Short description A must-have for students and novice researcher, this textbook explains current methods in terms of their reliability, limitations and user-friendliness, helping first-time users to become familiar with the possibilities and pitfalls of computer-based structure prediction.
From the 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 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
