This volume presents established bioinformatics tools and databases for function prediction of proteins. Reflecting the diversity of this active field in bioinformatics, the chapters in this book discuss a variety of tools and resources such as sequence-, structure-, systems-, and interaction-based function prediction methods, tools for functional analysis of metagenomics data, detecting moonlighting-proteins, sub-cellular localization prediction, and pathway and comparative genomics databases. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, step-by-step instructions of how to use software and web resources, use cases, and tips on troubleshooting and avoiding known pitfalls.

Thorough and cutting-edge, Protein Function Prediction: Methods and Protocols is a valuable and practical guide for using bioinformatics tools for investigating protein function

Using PFP and ESG Protein Function Prediction Web Servers.- GHOSTX: A Fast Sequence Homology Search Tool for Functional Annotation of Metagenomic Data.- From Gene Annotation to Function Prediction for Metagenomics.- An Agile Functional Analysis of Metagenomic Data using SUPER-FOCUS.- MPFit: Computational Tool for Predicting Moonlighting Proteins.- Predicting Secretory Proteins with SignalP.- The ProFunc Function Prediction Server.- G-LoSA for Prediction of Protein-Ligand Binding Sites and Structures.- Local Alignment of Ligand Binding Sites in Proteins for Polypharmacology and Drug Repositioning.- WATsite2.0 with PyMOL Plugin: Hydration Site Prediction and Visualization.- Enzyme Annotation and Metabolic Reconstruction Using KEGG.- Ortholog Identification and Comparative Analysis of Microbial Genomes using MBGD and RECOG.- Exploring Protein Function Using the
Saccharomyces
Genome Database.- Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates using MouseNet Server.- The FANTOM5 Computation Ecosystem: Genomic Information Hub for Promoters and Active Enhancers.- Multi-Algorithm Particle Simulations with Spatiocyte.