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2oty

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{{STRUCTURE_2oty| PDB=2oty | SCENE= }}
{{STRUCTURE_2oty| PDB=2oty | SCENE= }}
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'''1,2-dichlorobenzene in complex with T4 Lysozyme L99A'''
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===1,2-dichlorobenzene in complex with T4 Lysozyme L99A===
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==Overview==
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A central challenge in structure-based ligand design is the accurate prediction of binding free energies. Here we apply alchemical free energy calculations in explicit solvent to predict ligand binding in a model cavity in T4 lysozyme. Even in this simple site, there are challenges. We made systematic improvements, beginning with single poses from docking, then including multiple poses, additional protein conformational changes, and using an improved charge model. Computed absolute binding free energies had an RMS error of 1.9 kcal/mol relative to previously determined experimental values. In blind prospective tests, the methods correctly discriminated between several true ligands and decoys in a set of putative binders identified by docking. In these prospective tests, the RMS error in predicted binding free energies relative to those subsequently determined experimentally was only 0.6 kcal/mol. X-ray crystal structures of the new ligands bound in the cavity corresponded closely to predictions from the free energy calculations, but sometimes differed from those predicted by docking. Finally, we examined the impact of holding the protein rigid, as in docking, with a view to learning how approximations made in docking affect accuracy and how they may be improved.
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(as it appears on PubMed at http://www.pubmed.gov), where 17599350 is the PubMed ID number.
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{{ABSTRACT_PUBMED_17599350}}
==About this Structure==
==About this Structure==
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[[Category: Model system]]
[[Category: Model system]]
[[Category: Protein-ligand complex]]
[[Category: Protein-ligand complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 11:39:03 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 19:40:43 2008''

Revision as of 16:40, 27 July 2008

Image:2oty.png

Template:STRUCTURE 2oty

1,2-dichlorobenzene in complex with T4 Lysozyme L99A

Template:ABSTRACT PUBMED 17599350

About this Structure

2OTY is a Single protein structure of sequence from Enterobacteria phage t4. Full crystallographic information is available from OCA.

Reference

Predicting absolute ligand binding free energies to a simple model site., Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA, J Mol Biol. 2007 Aug 24;371(4):1118-34. Epub 2007 Jun 8. PMID:17599350

Page seeded by OCA on Sun Jul 27 19:40:43 2008

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