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In Silico Protein Motif Discovery and Structural Analysis

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In Silico Tools for Gene Discovery

Part of the book series: Methods in Molecular Biology ((MIMB,volume 760))

Abstract

A wealth of in silico tools is available for protein motif discovery and structural analysis. The aim of this chapter is to collect some of the most common and useful tools and to guide the biologist in their use. A detailed explanation is provided for the use of Distill, a suite of web servers for the prediction of protein structural features and the prediction of full-atom 3D models from a protein sequence. Besides this, we also provide pointers to many other tools available for motif discovery and secondary and tertiary structure prediction from a primary amino acid sequence. The prediction of protein intrinsic disorder and the prediction of functional sites and SLiMs are also briefly discussed. Given that user queries vary greatly in size, scope and character, the trade-offs in speed, accuracy and scale need to be considered when choosing which methods to adopt.

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Acknowledgements

C.M. is supported by Science Foundation Ireland (SFI) grant 08/IN.1/B1864. ND is supported by an EMBL Interdisciplinary Postdoc (EIPOD) fellowship. CM, GP, IW and AJMM were partly supported by SFI grant 05/RFP/CMS0029, grant RP/2005/219 from the Health Research Board of Ireland, a UCD President’s Award 2004 and UCD Seed Funding 2009 award SF371.

Author information

Authors and Affiliations

  1. Complex and Adaptive Systems Laboratory, University College Dublin, Belfield, Dublin 4, Ireland

    Catherine Mooney, Alberto J.M. Martin, Ian Walsh, Denis C. Shields & Gianluca Pollastri

  2. Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland

    Catherine Mooney & Denis C. Shields

  3. School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland

    Catherine Mooney & Denis C. Shields

  4. EMBL Structural and Computational Biology Unit, 69117, Heidelberg, Germany

    Norman Davey

  5. Biocomputing UP, Department of Biology, University of Padua, I-35131, Padova, Italy

    Alberto J.M. Martin & Ian Walsh

  6. School of Computer Science and Informatics, University College Dublin, Belfield, Dublin 4, Ireland

    Alberto J.M. Martin, Ian Walsh & Gianluca Pollastri

Authors
  1. Catherine Mooney
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  2. Norman Davey
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  3. Alberto J.M. Martin
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  4. Ian Walsh
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  5. Denis C. Shields
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  6. Gianluca Pollastri
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Corresponding author

Correspondence to Catherine Mooney .

Editor information

Editors and Affiliations

  1. Royal Prince Alfred Hospital, Dept. of Molecular & Clinical Genetics, University of Sydney, Missenden Road, Camperdown, 2050, New South Wales, Australia

    Bing Yu

  2. Royal Prince Alfred Hospital, Dept. Molecular & Clinical Genetics, University of Sydney, Missenden Road, Camperdown, 2050, New South Wales, Australia

    Marcus Hinchcliffe

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Mooney, C., Davey, N., Martin, A.J., Walsh, I., Shields, D.C., Pollastri, G. (2011). In Silico Protein Motif Discovery and Structural Analysis. In: Yu, B., Hinchcliffe, M. (eds) In Silico Tools for Gene Discovery. Methods in Molecular Biology, vol 760. Humana Press. https://doi.org/10.1007/978-1-61779-176-5_21

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  • DOI: https://doi.org/10.1007/978-1-61779-176-5_21

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-175-8

  • Online ISBN: 978-1-61779-176-5

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