DeepIEP: a Peptide Sequence Model of Isoelectric Point (IEP/pI) using Recurrent Neural Networks (RNNs)
This work provides a computational tool for predicting pI in biochemistry, but it is incremental as it applies an existing RNN method to a specific domain without introducing a new paradigm.
The paper tackled the problem of predicting the isoelectric point (pI) of peptides by training a recurrent neural network (RNN) with LSTM cells on a database of peptide sequences and pIs, achieving an RMSE of 0.28 and R² of 0.95 on an external test set.
The isoelectric point (IEP or pI) is the pH where the net charge on the molecular ensemble of peptides and proteins is zero. This physical-chemical property is dependent on protonable/deprotonable sidechains and their pKa values. Here an pI prediction model is trained from a database of peptide sequences and pIs using a recurrent neural network (RNN) with long short-term memory (LSTM) cells. The trained model obtains an RMSE and R$^2$ of 0.28 and 0.95 for the external test set. The model is not based on pKa values, but prediction of constructed test sequences show similar rankings as already known pKa values. The prediction depends mostly on the existence of known acidic and basic amino acids with fine-adjusted based on the neighboring sequence and position of the charged amino acids in the peptide chain.