From Protein Structure to Function with Bioinformatics.pdf

Contentsxi4.2.1 Alpha-Helical Bundles ......................................................... 924.2.2 Beta-Barrels .......................................................................... 924.3 Membrane Proteins Are Difficult to Crystallise ............................... 944.4 Databases .......................................................................................... 944.5 Multiple Sequence Alignments ......................................................... 964.6 Transmembrane Protein Topology Prediction .................................. 984.6.1 Alpha-Helical Proteins .......................................................... 984.6.2 Beta-Barrel Proteins .............................................................. 1024.6.3 Whole Genome Analysis ...................................................... 1024.6.4 Data Sets, Homology, Accuracyand Cross-Validation ............................................................. 1034.7 3D Structure Prediction ..................................................................... 1054.8 Future Developments ........................................................................ 1075 Bioinformatics Approaches to the Structureand Function of Intrinsically Disordered Proteins ............................... 113Peter Tompa5.1 The Concept of Protein Disorder ...................................................... 1135.2 Sequence Features of IDPs ............................................................... 1155.2.1 The Unusual Amino AcidComposition of IDPs ............................................................ 1155.2.2 Sequence Patterns of IDPs .................................................... 1155.2.3 Low Sequence Complexity and Disorder ............................. 1165.3 Prediction of Disorder ....................................................................... 1165.3.1 Prediction of Low-Complexity Regions ............................... 1165.3.2 Charge-Hydropathy Plot ....................................................... 1175.3.3 Propensity-Based Predictors ................................................. 1175.3.4 Predictors Based on the Lackof Secondary Structure .......................................................... 1185.3.5 Machine Learning Algorithms .............................................. 1195.3.6 Prediction Based on Contact Potentials ................................ 1205.3.7 A Reduced Alphabet Sufficesto Predict Disorder ................................................................ 1215.3.8 Comparison of Disorder Prediction Methods ....................... 1225.4 Functional Classification of IDPs ..................................................... 1225.4.1 Gene Ontology-Based FunctionalClassification of IDPs ........................................................... 1225.4.2 Classification of IDPs Basedon Their Mechanism of Action ............................................. 1235.4.3 Function-Related Structural Elements in IDPs ..................... 1265.5 Prediction of the Function of IDPs ................................................... 1285.5.1 Correlation of Disorder Pattern and Function ....................... 1285.5.2 Predicting Short Recognition Motifs in IDRs ....................... 1285.5.3 Prediction of MoRFs ............................................................. 129