Table of ContentsMolecular Biophysics & Biochemistry 447b3 / 747b3Bioinformatics Molecular Biology Information:Macromolecular Structure Molecular Biology Information: Protein Structure Details Sperm Whale Myoglobin Structure Comparison:AlignmentRigid-Body MovementsSuperpositionSignificance 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 Betweenan Atom in 2 Structures RMS Superposition (3):RMS Distance BetweenAligned Atoms in 2 Structures RMS Superposition (4):Rigid-Body Rotation and Translationof 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 Matrixfor 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 Featuresin Structural Similarity Some Similarities are Readily Apparent others are more Subtle Other Methodsof Structural Alignment Other Aspects of Structure, Besides just Comparing Atom Positions |
Author: Office97
Email: Mark.Gerstein@Yale.edu Home Page: http://bioinfo.mbb.yale.edu/course Other information: |