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  On-the-fly integration of data from a spin-diffusion-based NMR experiment into protein–ligand docking.

Onila, I., ten Brink, T., Fredriksson, K., Codutti, L., Mazur, A., Griesinger, C., et al. (2015). On-the-fly integration of data from a spin-diffusion-based NMR experiment into protein–ligand docking. Journal of Chemical Information and Modeling, 55(9), 1962-1972. doi:10.1021/acs.jcim.5b00235.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0028-9F78-0 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-002A-6051-E
Genre: Journal Article

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 Creators:
Onila, I., Author
ten Brink, T., Author
Fredriksson, K., Author
Codutti, L., Author
Mazur, A.1, Author              
Griesinger, C.1, Author              
Carlomagno, T., Author
Exner, T. E., Author
Affiliations:
1Department of NMR-Based Structural Biology, MPI for biophysical chemistry, Max Planck Society, ou_578567              

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 Abstract: INPHARMA (interligand nuclear Overhauser enhancement for pharmacophore mapping) determines the relative orientation of two competitive ligands in the protein binding pocket. It is based on the observation of interligand transferred NOEs mediated by spin diffusion through protons of the protein and is, therefore, sensitive to the specific interactions of each of the two ligands with the protein. We show how this information can be directly included into a protein ligand docking program to guide the prediction of the complex structures. Agreement between the experimental and back-calculated spectra based on the full relaxation matrix approach is translated into a score contribution that is combined with the scoring function ChemPLP of our docking tool PLANTS. This combined score is then used to predict the poses of five weakly bound cAMP-dependent protein kinase (PKA) ligands. After optimizing the setup, which finally also included trNOE data and optimized protonation states, very good success rates were obtained for all combinations of three ligands. For one additional ligand, no conclusive results could be obtained due to the ambiguous electron density of the ligand in the X-ray structure, which does not disprove alternative ligand poses. The failures of the remaining ligand are caused by suboptimal locations of specific protein side chains. Therefore, side-chain flexibility should be included in an improved INPHARMA-PLANTS version. This will reduce the strong dependence on the used protein input structure leading to improved scores overall, not only for this last ligand.

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Language(s): eng - English
 Dates: 2015-07-302015-09
 Publication Status: Published in print
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 Rev. Method: Peer
 Identifiers: DOI: 10.1021/acs.jcim.5b00235
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Title: Journal of Chemical Information and Modeling
Source Genre: Journal
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Pages: - Volume / Issue: 55 (9) Sequence Number: - Start / End Page: 1962 - 1972 Identifier: -