Contents
1 Using PFP and ESG Protein Function Prediction Web Servers
Qing Wei, Joshua McGraw, I*****a 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
I*****a 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
Index