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Biomedical Informatics pp 157–172Cite as

Applications of Bioinformatics to Protein Structures: How Protein Structure and Bioinformatics Overlap

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Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 569))

Summary

In this chapter, we will focus on the role of bioinformatics to analyze a protein after its protein structure has been determined. First, we present how to validate protein structures for quality assurance. Then, we discuss how to analyze protein–protein interfaces and how to predict the biomolecule which is the biological oligomeric state of the protein. Finally, we discuss how to search for homologs based on the 3-D structure which is an essential step for understanding protein function.

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Notes

  1. 1.

    The Quality Control Check program was developed at the Joint Center for Structural Genomics (JCSG). If you use this tool in preparing a structure please acknowledge the JCSG.

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Acknowledgment

G.W.H. and C.R. are affiliated with the JCSG, which is supported by the National Institute of General Medical Sciences, Protein Structure Initiative; Grant Numbers P50 GM62411, U54 GM074898. M.R.S. is supported by the Howard Hughes Medical Institute. We thank Ian Wilson, Anand Kolatkar, and Robyn Stanfield for their comments on this chapter. We also thank Lisa Van Veen for technical assistance. This is TSRI manuscript number 19238. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of General Medical Sciences or the National Institutes of Health.

Author information

Authors and Affiliations

  1. Join Center for Structural Genomics(JCSG), The Scripps Research Institute, La Jolla, CA, USA

    Gye Won Han

  2. Join Center for Structural Genomics(JCSG), Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, CA, USA

    Chris Rife

  3. UCLA-DOE Institute of Genomics and Proteomics, Howard Hughes Medical Institute, Los Angeles, CA, USA

    Michael R. Sawaya

Authors
  1. Gye Won Han
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  2. Chris Rife
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  3. Michael R. Sawaya
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Editors and Affiliations

  1. Biomedical Informatics Research Network, University of California, San Diego, Gilman Dr. 9500, La Jolla, 92093, U.S.A.

    Vadim Astakhov

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Han, G.W., Rife, C., Sawaya, M.R. (2009). Applications of Bioinformatics to Protein Structures: How Protein Structure and Bioinformatics Overlap. In: Astakhov, V. (eds) Biomedical Informatics. Methods in Molecular Biology™, vol 569. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-59745-524-4_8

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  • DOI: https://doi.org/10.1007/978-1-59745-524-4_8

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  • Publisher Name: Humana Press, Totowa, NJ

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