|
--- |
|
license: cc-by-4.0 |
|
--- |
|
|
|
Mirror of OpenFold parameters as provided in https://github.com/aqlaboratory/openfold. Stopgap solution as the original download link was down. Updated based on the s3 bucket parameter update. All rights to the authors. |
|
|
|
OpenFold model parameters, v. 06_22. |
|
|
|
# Training details: |
|
|
|
Trained using OpenFold on 44 A100s using the training schedule from Table 4 in |
|
the AlphaFold supplement. AlphaFold was used as the pre-distillation model. |
|
Training data is hosted publicly in the "OpenFold Training Data" RODA repository. |
|
|
|
To improve model diversity, we forked training after the initial training phase |
|
and finetuned an additonal branch without templates. |
|
|
|
# Parameter files: |
|
|
|
Parameter files fall into the following categories: |
|
|
|
initial_training.pt: |
|
OpenFold at the end of the initial training phase. |
|
finetuning_x.pt: |
|
Checkpoints in chronological order corresponding to peaks in the |
|
validation LDDT-Ca during the finetuning phase. Roughly evenly spaced |
|
across the 45 finetuning epochs. |
|
|
|
NOTE: finetuning_1.pt, which was included in a previous release, has |
|
been deprecated. |
|
finetuning_no_templ_x.pt |
|
Checkpoints in chronological order corresponding to peaks during an |
|
additional finetuning phase also starting from the 'initial_training.pt' |
|
checkpoint but with templates disabled. |
|
finetuning_no_templ_ptm_x.pt |
|
Checkpoints in chronological order corresponding to peaks during the |
|
pTM training phase of the `no_templ` branch. Models in this category |
|
include the pTM module and comprise the most recent of the checkpoints |
|
in said branch. |
|
finetuning_ptm_x.pt: |
|
Checkpoints in chronological order corresponding to peaks in the pTM |
|
training phase of the mainline branch. Models in this category include |
|
the pTM module and comprise the most recent of the checkpoints in said |
|
branch. |
|
|
|
Average validation LDDT-Ca scores for each of the checkpoints are listed below. |
|
The validation set contains approximately 180 chains drawn from CAMEO over a |
|
three-month period at the end of 2021. |
|
|
|
initial_training: 0.9088 |
|
finetuning_2: 0.9061 |
|
finetuning_3: 0.9075 |
|
finetuning_4: 0.9059 |
|
finetuning_5: 0.9054 |
|
finetuning_no_templ_1: 0.9014 |
|
finetuning_no_templ_2: 0.9032 |
|
finetuning_no_templ_ptm_1: 0.9025 |
|
finetuning_ptm_1: 0.9075 |
|
finetuning_ptm_2: 0.9097 |
|
|