Conclusion
Although this project investigates the use of the Side Chain Model in lieu of the standard HP Model, only specific scenarios were tested and as such it does only specific scenarios were tested, meaning it does not definitively prove one is superior.one model better that the other. Due to the Side Chain Model’s extra flexibility, a given sequence was more oft to conform totypically conforms to a lower energy state that in the HP Model. However, certain sequences ended up having more H-H contacts in the Side Chain Model but a more dense hydrophobic core in the HP Model. The Side Chain Model, unlike the HP model, considers both the number of contacts and the density of the hydrophobic core in determining the optimality of a fold.In the HP model, the number of H-H contacts is the only factor considered in determining the optimality of a fold because it is assumed that more H-H contacts result in a hydrophobic core. However, the Side Chain Model requires this assumption to be reexamined. Instead of just looking at contacts, taking into account centricity of peripheral H-nodes is in certain cases necessary to find the optimal folding with the Side Chain Model. Another area this project adds to the wealth of knowledge is with the definition of uniqueness in simple models. This project offers a revised definition of uniqueness, taking into account not only the backbone and H-H contacts, but neutral backbones, hydrophobic side chains, hydrophilic side chains, and centricity as well. Overall, for the majority of test cases, the Side Chain Model proved itself superior, and in light of these findings it should be studied further for potential use over the standard HP Model.
Citations