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Annotation of proteins of unknown function: initial enzyme results

Abstract

Working with a combination of ProMOL (a plugin for PyMOL that searches a library of enzymatic motifs for local structural homologs), BLAST and Pfam (servers that identify global sequence homologs), and Dali (a server that identifies global structural homologs), we have begun the process of assigning functional annotations to the approximately 3,500 structures in the Protein Data Bank that are currently classified as having “unknown function”. Using a limited template library of 388 motifs, over 500 promising in silico matches have been identified by ProMOL, among which 65 exceptionally good matches have been identified. The characteristics of the exceptionally good matches are discussed.

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Acknowledgments

NIGMS 2R15GM078077-02, NIGMS 3R15GM078077-02S1, NIGMS 3R15GM078077-02S2, Dowling College, Rochester Institute of Technology. We would like to thank the following team members who supported our efforts on this project: (from RIT) Weinishet Tedla-Boyd, Tananda Richards; (from Dowling College) Mogjan Asadi, Limone Rosa.

Conflict of interest

None of the authors have reported any conflicts of interest in the completion of the research described in this manuscript.

Author information

Correspondence to Paul A. Craig.

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Cite this article

McKay, T., Hart, K., Horn, A. et al. Annotation of proteins of unknown function: initial enzyme results. J Struct Funct Genomics 16, 43–54 (2015). https://doi.org/10.1007/s10969-015-9194-5

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Keywords

  • Bioinformatics
  • Catalytic motif
  • Enzyme
  • ProMOL
  • Protein function
  • PyMOL
  • Structural biology