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Exact(5)
Given this input, BowTieBuilder searches for the most probable pathway that connects the input and output proteins.
This information is then used to find the most probable pathway these genes come from by comparing the enriched protein-domain signature with all pathway domain signatures.
In the following section, we describe the formalism of the ADMD method used to obtain the most probable pathway connecting between a fully extended structure and the native structure.
That is, for two given states, we aim to obtain the most probable pathway smoothly connecting the two states, which approximately satisfies the Newtonian path conditions with a large-interval time step [ 15– 17].
In the ADMD formalism, we seek to find what one can do even when it is not known if the native state of the protein is the lowest-free-energy state of a given potential energy function by asking the question of obtaining the most probable pathway out of all possible paths connecting two-end states.
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Methods to discern these regulatory uncertainties (for example, through the identification of the most probable regulatory pathway from a set of different mechanistic pathway models), moreover have the potential to be used for reverse engineering of signaling and regulatory networks.
In order to obtain the most probable transition pathway, we searched for low-potential-energy-barrier pathways.
We quantify the most probable extinction pathway on the landscape and measure the extinction risk by the landscape topography.
We propose that the most probable reaction pathway is via CH3CH2O* on the basis of our mechanistic study: CH3CH2OH* → CH3CH2O* → CH2CH2O* → CH2CHO* → CH2CO* → CHCO* → CH* + CO* → C* + CO*.
In Fig. 2, the most probable metabolic pathway of the ionic liquid IL3 was proposed.
In this work, we refer to the trajectory with the lowest-potential-energy barrier as the most probable transition pathway model.
Related(20)
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