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

Jacquelyn S. Fetrow1

1 Wake Forest University, Winston‐Salem, North Carolina
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 8.10
DOI:  10.1002/0471250953.bi0810s14
Online Posting Date:  July, 2006
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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

     
 
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Table of Contents

  • Basic Protocol 1: Construction of the Active Site Profile for a Functional  Site
  • Basic Protocol 2: Use of the Functional Site Profile to Search the Sequence Database
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

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   Cammer, S.A., Hoffman, B.T., Speir, J.A., Canady, M.A., Nelson, M.R., Knutson, S., Gallina, M., Baxter, S.M., and Fetrow, J.S. 2003. Structure‐based active site profiles for genome analysis and functional family subclassification. J. Mol. Biol. 334:387‐401.
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Key References
   Cammer et al., 2003. See above.
  Describes original research leading to the development of the active site profiling method. Details are given about scoring and validation.
   Baxter et al., 2004. See above.
  Describes a computational method for profiling sequences with an experimental proteomics method. Detailed analysis of serine hydrolases in yeast is presented.
Internet Resources
   http://dasp.deac.wfu.edu
  This DASP Web site allows access to the active site profiling software.
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