We consider the problem of protein folding in the HP model on the 3D square lattice. This problem is combinatorially equivalent to folding a string of 0's and 1's so that the string forms a self-avoiding walk on the lattice and the number of adjacent pairs of 1's is maximized. The previously best-known approximation algorithm for this problem has a guarantee of 3/8 = .375 [HI95]. In this paper, we first present a new 3/8-approximation algorithm for the 3D folding problem that improves on the absolute approximation guarantee of the previous algorithm. We then show a connection between the 3D folding problem and a basic combinatorial problem on binary strings, which may be of independent interest. Given a binary string in {a, b}*, we want to find a long subsequence of the string in which every sequence of consecutive a's is followed by at least as many consecutive b's. We show a non-trivial lower-bound on the existence of such subsequences. Using this result, we obtain an algorithm with a slightly improved approximation ratio of at least .37501 for the 3D folding problem. All of our algorithms run in linear time. © Springer-Verlag 2004.
CITATION STYLE
Newman, A., & Ruhl, M. (2004). Combinatorial problems on strings with applications to protein folding. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2976, 369–378. https://doi.org/10.1007/978-3-540-24698-5_41
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