Abstract—The energy function of the off-lattice AB model
has a number of deep valleys and hills which usually leads the
search algorithms to trap into a local minimum point. Existing
studies usually performs algorithmic improvements on the
well-known search methods to avoid from these local minimum
points. However, these algorithmic improvements further
increase the computational time which is not desired for the
protein folding problem. In this study, it is aimed to smooth the
energy landscape of this energy function and thus, to find a
near optimal or optimal configuration without performing
algorithmic improvements on the search methods. This is
achieved by adding an additional term to the original energy
function by which a hydrophobic core is formed and a near
optimal and optimal configuration is found easily. In the
experiments, a newly proposed optimization algorithm, the
Vortex Search (VS) algorithm, is used to minimize both the
original and modified energy functions. Experimental results
showed that, the modified energy function helps the VS
algorithm to find the desired configurations much more easier
than the original function when the maximum number of
iterations is kept equal for both cases.
Index Terms—Off-lattice AB model, protein folding, vortex
search algorithm.
The authors are with the Istanbul Technical University, Istanbul,
SARIYER 34469, Turkey (e-mail: bdogan@ itu.edu.tr, olmezt@itu.edu.tr).
Cite: Berat Doğan and Tamer Ölmez, "Modified Off-lattice AB Model for Protein Folding Problem Using the Vortex Search Algorithm," International Journal of Machine Learning and Computing vol. 5, no. 4, pp. 329-333, 2015.