Keywords:
Computational biology.
;
Electronic books.
Type of Medium:
Online Resource
Pages:
1 online resource (334 pages)
Edition:
1st ed.
ISBN:
9780387688251
Series Statement:
Biological and Medical Physics, Biomedical Engineering Series
URL:
https://ebookcentral.proquest.com/lib/geomar/detail.action?docID=992957
DDC:
572.633
Language:
English
Note:
Intro -- Title Page -- Copyright Page -- Preface -- Acknowledgments -- Table of Contents -- Contributors -- 12 Protein Structure Prediction by Protein Threading -- 12.1 Introduction -- 12.2 Protein Domains, Structural Folds, and Structure Space -- 12.3 Fitting a Protein Sequence onto a Protein Structure -- 12.4 Calculating Optimal Sequence-Structure Alignments -- 12.4.1 PROSPECT -- 12.4.2 RAPTOR -- 12.4.3 Tree-Decomposition-Based Threading Algorithm -- 12.4.3.1 Graph Representation -- 12.4.3.2 Tree Decomposition of Structure Graph -- 12.4.3.3 Tree-Decomposition-Based Alignment Algorithm -- 12.4.3.4 Time Complexity Analysis -- 12.5 Assessing Statistical Significance of Threading Alignments -- 12.6 Structure Prediction Using Protein Threading -- 12.6.1 Database of Template Structures -- 12.6.2 Threading Energy Function -- 12.6.3 Threading Algorithm -- 12.6.4 Assessing Prediction Reliability -- 12.7 Improving Threading-Based Structure Prediction -- 12.7.1 Application of Experimental Data as Threading Constraints -- 12.7.2 Improving Structural Quality through Molecular Dynamics and Energy Minimization -- 12.8 Challenging Issues -- Energy Function -- Threading Algorithm and Implementation -- Statistical Significance Analysis of Threading Results -- Consensus Building and Subdomain Threading -- 12.9 Summary -- Suggested Further Reading -- Acknowledgments -- References -- 13 De Novo Protein Structure Prediction -- 13.1 Introduction -- 13.2 Methods and Algorithms -- 13.2.1 Energy Functions -- 13.2.2 Knowledge-Based Energies -- 13.2.3 Simplified Representations -- 13.2.4 Lattice Methods -- 13.2.5 Fragment Assembly -- 13.2.6 Continuous Torsional Distributions -- 13.2.7 Selection of the Best Conformers -- 13.2.8 PROTINFO, an Example de Novo Prediction Protocol -- 13.2.9 Other de Novo Structure Prediction Protocols -- 13.3 Discussion.
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13.3.1 Faster Computers and Larger Databases -- 13.3.2 Future Directions -- Acknowledgments -- References -- 14 Structure Prediction of Membrane Proteins -- 14.1 Introduction -- 14.2 Secondary Structure Prediction Methods for Membrane Proteins -- 14.2.1 Basic Characteristics -- 14.2.1.1 Hydrophobicity -- 14.2.1.2 Hydrophobic Moment -- 14.2.1.3 The Positive-Inside Rule -- 14.2.2 The Prediction Methods for the Topology of Transmembrane Helices -- 14.2.2.1 Physicochemical Methods Based on Various Hydrophobicity Scales -- Hydropathy Analysis -- An Example -- ALOM2 -- DAS -- PRED-TMR -- SOSUI -- TMFinder -- TopPred -- 14.2.2.2 Statistical (Propensity Based) Methods -- MEMSAT -- TMAP -- TMPRED -- SPLIT -- An Example -- 14.2.2.3 Learning Algorithm-Based Methods -- TMHMM -- HMMTOP -- PHDhtm -- ENSEMBLE -- SVMtm -- 14.2.2.4 Accessibility -- 14.2.3 The Prediction Methods for the Topology of Transmembrane Barrels -- 14.2.3.1 Methods -- B2TMPRED -- BBF -- BETA-TM -- BIOSINO-HMM -- BOMP -- HMM-B2TMR -- OM_Topo_predict -- PRED-TMBB -- ProfTMB -- TBBPred -- TMBETA-NET -- 14.2.3.2 Accessibility -- 14.2.4 Accuracy Measures of Secondary Structure Prediction Algorithms -- 14.2.4.1 Accuracy Measures -- Per-Residue Accuracy -- Per-Segment Accuracy -- 14.2.4.2 Performance of Secondary Structure Predictors -- 14.3 Tertiary Structure Prediction Methods for Membrane Proteins -- 14.3.1 Molecular Determinants of Helix-Helix Interactions -- 14.3.2 Potential (Scoring) Functions of Helix-Helix Interactions -- 14.3.2.1 Potential Functions Based on Physical Models -- 14.3.2.2 "Statistical Potentials -- 14.3.2.3 "Optimal Potential -- 14.3.3 Algorithms for Optimizing Helix-Helix Packing -- References -- 15 Structure Prediction of Protein Complexes -- 15.1 Introduction -- 15.1.1 Protein Docking: Definition -- 15.1.2 Protein-Protein Interactions: Underlying Principles.
