ProtGPT2-Oxido

Model

This is a fine-tuned version of ProtGPT2 : a language model that speaks the protein language and can be used for de novo protein design and engineering.

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Dataset

Protein data set retrieved from Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB).
Only the OXIDOREDUCTASE enzymes were used.
You can find the JSON formatted data @ oxidos.json

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How to Use?

>>> from transformers import pipeline
>>> pipe = pipeline("text-generation", model="zypchn/ProtGPT2-Oxido")
>>> sequences = pipe("", max_length=100, do_sample=True, top_k=950, repetition_penalty=1.2, num_return_sequences=5, eos_token_id=0)
# input field has left blank for diversity

[
  {"generated_text": "SNANQAPQPQTPTRATDAKKGSYGHPADRVGMEDNKYQVGVFYYDGPNPSYAEWNRDTQFWVETAKTAEKGKFDSIFFADTLGIYDSFKGSFEANLRHGAQFPVNDPLVAISAIAGATTKLGLVATASTTYSEPFHIARRFASLDHLSNGRAGWNIVTSYLDSAARNFGRTEQMEHDERYAIAEEYIDVVYKLWEGSWEDNAVIKDKETGLFTDPAKVHQINHEGEHFRVAGPLNIPRSPQGHPVIFQAGTSERGRDFAARHAEAVFTAQLDLEAGREFYEDIKSRAAKLGRDPDDVKILPGISVFVGKTREEAERKFRELQSLIDEEGALTRFSSYTGTDLSTYDPDGPLPELAGIDPTTPIAKLEGLLGKSKMTVREIALKQGGVSLREYQPFVGATAGSALVGGTPEQIADFMQDWFIEGTVDGFNIMPPYLPDGLEDFVDHVVPELQRRGLFRTEYEGTTLREHLGLAKPLEHHHHHH"},
  {"generated_text": "MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMGPCLICRSTSLKCVFCVRDPNGYKKCSKCDAFFCSRECQTEHWQRHHKFECPAAVAQPQIPPLPKPQQKQLTAAELGMFMEVRNQFALLKTNLERLDYEIFILERNVKLANTVTPPTNRTYFQSTMRYAPNPLRPNMTDAMRQQYLDKNKSSAALEHDLKELIKFKCYLLNDEYVEKEREENPFIWEYFLNKEWRKRNVWGNK\n"},
  {"generated_text": "MGHHHHHHSSGLVPRGSHMTVEQAKKLRAEAEAQAQIQDKAKAIAQTHGKVEVMVDGKHRVVDLDATTRRQLTDGELQAIVVAAQEAAAKQLKAQRQALLEQHQDAELRKLALEGEIV\nAVITGAAQGIGRAIALRLAKDGFRVAVADIDLAAAEAVAAEIEAKGGKALVIEGDVSREEDVKRLVRKAIDQFGRLDYAVNNAGIQGPLAPTEELPLALWNKVIDVNLTGVFLCMKYEIAQMVKQGRGGAIVNTASVAGLSGQPGMVAYCASKHGVVGLTKTVAIEYAKHGIRINAVAPGFIDTPMVQKLPEEKRARIAAAIPMRRLGQPDEIAAVVAFLLSDDASFITGQCIAVDGGFTAGLLA"},
  {"generated_text": "MAASKAADSLAEGAAKLEHHHHHH"},
  {"generated_text": "GSKPQPGVQVEGAKCQVLQAVYDFTVQSASELSFKAGDVICVTGQYDPTLGWWLAEERRTGKSGLVPENYVELLSTGPAQHHHHHH"}
]