Protein Function Prediction: Methods and Protocols

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