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Their SPACESHIP program generates a structural continuum between two molecules by the iterative application of mutation and selection cycles.
The SMSD calculates the MCS between two molecules by combining the power of the VF+ Lib, the MCS+, and the CDK based MCS algorithm.
The kernels that are used in this work describe the similarity between two molecules by considering pairwise atomic similarities and combining these in different ways to compare the molecular structure.
Also, 14-3-3 protwons help two molecules to interact or to interrupt the association between two molecules by functioning as molecular scaffolds [ 46].
To represent a diffusion dependent event (such as a translocation to a different compartment, or collision between two molecules) by means of a temporal delay, we generated appropriate probability and cumulative distribution functions (PDF and CDF, respectively).
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[See the Methods section for the definition of six 3-D similarity score types used in PubChem3D.] These distributions allow one to perform a statistical significance test that considers the null hypothesis that a particular similarity score between two molecules occurs by chance.
The triple-glutamate mutant crystallizes with a buried hydrophobic patch between two molecules related by a 2-fold rotation.
The similarity between two molecules is defined by any similarity coefficient (e.g. Tanimoto) available in SA2 applied to the selected fingerprint.
The other metric space is the data space, where the distance between two molecules is defined by the proximity of the corresponding numerical descriptors (such as expression profiles).
The reaction probability between two molecules is therefore given by the probability of the collision and the probability that a reaction occurs given that a collision is occurring.
The first one is the space of biological functions, where the distance between two molecules can be defined by the number of steps (edges) in a graph defining pairwise functional relations (such as protein-protein interactions) along the shortest path connecting them.
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