Improved prediction of the number of residue contacts in proteins by recurrent neural networks

Knowing the number of residue contacts in a protein is crucial for deriving constraints useful in modeling protein folding, protein structure, and/or scoring remote homology searches. Here we use an ensemble of bidirectional recurrent neural network architectures and evolutionary information to improve the state-of-the-art in contact prediction using a large corpus of curated data. The ensemble is used to discriminate between two different states of residue contacts, characterized by a contact number higher or lower than the average value of the residue distribution. The ensemble achieves performances ranging from 70.1% to 73.1% depending on the radius adopted to discriminate contacts (6Å to 12Å). These performances represent gains of 15% to 20% over the base line statistical predictors always assigning an aminoacid to the most numerous state, 3% to 7% better than any previous method. Combination of different radius predictors further improves the performance. © Oxford University Press 2001.