An algorithm for two-dimensional rigidity percolation: the pebble game
Journal of Computational Physics
Efficient algorithms to explore conformation spaces of flexible protein loops
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
BIBMW '12 Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
BIBMW '12 Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)
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We present a geometry-based, sampling based method to explore conformational pathways in medium and large proteins which undergo large-scale conformational transitions. In a past work we developed a coarse-grained geometry-based method that was able to trace large-scale conformational motions in proteins using residues between secondary structure elements as hinges, and a simple yet effective energy function. In this work we apply a rigidity-analysis tool to determine the rigid and flexible regions in protein structures, since hinges may not always lie on loops between secondary structure elements. This method allows for better accuracy in determining the rotational degrees of freedom of the proteins. We conducted a multi-resolution search scheme, as both C-α and backbone representations are used for sampling the protein conformational paths. Characteristic conformations detected by clustering the paths are converted to full atom protein structures and minimized to detect interesting intermediate conformations that may correspond to transition states or other events. Our algorithm was able to run efficiently on a proteins of various sizes and the results agree with experimentally determined intermediate protein structures.