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E-book

Title Structural bioinformatics of membrane proteins / Dmitrij Frishman, editor
Published Wien : Springer, ©2010

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Description 1 online resource (xi, 281 pages) : illustrations
Contents Cover -- Table of Contents -- Evolutionary Origins of Membrane Proteins -- 1 Introduction -- 2 Comparative Analysis of F/V-Type Atpases: Example of Function Cooption? -- 3 Emergence of Integral Membrane Proteins -- 4 Emergence of Lipid Membranes -- 5 Scenario for the Origin and Evolution of Membranes and Membrane Proteins -- Acknowledgments -- References -- Molecular Archeological Studies of Transmembrane Transport Systems -- 1 Introduction -- 2 Molecular Transport -- 3 Techniques to Establish Homology or the Lack of Homology -- 4 Transport Protein Diversity -- 5 The Abc Superfamily -- 6 Independent Origins for Abc Porters -- 7 The Phosphoenolpyruvate-Dependent Sugar Transporting Phosphotransferase System (Pts) -- 8 Independent Origins for Pts Permeases -- 9 Reverse (Retro)-Evolution -- 10 Conclusions and Perspectives -- References -- Resource for Structure Related Information on Transmembrane Proteins -- 1 Introduction -- 2 3D Structure Resources -- 2.1 Protein Data Bank -- 2.2 Manually Curated Structure Resources of Tmps -- 2.3 Tmdet Algorithm -- 2.4 Pdbtm Database -- 2.5 Opm Database -- 2.6 Modeling Protein8211;Lipid Assembly -- 3 2D Structure Resources -- 3.1 Topdb Database -- 3.2 Topdom Database -- 3.3 Prediction Methods Incorporating Experimental Results -- Acknowledgments -- References -- Topology Prediction of Membrane Proteins: How Distantly Related Homologs Come Into Play -- 1 Introduction -- 2 From Membrane Protein Sequence to Topologic Models -- 2.1 Datasets of Membrane Proteins -- 2.2 Scoring the Accuracy of Diff Erent Methods -- 2.3 Propensity Scales Versus Machine Learning-Based Methods -- 2.4 Methods for Optimizing Topologic Models -- 2.5 Single Sequence Versus Multiple Sequence Profi Le -- 2.6 Prediction of Signal Peptides and Gpi-Anchors -- 2.7 More Methods Are Bett Er Than One: Cinthia -- 2.8 A Large-Scale Annotator of the Human Proteome: the Pongo System -- 3 From Membrane Protein Sequence to Function and Structure -- 3.1 Membrane Proteins: How Many With Known Functions and Folds? -- 3.2 What Do Bar Clusters Contain? -- References -- Transmembrane Beta-Barrel Protein Structure Prediction -- 1 Introduction -- 1.1 1D Feature Prediction -- 1.2 946;-Contact and Tertiary Structure Prediction -- 2 Data -- 2.1 Benchmark Sets -- 2.2 Cross-Validation -- 2.3 Template Construction -- 3 Methods -- 3.1 Secondary Structure Prediction -- 3.2 946;-Contact Prediction -- 3.3 Tertiary Structure Prediction -- 4 Results -- 4.1 Secondary Structure Prediction Results -- 4.2 946;-Contact Prediction Results -- 4.3 Tertiary Structure Prediction Results -- 5 Discussion -- References -- Multiple Alignment of Transmembrane Protein Sequences -- 1 Introduction -- 2 Factors Influencing the Alignment of Transmembrane Proteins -- 2.1 Transmembrane Substitution Rates -- 2.2 Transmembrane Alignment Gaps -- 3 Overview of Tm Msa Methods -- 3.1 Tm-Aware Multiple Sequence Alignment By the Praline Method -- 3.2 Bipartite Msa Compared to Standard Msa -- 3.3 Comparing Pra Line-Tm With Non-Tm Msa Methods -- T$
Summary This book is the first one specifically dedicated to the structural bioinformatics of membrane proteins. With a focus on membrane proteins from the perspective of bioinformatics, the present work covers a broad spectrum of topics in evolution, structure, function, and bioinformatics of membrane proteins focusing on the most recent experimental results. Leaders in the field who have recently reported breakthrough advances cover algorithms, databases and their applications to the subject. The increasing number of recently solved membrane protein structures makes the expert coverage presented her
Bibliography Includes bibliographical references
Notes Print version record
Subject Membrane proteins.
Membrane Proteins
Computational Biology -- methods
MEDICAL -- Biochemistry.
Informatique.
Membrane proteins.
Form Electronic book
Author Frishman, Dmitrij
ISBN 9783709100455
3709100453