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This coefficient works with fingerprints (binary representation of molecules) and is defined as a ratio between the number of bits set on the same position in two fingerprints and the sum of bits set on different positions.
We define the fingerprint of each compound-protein pair as the tensor product of Φ(C) and Φ(P) as follows: Φ C, P = Φ C ⊗ Φ (P ) = (c 1 p 1, …, c 1 p D ′, …, c D p 1, …, c D p D ′ ) T. Φ(C, P) consists of all possible products of elements in two fingerprints Φ(C) and Φ(P), so the fingerprint is a D × D′ dimensional binary vector.
Similar(58)
The exact match operator required that the corresponding top three rows in two fingerprint matrices are exactly the same.
In order to compute fast and ensure the existence of cored substructures that are key for determining whether the two fingerprint are similar, the Exact match operator was firstly performed, which requires the layers in two fingerprint matrices to be exactly the same (top three layers were adopted in our method), thus the fingerprints that do not match top three layers can be rejected quickly.
In addition, two fingerprints were used for the experiments in order to study the effectiveness of consensus clustering on different representations of molecular dataset.
A Tanimoto similarity measure between two binary fingerprints is defined by the ratio of the number of common bits set to one to the total number of bits set to one in the two fingerprints [15].
In other words, that there is a large gain in similarity in having a bit (or equivalently a count of 1) in common between two fingerprints, but that increasing the count in common to 2 does not increase the similarity to the same extent.
In this study, two fingerprints were considered to be similar if the scoring function d total ≤ 3.5 [d total was range from 0 (identity) to ∞ (maximum diversity)].
The phase information is also used to confirm a match between two fingerprints in real time.
In a second step, the two fingerprints are concatenated into a complex-fingerprint which is flagged with 0 or 1 depending on whether the complex is reported in the MDDR database.
At least two fingerprints were matched in 393 (63.08%) cases.
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