Identifying Functional Sites Based on Prediction of Charged Group Behavior

Mary Jo Ondrechen1

1 Northeastern University, Boston, Massachusetts
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 8.6
DOI:  10.1002/0471250953.bi0806s6
Online Posting Date:  September, 2004
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This protocol describes the implementation and interpretation of THEMATICS, a simple computational predictor of functional information for proteins from the three‐dimensional structure. This method is based on the computation of the electrical potential function for the protein and the calculation of the predicted titration curves for each of the titratable groups in the protein. While most of the titratable residues in a protein have predicted titration behavior that fits the Henderson‐Hasselbalch equation, the ionizable residues in the active site generally deviate dramatically from the typical behavior. From the calculated titration curves, one identifies those residues that deviate significantly from Henderson‐Hasselbalch behavior. A cluster of two or more of such deviant titratable residues in physical proximity is a reliable predictor of active‐site location.

Keywords: THEMATICS; protein function prediction; active sites; titration; functional genomics

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Table of Contents

  • Basic Protocol 1: Thematics Analysis Using the UHBD Package
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

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