Protein Function Prediction: Methods and Protocols

✍ Scribed by Daisuke Kihara

• Publisher: Humana Press : Springer
• Year: 2017
• Tongue: English
• Leaves: 243
• Series: Methods in molecular biology (Clifton N.J.) 1611
• Edition: 1st ed. 2017
• Category: Library

✦ Synopsis

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

✦ Table of Contents

Content: Using PFP and ESG protein function prediction web servers / Qing Wei, Joshua McGraw, Ishita Khan, and Daisuke Kihara --
GHOSTX : a fast sequence homology search tool for functional annotation of metagenomic data / Shuji Suzuki, Takashi Ishida, Masahito Ohue, Masanori Kakuta, and Yutaka Akiyama --
From gene annotation to function prediction for metagenomics / Fatemeh Sharifi and Yuzhen Ye --
Agile functional analysis of metagenomic data using SUPER-FOCUS / Genivaldo Gueiros Z. Silva, Fabyano A.C. Lopes, and Robert A. Edwards --
MPFit : computational tool for predicting moonlighting proteins / Ishita Khan, Joshua McGraw, and Daisuke Kihara --
Predicting secretory proteins with SignalP / Henrik Nielsen --
ProFunc function prediction server / Roman A. Laskowski --
G-LoSA for prediction of protein-ligand binding sites and structures / Hui Sun Lee and Wonpil Im --
Local alignment of ligand binding sites in Proteins for polypharmacology and drug repositioning / Michal Brylinski --
WATsite2.0 with PyMOL plugin : hydration site prediction and visualization / Ying Yang, Bingjie Hu, and Markus A. Lill --
Enzyme annotation and metabolic reconstruction using KEGG / Minoru Kanehisa --
Ortholog identification and comparative analysis of microbial genomes using MBGD and RECOG / Ikuo Uchiyama --
Exploring protein function using the Saccharomyces genome database / Edith D. Wong --
Network-based gene function prediction in mouse and other model vertebrates using MouseNet server / Eiru Kim and Insuk Lee --
FANTOM5 computation ecosystem : genomic information hub for promoters and active enhancers / Imad Abugessaisa, Shuhei Noguchi, Piero Carninci, and Takeya Kasukawa --
Multi-algorithm particle simulations with spatiocyte / Satya N.V. Arjunan and Koichi Takahashi.

✦ Subjects

Proteins -- Laboratory manuals.;Protein-protein interactions -- Laboratory manuals.;Protein-protein interactions.;Proteins.;Protein Interaction Mapping.