Explicit Conformation Storage

At the simplest level, conformational flexibility has been represented through the explicit storage of multiple molecular conformations. - The problem with such an approach is that, if one wishes to keep the storage and search times down to a reasonable level, only a small number of con-formers may be stored per molecule. Thus, if this technique is to be successful, careful attention must be paid to which molecular conformations should be retained in the database. A general approach has been to apply conformational sampling methods 3.72-74 to search conformational space and then use a difference metric, for example, the root mean squared (RMS) difference in interatomic distances, to allow the clustering of conformations into families.  

Energy — Fbond f anglc f dihcd f VDW f coulomb f polc [ ] 

An alternative approach to the explicit storage of multiple conformations is the use of 3D distance screens. The ChemDBS-3D program provides a good example of such a technique and deals with the problem of conformational flexibility in the following manner  

Define ligands in terms of chemical centers as described in the earlier section on atom typing on compound registration. 

Determine the location of all these centers within the molecule. 

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