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Table of contents
Introduction
1 Fundamental reviewofproteins
1.1 Introduction
1.2 Proteins
1.2.1 Amino acids
1.2.2 Properties of amino acids
1.2.3 Peptide bond
1.2.4 Protein
1.2.5 Protein structure
1.3 Transmembrane proteins
1.3.1 Biological membrane
1.3.2 Transmembrane proteins
1.4 Folding energy
1.4.1 Partial charges
1.4.2 Electrostatic interaction
1.4.3 Hydrogen bond
1.4.4 Van der Waals forces and steric repulsion
1.4.5 Hydrophobic effect and interaction with the environment
1.4.6 Torsion energy around peptide bonds
1.4.7 Other interactions
1.5 Protein structure determination
1.5.1 Experimental methods
1.5.2 In silico prediction
2 Folding β-barrels
2.1 Introduction
2.2 Geometric framework for β-barrels
2.3 Physicochemical constraints
2.4 Classification filtering
2.5 Folding problem definition
2.5.1 Vertices
2.5.2 Edges
2.5.3 Energy attributes:
2.5.4 Protein folding problem
2.6 Dynamic programming approach
2.6.1 Solving as the longest path problem
2.6.2 Solving as the longest closed path problem
2.6.3 Generalization
2.7 Complexity on permuted structures
2.7.1 Preliminaries
3 Tree-decomposition basedalgorithm
3.1 Introduction
3.2 Graph-theory background
3.2.1 Tree decomposition
3.2.2 Modular decomposition
3.3 NP-Completeness
3.4 Algorithm for finding barrel structures of minimum energy
3.5 About Greek key motifs in β-barrels
4 Evaluation of performance of BBP
4.1 Introduction
4.2 Experimental setup
4.2.1 Software
4.2.2 Datasets
4.3 Implementation details
4.4 Method of evaluation
4.4.1 Concepts on predicted secondary structures
4.4.2 Measures of performance
4.5 Experimental results
4.5.1 Folding
4.5.2 Evaluation of the shear numbers
4.5.3 Influence of the filtering threshold
4.5.4 Evaluation on mutated sequences
4.5.5 Permuted structures
4.5.6 Classification
Conclusion and perspectives
Bibliography
