User:Pakpoom Subsoontorn/Notebook/general reading/2008/10/22: Difference between revisions
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# 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) | # 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 | #* 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 | * 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 | * 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 |
Revision as of 16:08, 23 October 2008
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Computational design of receptor and sensor proteins with novel functions(BioE300a presentation)Outline
Design Algorithm
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