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Fragment replacement for Medicinal Chemistry | ||||
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Fragment replacement for Medicinal Chemistry | ||||
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As mentioned in the theory section, Brood comes with two pregenerated, multiconformer fragment databases. Both of these databases are made of both simple and complex fragments that contain between 1 and 3 simple ring, functional-group and linker combinations. The databases are further limited to 15 heavy-atoms and 1-3 attachment sites.
The first of these contains the 29309 most common fragments identified from among 12 million vendor molecules (after filtering). This database takes only a few minutes to search using modern desktop computers. It is suitable for many preliminary inquiries, but 30,000 fragments excludes many medicinally interesting fragments.
The second database is a superset of the first database. The second database contains the most common 139061 fragment identified from among the 12 million available molecules (after filtering). This database can be searched in about fifteen minutes. This database should be sufficient for most purposes. With very large queries (around 15 heavy atoms) it is sometimes difficult to find interesting replacement fragments in this database. In these instances we suggest breaking the query into two or more sub-queries that can be searched separately.
Both of these fragment databases have been created by taking apart carefully
filtered, commercially available molecules. The conformers have been generated
with Omega2, using methyl groups to represent the attachment points. Each
fragment has MMFF partial charges attached for use with the -ET flag.
Brood can also search user-genergated fragment files. Details on how to create a custom database are included in a later chapter (vide infra).
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Fragment replacement for Medicinal Chemistry | ||||
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