Constrained structure generation

Constrained Structure Generation (CONGEN) Can generate all possible isomers if the substructure elements and the molecular formula are provided... 

Before moving on any further, we first consider the effectiveness of the mass spectral classifiers in reducing the number of candidates for selection. Of the 29 compounds, 15 were already reduced to the final, small (< 35) number of candidates using 95% probability classifiers alone. No additional classifiers were necessary (or possible) to reduce this number further, nor did calculated properties separate these candidates further. This means over half these compounds required only the default substructure information to constrain structure generation adequately. In a further 4 cases, the reduction in candidates to their final number (again below 35) was achieved by using an additional classifier or other restrictions, and no further elimination occurred with calculated properties. One further compound experienced only a slight additional re-... 

CASE = computer-assisted structure elucidation CHEM-ICS = combined handling of elucidation methods for interpretable chemical structures COCOA = constrained combination of atom-centered fragments CONGEN = constrained structure generator. 

It is obvious that any available spectral information can constrain the generation of an enormous number of structures, but its fuz2y character will greatly complicate the problem. Note that generators are created mostly for a simple enumeration of chemical structures. Therefore, they produce a crisp set of crisp structures. Each such structure is correlated to spectral information of a fuzzy nature. 

The number of calculated properties described in the previous sections require a logical approach for efficient and reproducible structure elucidation incorporating so many criteria. One approach is to use systematic filtering. This is best spUt into two basic parts structure generation (i.e. how to constrain the number of candidates using substructures and when to add additional constraints) and structure elimination (i.e. which is the best order to eliminate candidates using calculated properties). 

The surviving components, some of which are invalid, serve as the structural building units in the next step, structure generation. The process is constrained by user-entered macrocomponents (substructures) and some of the information... 

The average structure for the ADA-8H complex generated after energy minimization and equilibration with 20 ps of MD simulation showed considerable movement of atoms in the vicinity of the zinc ion when these residues were not constrained. Virtual bonds between zinc and the atoms that coordinate to the zinc ion were added to provide necessary atomic constraints prior to energy minimization and MD simulations. After constraints were applied, the average structure was similar to the X-ray... 

The Lys(Nic) and Dap(Nic) residues were incorporated into a simple hexa-peptide structure which contained a constrained type II -turn (Fig. 26). Dithionite reduction of both Lys(Nic) and Dap(Nic) peptides rapidly generated... 

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