Unit

UNIT 8.10 Active Site Profiling to Identify Protein Functional Sites in Sequences and Structures Using the Deacon Active Site Profiler (DASP)

  1. Jacquelyn S. Fetrow

Published Online: 1 JUL 2006

DOI: 10.1002/0471250953.bi0810s14

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Fetrow, J. S. 2006. Active Site Profiling to Identify Protein Functional Sites in Sequences and Structures Using the Deacon Active Site Profiler (DASP). Current Protocols in Bioinformatics. 14:8.10:8.10.1–8.10.16.

Author Information

  1. Wake Forest University, Winston-Salem, North Carolina

Publication History

  1. Published Online: 1 JUL 2006
  2. Published Print: JUN 2006

Abstract

Methods for the annotation and analysis of functional sites in proteins are an area of active research, and those methods that allow detailed characterization of functional site features are much needed. A Web site application, DASP, which implements a previously described method (Cammer, et al., 2003) to allow users to create an active site profile for any protein family, is described. Two protocols for functional site analysis of protein families using DASP are presented: 1) creation of functional site signatures and a profile from proteins of known structure and 2) utilization of the active site profile to search sequences that contain fragments similar to those found in the functional site signatures. The active site profile produced by Basic Protocol 1 allows the user to analyze the features of the functional site, i.e., those characteristics that are common across the family and those that are unique to one or several members of the family. The characteristics that are unique to a subfamily might be described as specificity determinants i.e., features that impart specificity to a particular function. Basic Protocol 2 provides instructions for searching for sequences that might contain a similar functional site.

Keywords:

  • active site profiling;
  • fuzzy functional form;
  • protein function prediction;
  • active site;
  • functional site;
  • functional specificity determinants