PARADE 3' UTR stability

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evo-design/proto-language/proto_language/constraint/rna_expression/parade_utr_stability_constraint.py

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@article{khoroshkin2024parade,
  title={A generative framework for enhanced cell-type specificity in rationally designed mRNAs},
  author={Khoroshkin, Matvei and Zinkevich, Arsenii and Aristova, Elizaveta and Yousefi, Hassan and Lee, Sean B. and Mittmann, Tabea and Manegold, Karoline and Penzar, Dmitry and Raleigh, David R. and Kulakovskiy, Ivan V. and Goodarzi, Hani},
  journal={bioRxiv},
  year={2024},
  publisher={Cold Spring Harbor Laboratory},
  doi={10.1101/2024.12.31.630783}
}

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Constraint contributors

Score 3’ UTR proposals by predicted mRNA stability.

API Reference

ConfigParadeUTRStabilityConfig Source

Configuration for the PARADE 3’ UTR mRNA-stability constraint.

enum

default:"max"

Whether to maximize (‘max’) or minimize (‘min’) predicted mRNA stability.Options: max, min

number

default:"0.0"

Raw PARADE log-ratio mapped to energy 0.5.

number

default:"1.0"

Positive float32-safe width of the sigmoid transform; larger is gentler.

string

default:"cuda"

Device used for PARADE inference.

integer

default:"1"

Number of sequences scored per PARADE GPU batch.

ReturnsConstraintOutput

One result per proposal. score is in [0.0, 1.0] (lower is better in the requested direction); metadata carries the raw log_ratio.

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import parade_utr_stability_constraint, ParadeUTRStabilityConfig

constraint = Constraint(
    inputs=[segment],
    function=parade_utr_stability_constraint,
    function_config=ParadeUTRStabilityConfig(
        # Configure parameters here
    ),
)

scores = constraint.evaluate()

Metadata

Property	Value
Key	`parade-utr-stability`
Function	`parade_utr_stability_constraint`
Category	`rna_expression`
Mode	`discrete`
Uses GPU	`True`
Supported Types	`dna`, `rna`

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PARADE 3' UTR stability

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