How Are the Best Designs Verified

It is also likely that the user will need to examine a given set of structures several times, using information gleaned by previous analyses to direct the current evaluation, perhaps in terms of setting values for additional rejection criteria. The tools that will serve these purposes must be flexible and modular as well as rapid and interactive in operation. 

The tools described in the sections above show that practical and helpful software protocols for structure evaluation exist. As the molecular design community gains more experience not only with de novo design but also with 3D database searching and combinatorial library management, such analysis tools are expected to develop significantly beyond what is currently available. 

For practical studies of large molecular systems including biological molecules (e.g., proteins, DNA, and their ligated complexes), classical mechanics based methods of molecular simulation have been used widely. This area of molecular simulation has been reviewed extensively in recent years, -and here we concentrate on a few approaches (rf relevance to de novo design. In particular, three areas will be considered molecular dynamics, docking methods, and free energy simulation. 

Are the average energies or scores stable under molecular dynamics  

How do particular intermolecular distances behave over a dynamics 

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