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.
- Publication Date:
- OSTI Identifier:
- Report Number(s):
- DOE Contract Number:
- 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
- 59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING
Enter terms in the toolbar above to search the full text of this document for pages containing specific keywords.