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MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization
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Question about how can i generate vector representations of proteins #10

Open xfy9 opened 2 years ago

xfy9 commented 2 years ago

Hi, I have a csv file that stores protein sequences，how can i generate vector representations of proteins，I would be very grateful if you could help me with my doubts

lxie21 commented 2 years ago

Hi,

You need to write a program following the steps below:

  1. Generate a multiple sequence alignment for your sequence of interest.
  2. Compute the conservation score for each position.
  3. Extract ~200 most conserved positions.
  4. Generate triplets for extracted positions.

Detailed procedure is in the published DISAE paper.

Best, Lei

On Sat, Feb 26, 2022 at 1:57 AM xfy9 @.***> wrote:

Hi, I have a csv file that stores protein sequences，how can i generate vector representations of proteins，I would be very grateful if you could help me with my doubts

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