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14 results on '"Vinkers, H.M."'

4. Ab Initio potential grid based docking: From High Performance Computing to In Silico Screening

Author

de Jonge, M.R., Vinkers, H.M., van Lenthe, J.H., Daeyaert, F.F.D., Bush, I.J., van Dam, H.J.J., Sherwood, P., Guest, M.F., Quantumchemie, and Dep Scheikunde

Abstract

We present a new method for the generation of potential grids for protein-ligand docking. The potential of the docking target structure is obtained directly from the electron density derived through an ab initio computation. A large subregion was selected to allow the full ab initio treatment of a the Isocitrate Lyase enzyme. The electrostatic potential is tested by docking a small charged molecule (succinate) into the binding site. The ab initio grid yields a superior result by producing the best binding orientation and position, and by recognizing it as the best. In contrast the same docking procedure, but using a classical point-charge based potential, produces a number of additional incorrect binding poses, and does not recognize the correct pose as the best solution.

Published
2007

11. SYNOPSIS: SYNthesize and OPtimize System in Silico

Author

Vinkers, H.M., de Jonge, M.R., Daeyaert, F.F.D., Heeres, J., Koymans, L.M.H., van Lenthe, J.H., Lewi, P.J., Timmerman, H., van Aken, K., Janssen, P.A.J., Quantumchemie, Universiteit Utrecht, and Dep Scheikunde

Published
2003

13. Inhibition and substrate recognition – a computational approach applied to HIV protease

Author

Quantumchemie, Universiteit Utrecht, Dep Scheikunde, Vinkers, H.M., de Jonge, M.R., Daeyaert, F.F.D., Heeres, J., Koymans, L.M.H., van Lenthe, J.H., Lewi, P.J., Timmerman, H., Janssen, P.A.J., Quantumchemie, Universiteit Utrecht, Dep Scheikunde, Vinkers, H.M., de Jonge, M.R., Daeyaert, F.F.D., Heeres, J., Koymans, L.M.H., van Lenthe, J.H., Lewi, P.J., Timmerman, H., and Janssen, P.A.J.

Published
2003

14. SYNOPSIS: SYNthesize and OPtimize System in Silico

Author

Quantumchemie, Universiteit Utrecht, Dep Scheikunde, Vinkers, H.M., de Jonge, M.R., Daeyaert, F.F.D., Heeres, J., Koymans, L.M.H., van Lenthe, J.H., Lewi, P.J., Timmerman, H., van Aken, K., Janssen, P.A.J., Quantumchemie, Universiteit Utrecht, Dep Scheikunde, Vinkers, H.M., de Jonge, M.R., Daeyaert, F.F.D., Heeres, J., Koymans, L.M.H., van Lenthe, J.H., Lewi, P.J., Timmerman, H., van Aken, K., and Janssen, P.A.J.

Published
2003

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