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Peter Kolb, Marco Cecchini, Danzhi Huang, pkolb, cecchini, majeux, dhuang, Department of Biochemistry, University of Zurich, Switzerland Fragment-Based Docking
Our approach consists of four modules (I-IV), which perform
IV. FFLD [4] uses a Genetic Algorithm to dock the whole – fully
different steps of the docking procedure.
flexible – molecules by trying to place the fragments identified by DAIM at the positions determined by SEED–SFI. The scoringfunction contains terms for van-der-Waals interaction, hydrogen I. DAIM preprocesses the molecules and decomposes them into
bonds and unfavorable polar contacts.
chemical fragments. It also allows to filter the molecules for theoccurence of certain fragments to reduce the library size.
FFLD generates a conformation and tries to put it on the corresponding Validation on HIV-1 Protease
molecule with the fragments identified by DAIM. A set of 4 different HIV-1 protease–ligand complexes was usedto test the docking approach. The number of ligand rotatablebonds (corresponding to the number of degrees of freedom, sincethe protein is kept rigid) ranged from 10 to 22. All ligands could II. SEED [1, 2] places the rigid fragments in the binding site us-
ing an accurate energy function including electrostatic solvation based on the generalized Born approach [3]. The electrostaticcomponent of the binding energy is approximated by the sum ofthe following terms: Screened receptor-fragment interaction: intermolecularelectrostatic energy between the fragment and the receptorin the solvent.
Partial desolvation of the receptor (fragment): electro- Structure of an HIV-1 protease inhibitor with 21 rotatable bonds docked static energy difference caused by the displacement of by FFLD (thick, yellow). The X-ray structure (thin, green) is shown as high dielectric solvent by the volume of the fragment (re- a basis of comparison. RMSD (heavy atoms) 1.05 ˚ Application on -Secretase (Alzheimer)
We have recently screened a library of 10’000 compounds (with2-11 rotatable bonds) for References
III. SFI clusters the geometrical centers found by SEED to re-
MAJEUX, N., SCARSI, M., APOSTOLAKIS, J., EHRHARDT, C., AND CAFLISCH, A. Exhaustive docking of molec-ular fragments with electrostatic solvation. Proteins 37 (1999), 88–105 MAJEUX, N., SCARSI, M., AND CAFLISCH, A. Efficient electrostatic solvation model for protein-fragment dock-ing. Proteins 42 (2001), 256–268 SCARSI, M., APOSTOLAKIS, A., AND CAFLISCH A. Continuum Electrostatic Energies of Macromolecules inAqueous Solutions. J. Phys. Chem. A 101 (1997), 8098–8106 BUDIN, N., MAJEUX, N., AND CAFLISCH, A. Fragment-based flexible ligand docking by evolutionary optimiza-tion. Biol. Chem. 382 (2001), 1365–1372


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