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.

2 items matching 1 filter

Mechanism Branch

Layer 1

Mechanisms

▾

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

Layer 2

Architectures

▾

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

Layer 3

Components

▾

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

Technique Branch

Layer 1

Approaches

▾

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

Layer 2

Methods

▾

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

Sort
structure-based fragment seeding

Showing 1-2 of 2

Loaditems
Page 1 / 1

FRASE-bot

Computational Method
Since 2024machine-learning-based fragment prioritizationstructural-environment similarity matchingstructure-based fragment seedingComputational DesignFunctional AssaySelection / EnrichmentStructural Characterization

FRASE-bot is an in silico fragment-based hit-finding method for drug discovery against unconventional therapeutic targets. It mines thousands of 3D protein-ligand complex structures to build a fragment-in-structural-environment database, matches target protein environments to that database, and uses machine learning to prioritize seeded fragments as candidate binders.

CFBacMamMusHumTxRep
Ev 37Rep 20Pr 83

FRASE

Computational Method
Since 2024neural-network-based binder prioritizationstructural-environment similarity matchingstructure-based fragment seedingComputational DesignFunctional AssaySelection / EnrichmentStructural Characterization

FRASE, also described as FRASE-bot, is a computational fragment-based ligand discovery method that mines 3D ligand–protein complex structures to build a database of fragments in structural environments. It screens this database against a target protein, seeds the target structure with relevant ligand fragments, and uses a neural network to prioritize fragments with the highest likelihood of being native binders.

CFBacMamMusHumTxRep
Ev 28Rep 9Pr 71
Page 1 / 1