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A negative scoring value indicates that the leaf contains mainly equally populated contacts.
Additionally, removing equally populated contacts can improve scoring and significantly simplifies visual identification of key contacts on the heat maps.
Removing weakly populated contacts does not influence clustering or scoring, but simultaneously simplifies the analysis of the heat maps.
The absence of populated contacts made it possible to cluster 55.2% of the active compounds in one leaf for the filtered matrix of coulomb contact selection.
The technique is especially useful when the number of equally populated contacts is much higher than the number of specific contacts.
For HIV RT, HIV protease, CDK2, and COX1 datasets, the best leaf ligands' clustering is mainly provided by highly populated contacts.
Similar(53)
If I contact mean leaf is higher than 90% of the maximum population, the contact is described as a highly populated contact and the assigned weight is increased: (4) W c o n t a c t l e a f n e w = W c o n t a c t l e a f + I c o n t a c t m e a n l e a f.
Active compounds have a high affinity for the receptor and are expected to form the largest number of high-populated contacts corresponding to the decoys.
The clustering was efficient in cases where the difference between contact sets of active compounds and decoys was significant, while the presence of well-populated contacts for active compounds was additionally required for successful scoring.
The HSP dataset was the most difficult for scoring, as active compounds did not contain remarkably populated HB contacts.
In this case high-populated non selective contacts mask the difference in binding modes and decrease the efficiency of AuPosSOM.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com