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15.1.3 Will the Proteins Interact? -- 15.1.4 Input Structures -- 15.1.5 History of Docking -- 15.2 Unbound Docking: Current Approaches -- 15.2.1 Rigid Body Docking: Search -- 15.2.1.1 Fast Fourier Transform -- 15.2.1.2 Other Search Techniques -- 15.2.2 Rigid Body Docking: Scoring -- 15.2.2.1 Shape Complementarity -- 15.2.2.2 Electrostatics -- 15.2.2.3 Desolvation and Statistical Potentials -- 15.2.2.4 Hydrogen Bonding -- 15.2.3 Refinement -- 15.2.4 Clustering -- 15.2.5 Side Chain Searching -- 15.2.6 Backbone Searching -- 15.3 Evaluation of Docking Algorithms -- 15.3.1 Determining Accuracy of Predictions -- 15.3.2 Docking Benchmark -- 15.3.3 CAPRI Experiment -- 15.4 Case Study: ZDOCK and RDOCK -- 15.4.1 ZDOCK Algorithm -- 15.4.1.1 Angular Search -- 15.4.1.2 ZDOCK Scoring -- 15.4.2 RDOCK -- 15.4.2.1 RDOCK: Energy Minimization -- 15.4.2.2 RDOCK: Scoring -- 15.4.3 6D Refinement -- 15.4.3.1 Development of a Scoring Function -- 15.4.3.2 Exploring the Search Space -- 15.4.3.3 Results -- 15.5 Summary/Future Directions -- 15.5.1 CAPRI Success/Lessons -- 15.5.2 New Developments -- Recommended Reading -- Books -- Review Articles -- References -- 16 Structure-Based Drug Design -- 16.1 Introduction to Modern Drug Discovery -- 16.1.1 Current Drug Discovery Process -- 16.1.2 Role of Protein Structure in Modern Pharmaceutical Sciences -- 16.1.3 Structure-Based Drug Design -- 16.2 Protein Therapeutics -- 16.2.1 Cytokines -- 16.2.2 Antibodies -- 16.2.3 Engineered Enzymes -- 16.2.4 Summary of Protein Therapeutics -- 16.3 Receptor-Based Drug Design -- 16.3.1 Docking -- 16.3.1.1 Search Algorithms -- 16.3.1.2 Scoring Functions -- 16.3.1.3 Input Receptor Structures -- 16.3.1.4 Validation of Docking Algorithms -- 16.3.2 Lead Discovery -- 16.3.2.1 VS Library Generation -- 16.3.2.2 Validation of Docking as a VS Tool -- 16.3.3 Lead Optimization.
