ASMscan-LSTM

Bidirectional LSTM model for detection of amyloid signaling motifs (ASMs).

Installation

pip install asmscan-lstm

Usage

from asmscanlstm import ASMscanLSTM

aa_seqs = [
    "MEGRASGSARIYQAGGDQYIEE",
    "VSLRAGAHDGGRIYQAVGDQYIYE",
    "HASGHGRVFQSAGDQHITEH"
]

model = ASMscanLSTM()
pred, frags = model.predict(aa_seqs)

References

ASMscan-LSTM model is part of the ASMscan project:

• Not yet published.

ASMscan project is an extension of the ASMs analysis conducted with the PCFG-CM model:

• W. Dyrka, M. Gąsior-Głogowska, M. Szefczyk, N. Szulc, "Searching for universal model of amyloid signaling motifs using probabilistic context-free grammars", BMC Bioinformatics, 22, 222, 2021.

• W. Dyrka, M. Pyzik, F. Coste, H. Talibart, "Estimating probabilistic context-free grammars for proteins using contact map constraints", PeerJ, 7, e6559, 2019.