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Evolutionary Scale Modeling (esm): Pretrained language models for proteins
MIT License
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Out of memory - upper limit on sequence length?
#457
jennastanislaw
opened
1 year ago
4
openfold installation
#456
saeid976
opened
1 year ago
11
Update data.py
#455
Chenjw99
closed
1 year ago
2
ESM-2 Model checkpoints during training run
#453
tomsercu
closed
1 year ago
0
Only CPU Malfunction -- HF Colab Notebook
#451
coopersvajda
opened
1 year ago
1
Protein design papers added
#448
tomsercu
closed
1 year ago
0
download model from huggingface
#447
saeid976
closed
1 year ago
3
Adjust header in output file
#445
dawsonhunt
closed
1 year ago
6
EMSIF1-Encoder output as structure representation
#443
LDAIprotein
opened
1 year ago
0
can't download the contact-regression.pt for those ESM models
#442
imSeaton
opened
1 year ago
1
Fix sampling error with partial_seq
#438
chloechsu
closed
1 year ago
0
Keys 'trunk.structure_module.ipa.linear_q_points.linear.weight, trunk.structure_module.ipa.linear_q_points.linear.bias, trunk.structure_module.ipa.linear_kv_points.linear.weight, trunk.structure_module.ipa.linear_kv_points.linear.bias' are missing.
#435
nibtehaz
closed
1 year ago
12
atom name all left justified
#431
kad-ecoli
opened
1 year ago
2
Question about confidence determination
#426
alpha-omega-labs
closed
1 year ago
3
Question about mean-pooled protein embeddings
#423
y-hwang
closed
1 year ago
0
RuntimeError: view size is not compatible with input tensor's on MPS backend
#421
shaharec
closed
1 year ago
1
Why is `lm_head` in ESM-2 (35M) (480, 480)?
#418
jasperhyp
closed
1 year ago
1
name of protein != entirety of header
#410
flowers9
opened
1 year ago
1
fix typo in README.md
#408
eltociear
closed
1 year ago
1
CUDA out of memory error for long sequences
#407
gbrown40
closed
1 year ago
5
High quality ESM atlas contains some pdb files without ATOM records.
#405
khb7840
opened
1 year ago
1
Some pdbfile ATOM sections are missing Spaces
#404
OrangeCatzhang
opened
1 year ago
1
Some pdbfile ATOM sections are missing Spaces
#402
OrangeCatzhang
closed
1 year ago
0
Strict length requirement for mutant sequence scoring via score_log_likelihood
#401
adalisan
opened
1 year ago
0
Issue with ESM_advanced Colab
#399
jfbazan
opened
1 year ago
0
document esmfold version
#398
tomsercu
closed
1 year ago
0
Separation of model config and weights
#395
kklemon
closed
1 year ago
2
Can esm model predict multi sequence protein like alphafold-multimer?
#392
hokiwood-geek
closed
1 year ago
2
Further CUDA support for IF-1
#386
naailkhan28
closed
1 year ago
5
Is the current ESM Metagenomic Atlas called version 0 or version 1?
#384
tomgoddard
closed
1 year ago
2
Documenting stats.parquet and atlas.fasta, see #366 and #376
#383
tomsercu
closed
1 year ago
0
update IF1 readme colab link to multichain
#379
tomsercu
closed
1 year ago
1
Issues with fixed position
#377
yzhang-github-pub
closed
1 year ago
2
stats.parquet file for ESM Metagenomic Atlas has duplicate entries
#376
tomgoddard
closed
1 year ago
5
ESMAtlas api access: Rate limit?
#375
fteufel
closed
1 year ago
11
Configuring device in Inverse Folding model
#374
adrienchaton
closed
1 year ago
4
ESM Metagenomic Atlas website not working
#373
KexinNiu
closed
1 year ago
2
download pretrained models in a local disk storage?
#372
ryao-mdanderson
opened
1 year ago
11
re-PR for pretrained ESM weights issue.
#371
YaoYinYing
closed
1 year ago
5
Provide predicted aligned error (PAE) from the ESM Metagenomic Atlas prediction API
#370
tomgoddard
closed
1 year ago
3
Provide predicted aligned error (PAE) json file download on atlas web pages
#369
tomgoddard
closed
1 year ago
3
document the fasta paths from #341 and `pip install` fix
#367
tomsercu
closed
1 year ago
0
Provide MGnify sequences available in ESM Metagenomic Atlas
#366
tomgoddard
closed
1 year ago
8
no matches found: fair-esm[esmfold]
#365
tdiethe
closed
1 year ago
3
Error when setting chunk size for ESMFold
#364
martinez-zacharya
closed
1 year ago
5
Confidence level for structures predicted via API
#363
alpha-omega-labs
closed
1 year ago
1
Fix typo in README.md
#362
amorehead
closed
1 year ago
0
Fix sequence lengths in README & notebooks
#361
nikitos9000
closed
1 year ago
1
CPU-only mode fix
#360
nikitos9000
closed
1 year ago
0
Mapping between MGYP ID and Uniprot ID
#357
blackjack6666
closed
1 year ago
2
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