UNRES web server: Extensions to nucleic acids, prediction of peptide aggregation, and new types of restrained...

The third version of the UNRES web server is described, in which the range of biological macromolecules treated and calculation types has been extended significantly. DNA and RNA molecules have been added to enable the user to run simulations of their folding/hybridization and dynamics. To increase the accuracy of the simulated proteins models, the restraints on secondary structure have been enhanced to include the probabilities of the coil, extended and helical state, which are taken from the PSIPRED or HHpred raw input and the restraints from multiple bioinformatics models have been added. The NMR-data-assisted functionality has been extended to include time-averaged restraints, this feature enabling the user to model multistate and intrinsically-disordered proteins and those with intrinsically-disordered regions. Finally, the prediction of the propensity of peptides to aggregation has been included to enable the user to predict peptide solubility and aggregation, including the character and the structures of the aggregates.