Protein Structure Prediction

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 Method of Prediction
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 and 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
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