Molecular Biophysics & Biochemistry 447b3 / 747b3 Bioinformatics

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Table of Contents

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

Author: Office97

Email: Mark.Gerstein@Yale.edu

Home Page: http://bioinfo.mbb.yale.edu/course

Other information:
All overheads are copyright 1998, Mark Gerstein, All Rights Reserved