NovoB

algorithm · Transformer (AR)

NovoB: algorithm · Transformer (AR). Bidirectional decoding

Bidirectional decoding

Kind	algorithm
Deep learning	yes
Acquisition	DDA
Family	Transformer (AR)

Code

• https://github.com/ProteomeTeam/NovoB

Live stars, open issues and last-push figures are on the Code activity chart.

Data

What the papers describing this method trained it on and reported its results on, as each paper states it. A version is named only where the paper names one.

Trained on

• BoxCar acquisition method enables single shot proteomics at a depth of 10,000 proteins in 100 minutes (as deposited)
• Nine-species benchmark (version not stated)

Evaluated on

• NFYB-1 regulates mitochondrial function and longevity via lysosomal prosaposin (as deposited)
• Nine-species benchmark (version not stated)
• Predictive signatures of 19 antibiotics-induced Escherichia coli proteomes (as deposited)
• The beta subunit of nascent polypeptide associated complex plays a role in flowers and siliques development of Arabidops (as deposited)

Deposited

• NovoB DataSets & Trained Models (as deposited)

Paper describing it

• Bidirectional de novo peptide sequencing using a transformer model (2024, PLOS Computational Biology, peer-reviewed)

Authors (2)

Sangjeong Lee, Hyunwoo Kim

Seen in the charts

• The architectures
• Code activity

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