Preface
The Study of Structural Bioinformatics
Motivation
Small Beginnings
Structural Bioinformatics and the Scientific Method
A More Detailed Problem Analysis: Force Fields
Modeling Issues
Sources of Error
Summary
Introduction to Macromolecular Structure
Motivation
Overview of Protein Structure
Overview of RNA Structure
Data Sources, Formats, and Applications
Motivation
Sources of Structural Data
PDB File Format
Visualization of Molecular Data
Software for Structural Bioinformatics
Dynamic Programming
Motivation
Introduction
A DP Example: The Al Gore Rhythm for Giving Talks
A Recipe for Dynamic Programming
Longest Common Subsequence
RNA Secondary Structure Prediction
Motivation
Introduction to the Problem
The Nussinov Dynamic Programming
The MFOLD Algorithm: Terminology
Protein Sequence Alignment
Protein Homology
Variations in the Global Alignment Algorithm
The Significance of a Global Alignment
Local Alignment
Protein Geometry
Introduction
Calculations Related to Protein Geometry
Ramachandran Plots
Inertial Axes
Coordinate Transformations
Motivation
Introduction
Translation Transformations
Rotation Transformations
Isometric Transformations
Structure Comparison, Alignment, and Superposition
Motivation
Introduction
Techniques for Structural Comparison
Scoring Similarities and Optimizing Scores
Superposition Algorithms
Algorithms Comparing Relationships within a Protein
Machine Learning
Motivation
Issues of Complexity
Prediction via Machine Learning
Data Used during Training and Testing
Objectives of the Learning Algorithm
Linear Regression
Ridge Regression
Preamble for Kernel Methods
Kernel Functions
Classification
Heuristics for Classification
Nearest Neighbor Classification
Support Vector Machines
Linearly Nonseparable Data
Support Vector Machines and Kernels
Expected Test Error
Transparency
Overview of the Appendices
Index
Biography
Forbes J. Burkowski
… the book presents a number of topics in structural bioinformatics, aiming to emphasize the beauty of the area as well as some of the main problems. It targets advanced undergraduate students and hence the description of more complicated algorithms is avoided. It nevertheless provides an interesting introduction to the area.
—Lucian Ilie, Mathematical Reviews, Issue 2009k
