Abstract
The protein conformational space is characterized as a multi-dimensional funnel-like energy surface with conformations corresponding to the native state around the energy basin [1]. The dimensionally and ruggedness of this energy surface are primary why computationally determining the biologically active or native state of a protein remains a difficult challenge. A common template among structure prediction protocols begins by sampling many local minima in the energy surface. Basin Hopping (BH) has emerged as a suitable framework for effectively sampling these coarsegrained local minima [2], [3]. BH consists of a series structural perturbations followed by minimizations, forming a trajectory of local minima with the Metropolis criterion biasing it towards increasingly low-energy minima.
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