V.D.)
Score Significance (P-value) derived from Extreme Value Distribution (just like BLAST, FASTA)
Significance Ignoring Crucial Features in Structural Similarity
Some Similarities are Readily Apparent others are more Subtle
Other Methods of Structural Alignment
Other Aspects of Structure, Besides just Comparing Atom Positions