Abstract
Understanding how protein folds into a functional and structural configuration is arguably one of themost important and challenging problems in computational biology. Currently, the protein foldingmechanism is often characterized by calculating the free energy landscape versus the reaction coordi-nates such as the fraction of native contacts, the radius of gyration, the principal components and soon. In this paper, we present a combinatorial algorithmic approach towards understanding the globalstate changes of the configurations. The approach is based on cluster computation, each cluster beingdefined by a pattern of a combination of various reaction coordinates. We present an algorithm oftime complexity
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