Ke-Song Liu

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The Miyazawa-Jernigan (MJ) contact potential for globular proteins is a widely used knowledge-based potential. It is well known that MJ's contact energies mainly come from one-body terms. Directly in the framework of the MJ energy for a protein, we derive the one-body term based on a probabilistic model, and compare the term with several hydrophobicity(More)
Lattice-model simulations and experiments of some small proteins suggest that folding is essentially controlled by a few conserved contacts. Residues of these conserved contacts form the minimum set of native contacts needed to ensure foldability. Keeping such conserved specific contacts in mind, we examine contacts made by two secondary structure elements(More)
Overlap of words complicates the problem of word counting. The technique of the imbedded Markov chain (IMC) uses an enlarged state space to recover the Markovian property for the word counting problem. A degenerate word represents multiple non-degenerate words. An efficient way to decompose a degenerate word according to its overlapping pattern for(More)
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