| Popis: |
We describe an approach for predicting protein folding pathways and tertiary structure from a primary sequence. The method integrates our existing Monte Carlo Simulated Annealing (MCSA) TerItFix algorithm and Upside, a new continuous staEsEcal potential enabling Molecular Dynamics (spMD) type simulations. By iteratively fixing the secondary structure, hydrogen bonds, and tertiary contacts, our model can predict the tertiary structure with high precision. The algorithm only samples Ramachandran maps by launching MCSA folding simulations as previous stages and spMD simulations are run with bias sampling strategies, such as employing ranges of backbone dihedral angles and incorporating contact maps generated from previous stages of TerItFix as constraints. The integrated approach is capable of accurately predicting secondary and tertiary structures for several small proteins, and the method also can be used for analysis of energy surfaces near transiEon states. |
