Protein Function Prediction: Methods and Protocols (Paperback)

Preface... Table of Contents... Contributing Authors... 1. Using PFP and ESG Protein Function Prediction Web Servers Qing Wei, Joshua McGraw, Ishita Khan, and Daisuke Kihara 2. GHOSTX: A Fast Sequence Homology Search Tool for Functional Annotation of Metagenomic Data Shuji Suzuki, Takashi Ishida, Masahito Ohue, Masanori Kakuta, and Yutaka Akiyama 3. From Gene Annotation to Function Prediction for Metagenomics Fatemeh Sharifi and Yuzhen Ye 4. An Agile Functional Analysis of Metagenomic Data using SUPER-FOCUS Genivaldo Gueiros Z. Silva, Fabyano A. C. Lopes, and Robert A. Edwards 5. MPFit: Computational Tool for Predicting Moonlighting Proteins Ishita Khan, Joshua McGraw, and Daisuke Kihara 6. Predicting Secretory Proteins with SignalP Henrik Nielsen 7. The ProFunc Function Prediction Server Roman A. Laskowski 8. G-LoSA for Prediction of Protein-Ligand Binding Sites and Structures Hui Sun Lee and Wonpil Im 9. Local Alignment of Ligand Binding Sites in Proteins for Polypharmacology and Drug Repositioning Michal Brylinski 10. WATsite2.0 with PyMOL Plugin: Hydration Site Prediction and Visualization Ying Yang, Bingjie Hu, and Markus A. Lill 11. Enzyme Annotation and Metabolic Reconstruction Using KEGG Minoru Kanehisa 12. Ortholog Identification and Comparative Analysis of Microbial Genomes using MBGD and RECOG Ikuo Uchiyama 13. Exploring Protein Function Using the Saccharomyces Genome Database Edith D. Wong 14. Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates using MouseNet Server Eiru Kim and Insuk Lee 15. The FANTOM5 Computation Ecosystem: Genomic Information Hub for Promoters and Active Enhancers Imad Abugessaisa, Shuhei Noguchi, Piero Carninci, and Takeya Kasukawa 16. Multi-Algorithm Particle Simulations with Spatiocyte Satya N. V. Arjunan and Koichi Takahashi