http://www.cs.ucdavis.edu/~koehl/
| |
http://www.cs.ucdavis.edu/~koehl/ |
|
Homology Modeling4. Homology Modeling: A Self Consistent Mean Field Approach Here I focus on the SCMF method that Marc Delarue and myself originally developed for protein sidechain modeling [1], and later applied to comparative protein structure modelling [2]. An overview of the Mean Field Theory is available here, and its application to sidechain prediction is described here. We suppose given a framework for the target protein, as well as multiple candidate fragments for each gap in the framework. The framework was obtained from the sequence alignment between the template protein and the target protein (see here) while the candidate fragments were selected from a library of protein fragments. 
References1. Koehl, P and Delarue, M. Application of a self consistent mean field theo ry to predict protein side-chain conformations and estimate their conformationalentropy. J. Mol. Biol., 239, 249-275 (1994). 2. Koehl, P and Delarue, M. A self-consistent meanfield approach t simultaneous gap closure and side-chain positioning in homology modeling. Nature Struct. Bio., 2, 163-170 (1995).
|