User:Pakpoom Subsoontorn/Notebook/general reading/2008/10/22: Difference between revisions
From OpenWetWare
Line 37: | Line 37: | ||
# Place a cubic grid for docking ligands with in a convex hull encompassing with wild-type ligand | # Place a cubic grid for docking ligands with in a convex hull encompassing with wild-type ligand | ||
# Construct an ensemble representing all rotational and internal degrees of freedom of ligand | # Construct an ensemble representing all rotational and internal degrees of freedom of ligand | ||
# Place the rotational ensemble onto the grid and select pose that do not form unfavorable steric interactions and are partially confined within the convex hull. This will be the "doced ligand conformations" | # Place the rotational ensemble onto the grid and select pose that do not form unfavorable steric interactions and are partially confined within the convex hull. This will be the "doced ligand conformations" (Parallelized) | ||
# Rank the docked ensemble by the interaction energy between the ligands and the receptor | # Rank the docked ensemble by the interaction energy between the ligands and the receptor | ||
# | # Calculate PCS of the top N (~10,000) docked ligands, using DEE (Parallelized) | ||
* Place side-chain rotamer library representing all possible mutation and side-chain conformation (except cys, pro) at all position in the PCS | |||
* Identify optimal sequence by determining the global minimum energy functions of interaction | |||
* Potential function is based on semi-empirical force field, a modified Lennard-Jones potential representing van der Waals interaction. Satisfy potential hydrogen bonds donors and acceptors in the ligand | |||
*As additional filter in DEE: should all non-eliminated hydrogen bond partners for a demanded atom arise from a single residue position, all non-hydrogen-bonding side-chains at this position are eliminated | |||
*Keep protein backbone fix | |||
# Rank predicted design based on should all non-eliminated hydrogen bond partners for a demanded atom arise from a single residue position, all non-hydrogen-bonding side-chains at this position are eliminated. | |||
#a small number of the top-ranked designs are experimentally tested. | |||
Revision as of 16:08, 23 October 2008
Project name | <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page <html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html> </html>Next entry<html><img src="/images/5/5c/Resultset_next.png" border="0" /></html> |
Computational design of receptor and sensor proteins with novel functions(BioE300a presentation)Outline
Design Algorithm
|