From Protein Structure to Function with Bioinformatics.pdf

Contentsxiii7.4.2 Predicting Binding Site Locations ........................................ 1757.4.3 Predictions of Druggability ................................................... 1787.4.4 Annotation of Ligand Binding Sites ..................................... 1787.5 Protein-Protein Interfaces ................................................................. 1807.5.1 Properties of Protein-Protein Interfaces ................................ 1807.5.2 Hot-Spot Regions in Protein Interfaces ................................ 1817.5.3 Predictions of Interface Location .......................................... 1827.6 Summary ........................................................................................... 1848 3D Motifs ................................................................................................... 187Elaine C. Meng, Benjamin J. Polacco,and Patricia C. Babbitt8.1 Background and Significance ........................................................... 1888.1.1 What Is Function? ................................................................. 1898.1.2 Three-Dimensional Motifs: Definitionand Scope .............................................................................. 1908.2 Overview of Methods ........................................................................ 1908.2.1 Motif Discovery .................................................................... 1908.2.2 Motif Description and Matching ........................................... 1918.2.3 Interpretation of Results ........................................................ 1938.3 Specific Methods ............................................................................... 1968.3.1 User-Defined Motifs ............................................................. 1978.3.2 Motif Discovery .................................................................... 2018.4 Related Methods ............................................................................... 2088.4.1 Hybrid (Point-Surface) Descriptions .................................... 2088.4.2 Single-Point-Centred Descriptions ....................................... 2088.5 Docking for Functional Annotation .................................................. 2108.6 Discussion ......................................................................................... 2128.7 Conclusions ....................................................................................... 2129 Protein Dynamics: From Structure to Function ................................... 217Marcus B. Kubitzki, Bert L. de Groot,and Daniel Seeliger9.1 Molecular Dynamics Simulations ..................................................... 2179.1.1 Principles and Approximations ............................................. 2189.1.2 Applications .......................................................................... 2209.1.3 Limitations – Enhanced SamplingAlgorithms ............................................................................ 2269.2 Principal Component Analysis ......................................................... 2309.3 Collective Coordinate Sampling Algorithms .................................... 2339.3.1 Essential Dynamics ............................................................... 2339.3.2 TEE-REX .............................................................................. 2349.4 Methods for Functional Mode Prediction ......................................... 2379.4.1 Normal Mode Analysis ......................................................... 237