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Title: Genomic Functionalization: The Next Revolution In Biology

We have implemented a ligand-alignment algorithm into our developed computational pipeline for identifying specificity-determining features (SDFs) in protein-ligand complexes. Given a set of protein-ligand complex structures, the algorithm aligns the complexes by ligand rather than by the C -RMSD or standard approach, providing a single reference frame for extracting SDFs. We anticipate that this ligand-alignment capability will be highly useful for protein function prediction. We already have a database containing > 20 K ligand-protein complex crystal structures taken from the Protein Data Bank. By aligning these proteins to single reference frames using ligand alignment, we can submit the complexes to our pipeline for SDF extraction. The SDFs derived from this training procedure can be used as thumbprints that are hallmarks of individual enzyme classes. These SDF thumbprints may then serve as guides to the prediction of function of new unknown proteins.
Authors:
 [1] ;  [1] ;  [1]
  1. Sandia National Lab. (SNL-CA), Livermore, CA (United States)
Publication Date:
OSTI Identifier:
1322289
Report Number(s):
SAND2014--16084
533045
DOE Contract Number:
AC04-94AL85000
Resource Type:
Technical Report
Research Org:
Sandia National Laboratories (SNL-CA), Livermore, CA (United States)
Sponsoring Org:
USDOE National Nuclear Security Administration (NNSA)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING