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Tue, 20 August 2024 12:19

sansun
Messages: 50
Registered: April 2019

Member

Hi Thomas,

I have created a similarity chart using Similarity Analysis/Activity Cliff. With no activity data, I have created only the similarity chart (attached). I have two questions regarding the interpretation.

/forum/index.php?t=getfile&id=878&private=0

/forum/index.php?t=getfile&id=878&private=0

1) After reading the original paper I understand that molecules with >80% similarity (w.r.t. to the chosen descriptor) show connection lines. Is this a correct interpretation? I have manually checked some of the connected compounds and have not seen any that display similarity lower than 80% to each other.

2) Can it be said that molecules not connected to any other and occupy space towards the edge (e.g. red square) are unique since they do not have close neighbours? This is based on the following sentence in the original paper.

"Therefore, an individual compound, when being dragged toward the mean location of its neighbors, is often dragged toward the center"

However, the next sentence also says that a remedy is included in the algorithm to avoid crowding at the center. Therefore, I am little confused about the second interpretation.

Sorry, for the long message.
Thank you