Increasing the accuracy of protein loop structure prediction with evolutionary constraints.

摘要: MOTIVATION Accurate prediction of loop structures remains challenging. This is especially true for long loops where the large conformational space and limited coverage experimentally determined often leads to low accuracy. Co-evolutionary contact predictors, which provide information about proximity pairs residues, have been used improve whole-protein models generated through de novo techniques. Here we investigate whether these evolutionary constraints can enhance structures. RESULTS As a first stage, assess accuracy predicted contacts that involve regions. We find are less accurate than in general. also observe some incorrectly be identified as they never satisfied any our conformations. examined two different strategies incorporating contacts, on test set (10 residues or more), both approaches prediction. For 135 loops, were hence methods applicable 97 cases. Both result an increase proportion near-native decoys ensemble, leading more predictions cases improving root-mean-square deviation final model by 3 A. SUPPLEMENTARY INFORMATION Supplementary data available at Bioinformatics online.