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16.3.4 Comparison Studies of Docking Tools -- 16.3.5 Summary of Receptor-Based Drug Design -- 16.4 Ligand-Based Drug Design -- 16.4.1 Pharmacophore Modeling -- 16.4.2 Quantitative Structure-Activity Relationship (QSAR) -- 16.4.2.1 Training Set Compilation -- 16.4.2.2 Descriptor Selection -- 16.4.2.3 Model Generation -- A. Linear Models -- B. Nonlinear Models -- 16.4.2.4 Model Validation -- 16.4.2.5 3D-QSAR -- 16.4.2.6 QSAR Summary -- 16.4.3 Summary of Ligand-Based Drug Design -- 16.5 Future Reading -- 16.6 Conclusions -- References -- 17 Protein Structure Prediction as a Systems Problem -- 17.1 Introduction: The Complexity of Protein Structure Prediction -- 17.2 Consensus-Based Approach for Protein Structure Prediction -- 17.3 Pipeline Approach for Protein Structure Prediction -- 17.4 Expert System for Protein Structure Prediction -- 17.5 From Structure to Function -- 17.6 Benchmark and Evaluation -- 17.7 Genome-Scale Protein Structure Prediction -- 17.7.1 Overview of Three Cyanobacterial Genomes -- 17.7.2 Global Analysis of Protein Structural Folds in Three Genomes -- 17.7.3 Computational Analysis of Predicted Carboxysome Proteins -- 17.8 Summary -- 1. Protein representation -- 2. High-resolution protein structure prediction -- 3. Membrane protein structure prediction -- 4. Effects of protein interaction -- 5. New computational technology development -- Suggested Further Reading -- Acknowledgments -- References -- 18 Resources and Infrastructure for Structural Bioinformatics -- 18.1 Introduction -- 18.2 PDB and Related Databases/Servers -- 18.3 Structure Visualization -- 18.4 Protein Sequence and Function Databases -- 18.5 Structural Bioinformatics Tools -- 18.6 RNA Structure Modeling and Prediction -- 18.7 General Online Resources -- 18.8 Major Journals and Further Readings -- 18.9 Professional Societies, Conferences, and Events -- 18.10 Summary.
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Acknowledgments -- References -- Appendix 1 Biological and Chemical Basics Related to Protein Structures -- A 1.1 Amino Acid Residues -- A 1.2 Nucleic Acids -- A 1.3 Protein Structures -- Suggested Further Readings -- Appendix 2 Computer Science for Structural Informatics -- A 2.1 Introduction -- A 2.2 Efficient Data Structures -- A 2.2.1 Hash Tables -- A 2.2.2 Suffix Trees -- A 2.2.3 Disjoint Sets -- A 2.2.4 Heaps -- A 2.2.5 Other Data Structures -- A 2.3 Computational Complexity and NP-Hardness -- A 2.3.1 Concept of Computational Complexity -- A 2.3.2 Optimization Problems -- A 2.4 Algorithmic Techniques -- A 2.4.1 Exhaustive Enumeration -- A 2.4.2 Dynamic Programming -- A 2.4.3 Integer Programming -- A 2.4.4 Branch-and-Bound -- A 2.4.5 A* Search -- A 2.4.6 Dead-End-Elimination Algorithm -- A 2.4.7 Greedy Algorithms -- A 2.4.8 Reduction Techniques -- A 2.4.9 Divide-and-Conquer Algorithms -- A 2.5 Parallel Computing -- A 2.6 Programming -- A 2.7 Summary -- Further Reading -- A 2.8 Acknowledgments -- References -- Appendix 3 Physical and Chemical Basis for Structural Bioinformatics -- A 3.1 Introduction -- A 3.2 Physics Concepts -- A 3.2.1 Units -- A 3.2.2 Potential Energy Surface -- A 3.2.3 Coordinate Systems -- A 3.3 Basic Chemistry -- A 3.3.1 Chemical Reactions -- A 3.3.2 Formation of the Peptide Bond -- A 3.4 Physical Forces in Proteins and Nucleic Acids -- A 3.4.1 Covalent Bond -- A 3.4.2 Electrostatic Interactions -- A 3.4.3 van der Waals Interactions -- A 3.4.4 Hydrogen Bond -- A 3.4.5 Disulfide Bond -- A 3.4.6 Solvation -- A 3.4.7 Hydrophobic Interactions -- A 3.5 Concepts from Statistical Physics and Thermodynamics -- A 3.5.1 Temperature -- A 3.5.2 The Most Probable Distribution -- A 3.5.3 Entropy -- A 3.5.4 Information Entropy -- A 3.5.5 Enthalpy -- A 3.5.6 Free Energy -- A 3.5.6.1 Helmholtz Free Energy -- A 3.5.6.2 Gibbs Free Energy.
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A 3.5.7 Kinetic Barrier.
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