Introduction to Computational Structural Biology

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Introduction to Computational Structural Biology
http//www.math.iastate.edu/wu/math597.html

• Math/BCB/ComS597
• Zhijun Wu
• Department of Mathematics

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Time and Place

• Lectures MWF, 2 3 pm
• Class Room Carver Hall 290
• Office Hours MWF, 3 4 pm
• Office Carver Hall 370

515-294-8165 / zhijun_at_iastate.edu
? Phone / Email
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Pre-requisite

• Knowledge of Molecular Biology
• General Computer Programming Skills
• Multi-variable Calculus
• Numerical Analysis
• Design and Analysis of Computer Algorithms

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Course Work

• Class participation (10)
• 4 homework assignments (20)
• 3 computer projects (60)
• 1 oral presentation (10)

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Course Material and Content

• Lecture notes
• General references
• RasMol
• Matlab
• PDB Data Bank

Content ?
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Reference Books

• Molecular Modeling and Simulation
• Tamar Schlick
• Structural Bioinformatics
• Philip Bourne and Helge Weissig

Content ?
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Section 1. Introduction

• DNA, RNA, and Protein
• Protein Structure Determination
• Experimental and Theoretical Approaches
• Role of Computation
• Further Reading

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Section 2. Computational Background

• Matrix-Vector Calculation
• Matlab Introduction
• Local and Global Optimization
• Design and Analysis of Computer Algorithms
• Further Reading

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Section 3. Structural Representation

• Cartesian Coordinates
• Inter-Atomic Distances
• Dihedral Angles
• Electron Density Distributions
• Coordinate Transformation
• Further Reading

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Section 4. Distance Geometry

• Exact, Inexact, Dense, Sparse Distances
• Computational Complexities
• Algorithms SVD, Build-Up, Least-Squares
• Applications to Prediction Determination
• Further Reading

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Section 5. Energy Minimization

• All-Atom Potentials
• Reduced Energy Models
• Local Optimization Structure Refinement
• Global Optimization Structure Prediction
• Further Reading

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Section 6. Dynamics Simulation

• Mathematical and Physical Models
• Numerical Algorithms
• Initial Boundary Value Problems
• Normal Mode Analysis
• Gaussian Network Model
• Further Reading

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Section 7. Structure Prediction

• Homology Modeling
• Structural Alignment
• Inverse Folding
• Secondary Structure Prediction
• Further Reading

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Section 8. Literature Review

• Distance Geometry Future Development
• Protein Folding Theory Methods
• Dynamic Simulation Problems Challenges
• Structure Prediction Future Direction
• Systems Biology Beyond DNA Protein