Abstract
Many proteins undergo conformational changes to perform their functions. A simple mechanism of conformational change in proteins is a rigid domain motion, in which two parts of a structure move rigidly with respect to each other. The identification of rigid domains is therefore useful in understanding the structure-function relationship of proteins. Many algorithms, including those in [16], [22], [13], [10], and [19], have been developed to identify rigid domains. In this paper we complement these works by proposing a mathematical definition of a rigid domain. We argue that our definition more accurately captures the intuitive notion of rigid domain in the previous work, than the quantitative definition of a rigid domain introduced by Nichols et al. [19]. Furthermore, our definition admits a practical approximation algorithm. We can prove theoretical guarantee on the quality of the output of our algorithm. We implement a randomized version of our algorithm, and demonstrate its effectiveness on several known protein complexes.
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Choi, V., Goyal, N. An Algorithmic Approach to the Identification of Rigid Domains in Proteins. Algorithmica 48, 343–362 (2007). https://doi.org/10.1007/s00453-007-0186-0
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DOI: https://doi.org/10.1007/s00453-007-0186-0