Table of Content: Part 1: Proteomics analysisChapter 1 Predict protein structure1.1 Protein structure layers1.2 Secondary structures1.3 Secondary structure testing1.4 Algorithms for predicting protein structure 1.5 Evaluation of prediction algorithms1.6 Protein comparisonChapter 2 Mass spectrometry (MS) analysis for protein sequences2.1 MS2.2 MS data analysis2.3 Pre-treatment for MS data2.4 Scoring methods2.5 de novo sequencingPart 2 Biological network analysisChapter 3 Protein-Protein interaction prediction3.1 Protein-Protein interaction3.2 Experimental methods for Protein-Protein interaction detection3.3 Bioinformatics application in Protein-Protein interaction analysis3.4 Domain interaction prediction3.5 SummaryChapter 4 Functional modules in biological networks4.1 Introduction4.2 Structure characteristics for complex networks4.3 Network parameters and calculation4.4 Parallel analysis for biological networks4.5 Module partition 4.6 Clustering4.7 Spectral analysis4.8 Evaluation for module partitionChapter 5 Data mining for large-scale network5.1 Clustering analysis5.2 Linkage clustering - single, complete, average 5.3 Kernel function5.4 Spectral clustering
