UNIT 8.6 Identifying Functional Sites Based on Prediction of Charged Group Behavior
Published Online: 1 SEP 2004
Copyright © 2003 by John Wiley and Sons, Inc.
Lab Protocol Title
Current Protocols in Bioinformatics
How to Cite
Ondrechen, M. J. 2004. Identifying Functional Sites Based on Prediction of Charged Group Behavior. Current Protocols in Bioinformatics. 6:8.6:8.6.1–8.6.10.
- Published Online: 1 SEP 2004
- Published Print: JUN 2004
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.
- protein function prediction;
- active sites;
- functional genomics