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The proneously minimize or ofuench many identical

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Unformatted text preview: ally favoron energy minimizatiodquenched i nolecular dyable positions of functional groups m the binding i n the force field of a single protein or of a protein with multiple copies q important residues. The proneously minimize or ofuench many identical groups iposed method provides ingle protein or of a to more n the force field of a s a useful supplement protein standard visual (graphical) approaches3 The grid with multiple copies of important residues. and prosearch t echniques.*~~ posed method provides a useful supplement to more standard visual (graphical) approaches3 and grid METHOD search t echniques.*~~ Implementation of t he multiple copy simultaM (MCSS) neous search method ETHOD requires a choice of functional groups and ahe olecular mechanics model Implementation of t m multiple copy simultaf eous search method MCSS) r enough t be easily nor them. Groups must (be simpleequires aochoice of characterized and nd a molecular mechanics model functional groups amanipulated (3-6 atoms, few or no them. G degrees of be simple enough to b eeasily for dihedralroups must freedom),yet complexe nough t haracterized a t he anipulated (3-6 atoms, few or co approximatend msteric and electrostatic interact o dihedral degrees of freedom),yet complex n bindnions t hat t he functional group would have ienough ng to t he site t interest. An electrostatic interactio approximateof he steric and appropriate set is one n w t hat t he organic molecules ould h described a s tiionshich most functional group wcan be ave i n bindia collectionite such group^.^ n his includes fset is one ng to t he s of of interest. AT appropriate ragments uch a s cetonitrile, methanol, acetate, escribed a s isn whichamost organic molecules can be dmethyl ammonium, dimethyl roup^.^ This includes acetaldea collection of such gether, methane, andfragments h ~ s . thers have methanol, acetate, methyl amsuchdae Ocetonitrile, used functionality descriptions a~ with fewer atoms: r a spherical approximation to a monium, dimethyl oether, methane, and acetaldemulti-atom h ~ d e Others have Asedpplication of such a n atom.~ un a functionality descriptions b ith f grid atoms: or a pherical approximation to a wasedewer search t o t hesdocking of molecules by simu ulti-atom h n been described e e n t l mlated annealing Aasapplication of such ra n~atom-y . ~ Whereas...
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