Prediction of the Number of Residue Contacts in Proteins

Piero Fariselli and Rita Casadio, University of Bologna

Knowing the number of residue contacts in a protein is crucial for deriving constraints useful in modeling protein folding and/or scoring remote homology search. Here we focus on the prediction of residue contacts and show that this figure can be predicted with a neural network based method. The accuracy of the prediction is 12 percentage points higher than that of a simple statistical method. The neural network 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. When evolutionary information is taken into account, our method correctly predicts 69% of the residue states in the data base and it adds to the prediction of residue solvent accessibility. The predictor is available at htpp://www.biocomp.unibo.it


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