PsiFold is a pytorch library for protein structure prediction which implements the RGN method as well a novel variant based on the transformer architecture.
pip install git+https://git@github.com/kleinhenz/psifold.git
The following script downloads the ProteinNet casp7 dataset, trains a RGN model for 5 epochs, and evaluates the trained model.
In addition to computing the dRMSD loss, the evaluation step computes the TMscore for each predicted structure (the TMscore program must be in the PATH or else provided via the tmscore_path argument).
# download tensorflow records
curl -LO "https://sharehost.hms.harvard.edu/sysbio/alquraishi/proteinnet/tfrecords/casp7.tar.gz"
tar -xvzf casp7.tar.gz
# convert tensorflow records to hdf5 file
# note this is the only part of psifold which requires tensorflow
proteinnet2hdf --output="casp7.h5" casp7
# tensorflow records are no longer needed
rm -r casp7 casp7.tar.gz
# train rgn model
run_rgn \
--train \
--input.file=casp7.h5 \
--train.section=/training/90 \
--batch_size=32 \
--epochs=5 \
--learning_rate=1e-3
# evaluate the model
# choose --test.section="/testing" to evaluate the test set
run_rgn \
--test \
--compute_tm \
--input.file=casp7.h5 \
--load_checkpoint=checkpoints/{uuid}/latest.pt \
--test.section=/validation
Given the recent advances in NLP from the introduction of transformers, it is interesting to see if they may be beneficial in other problem domains. PsiFold implements a variant of the RGN method which replaces the LSTM with a transformer encoder stack similar to BERT. Additionally this variant replaces the global dRMSD loss with a local cosine similarity loss on the alpha carbon SRF coordinates. The reason for the local loss function is to try to ameliorate the vanishing/exploding gradient problems that come from backpropagation through the sequential NERF reconstruction algorithm that is necessary for computing global loss functions such as dRMSD. Additionally, the experience of NLP shows that transformers can show very good performance on problems with long range correlations even when the loss is completely local.
After the input data has been downloaded, a psifold model can be trained similarly to an RGN model using the run_psifold command as shown below
run_psifold \
--train \
--input.file=casp7.h5 \
--train.section=/training/90 \
--enable_amp \
--epochs=10 \
--accumulate_steps=8 \
--batch_size=16 \
--learning_rate=1e-3 \
--max_len=512 \
transformer \
--n_layers=12 \
--hidden_size=768
Unfortunately, these models appear to still be difficult to train and I have not yet obtained a good set of weights. I had hoped that the use of the local loss function would fix the training difficulties of the RGN models but this seems to not be the case.