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Protein Structure Prediction: Concepts and Applications

ISBN: 978-3-527-31167-5
228 pages
February 2006
Protein Structure Prediction: Concepts and Applications (352731167X) cover image
While most textbooks on bioinformatics focus on genetic algorithms and treat protein structure prediction only superficially, this course book assumes a novel and unique focus. Adopting a didactic approach, the author explains all the current methods in terms of their reliability, limitations and user-friendliness. She provides practical examples to help first-time users become familiar with the possibilities and pitfalls of computer-based structure prediction, making this a must-have for students and researchers.
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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
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Anna Tramontano is Professor of Biochemistry at the Medical Faculty of the University of Rome "La Sapienza" since 2001. She received her PhD in Physics from the University of Naples (Italy) in 1980 and held various appointments at research institutes in Europe and in the U.S. before becoming Professor of Bioinformatics at the University of Milan in 1990. From 1996 to 2001 she held the position as director of Computational Biology and Chemistry at the Merck Research Laboratories in Rome.
Anna Tramontano is among the organizers of the CASP (critical assessment of protein structure prediction) conferences and is on the editorial boards of several journals.
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"...this is a uniquely educational book, ideal as a teaching manual, especially for undergraduate students studying this fast-changing discipline, and for graduate students from other areas of science who want to quickly grasp the basics of protein structure prediction. Excellent value for money!" ChemBioChem

"... a good review of how the field has progressed and what one can expect with current methodologies."
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