Chemistry Reference
In-Depth Information
done 'on-the-fly' by the software and are not included in public and free-access
software. The calculations involved are complex/time consuming/ requiring large
storage space/efficient sharing of data.
There are also controversial points regarding restriction of database's dramatic
increase. How much study is required using diversified methods (distance-
dependent, random torsional angle changes, normal modes and Monte Carlo
minima, conformation generators) which may be only considered explicitly by
few databases?
Database size increase is sometimes addressed by using compressed files from
broadband capabilities yielding significant preparation speed-up with pre-
calculated multi-conformation databases.
The global hit rate for the development of new therapeutics still indicates major
failures in converting new ligands into drugs. This is often attributed to more
difficult to predict ADMET profiles (toxicity, metabolism, excretion, distribution,
absorption). It is important to discard virtual screened compounds with poor
physicochemical/ADMET properties, even before experiments are performed.
Sdf files are not cheap for storing large information, inclusion of annotations and
chemical information. The virtual screening on plain text formats can be parsed
sequentially. This yields inefficient/time expensive or reduced parallel
calculations potential. One solution is binary format files that can include more
information that is chemical, store and organize large numerical data.
Disadvantage of binary formats is that they are not readable with other software.
They also offers challenges involving management, merging and tools for
upgrading.
Of considerable importance are web servers of databases that may include
facilities for display, substructure, preliminary searches, compound retrieval and
physicochemical, pharmacokinetic properties. These are widely used to store and
retrieve molecular data. There are free access and commercial servers (database
management systems) that can optionally perform the following tasks. They can
compress archive files libraries, perform re-filtering, improve visualization, do
