Protein Structure Prediction explains all the current methods in terms of their reliability, limitations and user-friendliness.

Features:

• Provides practical examples to help first-time users become familiar with the possibilities and pitfalls of computer-based structure prediction
• Explains information in a didactic approach

Contents

Sequence, Function, and Structure Relationships

• Protein Structure
• The Properties of Amino Acids
• Experimental Determination of Protein Structures
• The PDB Protein Structure Data Archive
• Classification of Protein Structures
• The Protein-folding Problem
• Inference of Function from Structure
• The Evolution of Protein Function
• The Evolution of Protein Structure
• Relationship Between Evolution of Sequence and Evolution of Structure

Reliability of Methods for Prediction of Protein Structure

• Prediction of Secondary Structure
• Prediction of Tertiary Structure
• Benchmarking a Prediction Method
• Blind Automatic Assessments
• The CASP Experiments

Ab-initio Methods for Prediction of Protein Structures

• The Energy of a Protein Configuration
• Interactions and Energies
• Covalent Interactions
• Electrostatic Interactions
• Potential-energy Functions
• Statistical-mechanics Potentials
• Energy Minimization
• Molecular Dynamics
• Other Search Methods: Monte Carlo and Genetic Algorithms
• Effectiveness of Ab-initio Methods for Folding a Protein

Evolutionary-based Methods for Predicting Protein Structure: Comparative Modeling

• Theoretical Basis of Comparative Modeling
• Detection of Evolutionary Relationships from Sequences
• The Needleman and Wunsch Algorithm
• Substitution Matrices
• Template(s) Identification Part I
• The Problem of Domains
• Alignment
• Template(s) Identification Part II
• Building the Main Chain of the Core
• Building Structurally Divergent Regions
• A Special Case: Immunoglobulins
• Side-chains
• Model Optimization
• Other Approaches
• Effectiveness of Comparative Modeling Methods

Sequence-Structure Fitness Identification: Fold-recognition Methods

• The Theoretical Basis of Fold-recognition
• Profile-based Methods for Fold-recognition
• Threading Methods
• Profile–Profile Methods
• Construction and Optimization of the Model

Methods Used to Predict New Folds: Fragment-based Methods

• Fragment-based Methods
• Splitting the Sequence into Fragments and Selecting Fragments from the Database
• Generation of Structures

Low-dimensionality Prediction: Secondary Structure and Contact Prediction

• A Short History of Secondary structure Prediction Methods
• Automatic learning Methods.
• Artificial Neural Networks
• Support Vector Machines
• Secondary structure Prediction Methods Based on Automatic Learning Techniques
• Prediction of Long-range Contacts

Membrane Proteins

• Prediction of the Secondary Structure of Membrane Proteins
• The Hydrophobic Moment
• Prediction of the Topology of Membrane Proteins

Applications and Examples

• Early Attempts
• The HIV Protease
• Leptin and Obesity
• The Envelope Glycoprotein of the Hepatitis C Virus
• HCV Protease
• Cyclic Nucleotide Gated Channels
• The Effectiveness of Models of Proteins in Drug Discovery
• The Effectiveness of Models of Proteins in X-ray Structure Solution

Index

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