From Protein Structure to Function with Bioinformatics

✍ Scribed by Daniel J. Rigden (eds.)

• Publisher: Springer Netherlands
• Year: 2017
• Tongue: English
• Leaves: 509
• Edition: 2
• Category: Library

✦ Synopsis

This book is about protein structural bioinformatics and how it can help understand and predict protein function. It covers structure-based methods that can assign and explain protein function based on overall folds, characteristics of protein surfaces, occurrence of small 3D motifs, protein-protein interactions and on dynamic properties. Such methods help extract maximum value from new experimental structures, but can often be applied to protein models. The book also, therefore, provides comprehensive coverage of methods for predicting or inferring protein structure, covering all structural classes from globular proteins and their membrane-resident counterparts to amyloid structures and intrinsically disordered proteins.

The book is split into two broad sections, the first covering methods to generate or infer protein structure, the second dealing with structure-based function annotation. Each chapter is written by world experts in the field. The first section covers methods ranging from traditional homology modelling and fold recognition to fragment-based ab initio methods, and includes a chapter, new for the second edition, on structure prediction using evolutionary covariance. Membrane proteins and intrinsically disordered proteins are each assigned chapters, while two new chapters deal with amyloid structures and means to predict modes of protein-protein interaction. The second section includes chapters covering functional diversity within protein folds and means to assign function based on surface properties and recurring motifs. Further chapters cover the key roles of protein dynamics in protein function and use of automated servers for function inference. The book concludes with two chapters covering case studies of structure prediction, based respectively on crystal structures and protein models, providing numerous examples of real-world usage of the methods mentioned previously.

This book is targeted at postgraduate students and academic researchers. It is most obviously of interest to protein bioinformaticians and structural biologists, but should also serve as a guide to biologists more broadly by highlighting the insights that structural bioinformatics can provide into proteins of their interest.

✦ Table of Contents

Front Matter....Pages i-xv
Front Matter....Pages 1-1
Ab Initio Protein Structure Prediction....Pages 3-35
Protein Structures, Interactions and Function from Evolutionary Couplings....Pages 37-58
Fold Recognition....Pages 59-90
Comparative Protein Structure Modelling....Pages 91-134
Advances in Computational Methods for Transmembrane Protein Structure Prediction....Pages 135-165
Bioinformatics Approaches to the Structure and Function of Intrinsically Disordered Proteins....Pages 167-203
Prediction of Protein Aggregation and Amyloid Formation....Pages 205-263
Prediction of Biomolecular Complexes....Pages 265-292
Front Matter....Pages 293-293
Function Diversity Within Folds and Superfamilies....Pages 295-325
Function Prediction Using Patches, Pockets and Other Surface Properties....Pages 327-360
3D Motifs....Pages 361-392
Protein Dynamics : From Structure to Function....Pages 393-425
Integrated Servers for Structure-Informed Function Prediction....Pages 427-448
Case Studies: Function Predictions of Structural Genomics Results....Pages 449-465
Prediction of Protein Function from Theoretical Models....Pages 467-498
Back Matter....Pages 499-503

✦ Subjects

Protein Science;Biomedicine general;Bioinformatics;Computer Appl. in Life Sciences;Proteomics