Format

Send to:

Choose Destination
See comment in PubMed Commons below
Proteins. 2011 Sep;79(9):2746-63. doi: 10.1002/prot.23103. Epub 2011 Jul 18.

Surface-based protein binding pocket similarity.

Author information

  • 1Department of Bioengineering and Therapeutic Sciences, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158-9001, USA.

Abstract

Protein similarity comparisons may be made on a local or global basis and may consider sequence information or differing levels of structural information. We present a local three-dimensional method that compares protein binding site surfaces in full atomic detail. The approach is based on the morphological similarity method which has been widely applied for global comparison of small molecules. We apply the method to all-by-all comparisons two sets of human protein kinases, a very diverse set of ATP-bound proteins from multiple species, and three heterogeneous benchmark protein binding site data sets. Cases of disagreement between sequence-based similarity and binding site similarity yield informative examples. Where sequence similarity is very low, high pocket similarity can reliably identify important binding motifs. Where sequence similarity is very high, significant differences in pocket similarity are related to ligand binding specificity and similarity. Local protein binding pocket similarity provides qualitatively complementary information to other approaches, and it can yield quantitative information in support of functional annotation.

Copyright © 2011 Wiley-Liss, Inc.

PMID:
21769944
[PubMed - indexed for MEDLINE]
PMCID:
PMC3155014
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for John Wiley & Sons, Inc. Icon for PubMed Central
    Loading ...
    Write to the Help Desk