microsoft / microsoft/Graphormer
Lack of diversity in the 1ake example prediction by DiG
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 2.5k
- Forks
- 374
- PR merge metrics
- No merged PRs in 30d
Description
I tried to use the newly open-sourced DiG code to make 1ake example prediction for 100 samples, but all conformations are mainly around 1ake experimental structure, deviate away from 4ake structure. I think the result is contradictory with the result in your paper. The result is shown in the figure.
To be more specific, the command I used for prediction is
PDBID="1ake"
CKPT_PATH=./checkpoints/checkpoint-520k.pth
FEATURE_PATH=./dataset/${PDBID}.pkl
FASTA_PATH=./dataset/${PDBID}.fasta
OUTDIR=./output/${PDBID}/
mkdir -p ${OUTDIR}
python run_inference.py -c ${CKPT_PATH} -i ${FEATURE_PATH}\
-s ${FASTA_PATH} -o ${PDBID} --output-prefix ${OUTDIR}\
-n 100 --use-gpu --use-tqdm
Contributor guide
No contributing guide indexed for this repository
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with run_inference.py and reproduce the 100-sample 1ake prediction using checkpoint-520k.pth, the supplied feature and FASTA files, and the command in the report. Compare the generated conformations with the 1ake and 4ake structures and the paper's result; done means the discrepancy is explained and the appropriate correction or documentation is identified.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100