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Protein Structure Prediction
Concepts and Applications
by Anna Tramontano

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


  • 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


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


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Protein Structure Prediction
Concepts and Applications
by Anna Tramontano

2006 • 228 pages • $79.00 + shipping
Texas residents please add 6.75 % sales tax

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