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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transition path sampling

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transition path sampling

Computational Method
Since 2010reaction coordinate inference by likelihood maximizationtransition path samplingComputational Design

Transition path sampling is a computational method applied to explicit-solvent molecular dynamics trajectories to extract atomistic features of conformational reaction networks. In the cited study, it was used to analyze the millisecond partial unfolding transition in the light-driven photocycle of photoactive yellow protein and to predict reaction coordinate models and tentative transition states.

CFBacMamMusHumTxRep
Ev 28Rep 9Pr 59
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