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Protein Function Prediction

Methods and Protocols

  • Book
  • © 2017

Overview

Editors:
  1. Daisuke Kihara

    1. Department of Biological Sciences and Computer Science, Purdue University, West Lafayette, USA

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1611)

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Table of contents (16 protocols)

  1. Front Matter

    Pages i-x
    Download chapter PDF

  2. Using PFP and ESG Protein Function Prediction Web Servers

    • Qing Wei, Joshua McGraw, Ishita Khan, Daisuke Kihara
    Pages 1-14

  3. GHOSTX: A Fast Sequence Homology Search Tool for Functional Annotation of Metagenomic Data

    • Shuji Suzuki, Takashi Ishida, Masahito Ohue, Masanori Kakuta, Yutaka Akiyama
    Pages 15-25

  4. From Gene Annotation to Function Prediction for Metagenomics

    • Fatemeh Sharifi, Yuzhen Ye
    Pages 27-34

  5. An Agile Functional Analysis of Metagenomic Data Using SUPER-FOCUS

    • Genivaldo Gueiros Z. Silva, Fabyano A. C. Lopes, Robert A. Edwards
    Pages 35-44

  6. MPFit: Computational Tool for Predicting Moonlighting Proteins

    • Ishita Khan, Joshua McGraw, Daisuke Kihara
    Pages 45-57

  7. Predicting Secretory Proteins with SignalP

    • Henrik Nielsen
    Pages 59-73

  8. The ProFunc Function Prediction Server

    • Roman A. Laskowski
    Pages 75-95

  9. G-LoSA for Prediction of Protein-Ligand Binding Sites and Structures

    • Hui Sun Lee, Wonpil Im
    Pages 97-108

  10. Local Alignment of Ligand Binding Sites in Proteins for Polypharmacology and Drug Repositioning

    • Michal Brylinski
    Pages 109-122

  11. WATsite2.0 with PyMOL Plugin: Hydration Site Prediction and Visualization

    • Ying Yang, Bingjie Hu, Markus A. Lill
    Pages 123-134

  12. Enzyme Annotation and Metabolic Reconstruction Using KEGG

    • Minoru Kanehisa
    Pages 135-145

  13. Ortholog Identification and Comparative Analysis of Microbial Genomes Using MBGD and RECOG

    • Ikuo Uchiyama
    Pages 147-168

  14. Exploring Protein Function Using the Saccharomyces Genome Database

    • Edith D. Wong
    Pages 169-182

  15. Network-Based Gene Function Prediction in Mouse and Other Model Vertebrates Using MouseNet Server

    • Eiru Kim, Insuk Lee
    Pages 183-198

  16. The FANTOM5 Computation Ecosystem: Genomic Information Hub for Promoters and Active Enhancers

    • Imad Abugessaisa, Shuhei Noguchi, Piero Carninci, Takeya Kasukawa
    Pages 199-217

  17. Multi-Algorithm Particle Simulations with Spatiocyte

    • Satya N. V. Arjunan, Koichi Takahashi
    Pages 219-236

  18. Back Matter

    Pages 237-239
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Keywords

About this book

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</p>

Editors and Affiliations

  • Department of Biological Sciences and Computer Science, Purdue University, West Lafayette, USA

    Daisuke Kihara

Bibliographic Information

  • Book Title: Protein Function Prediction

  • Book Subtitle: Methods and Protocols

  • Editors: Daisuke Kihara

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7015-5

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2017

  • Hardcover ISBN: 978-1-4939-7013-1Published: 28 April 2017

  • Softcover ISBN: 978-1-4939-8368-1Published: 17 July 2018

  • eBook ISBN: 978-1-4939-7015-5Published: 27 April 2017

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: X, 239

  • Number of Illustrations: 11 b/w illustrations, 71 illustrations in colour

  • Topics: Protein Science

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