Toolkit Items

Browse the toolkit beneath workflows. The mechanism branch runs mechanism -> architecture -> component, while the technique branch runs from high-level approaches down to concrete methods.

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Mechanism Branch

Layer 1

Mechanisms

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Top-level concepts: biophysical action modes such as heterodimerization, photocleavage, or RNA binding.

Layer 2

Architectures

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Arrangements that realize or deploy mechanisms, including switches, construct patterns, and delivery strategies.

Layer 3

Components

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Low-level parts and sequence-defined elements used inside architectures, including protein domains and RNA elements.

Technique Branch

Layer 1

Approaches

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High-level engineering practices such as computational design, directed evolution, sequence verification, and functional assay.

Layer 2

Methods

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Concrete methods used to design, build, verify, or characterize engineered systems.

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likelihood maximization

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likelihood maximization analysis

Computational Method
Since 2010likelihood maximizationreaction coordinate model selectiontransition state inferenceComputational Design

Likelihood maximization analysis is a computational method for selecting reaction coordinate models for individual substeps of a conformational transition and inferring tentative transition states. In the cited application, it was applied to transition path sampling data from explicit-solvent molecular dynamics of the millisecond partial unfolding transition in the photoactive yellow protein photocycle.

CFBacMamMusHumTxRep
Ev 28Rep 9Pr 71
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