1. Annotation of proteins of unknown function: initial enzyme results.
- Author
-
McKay T, Hart K, Horn A, Kessler H, Dodge G, Bardhi K, Bardhi K, Mills JL, Bernstein HJ, and Craig PA
- Subjects
- Algorithms, Amino Acid Motifs genetics, Amino Acid Sequence, Binding Sites genetics, Computer Simulation, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Structure, Tertiary, Proteins genetics, Proteins metabolism, Reproducibility of Results, Sequence Homology, Amino Acid, Computational Biology methods, Databases, Protein, Molecular Sequence Annotation methods, Proteins chemistry, Software
- 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.
- Published
- 2015
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