Parameter switching in a generalized Duffing system: Finding the stable attractors

This paper presents a simple periodic parameter-switching method which can find any stable limit cycle that can be numerically approximated in a generalized Duffing system. In this method, the initial value problem of the system is numerically integrated and the control parameter is switched periodically within a chosen set of parameter values. The resulted attractor matches with the attractor obtained by using the average of the switched values. The accurate match is verified by phase plots and Hausdorff distance measure in extensive simulations

SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures

Similarities in the 3D patterns of amino acid side chains can provide insights into their function despite the absence of any detectable sequence or fold similarities. Search for protein sites (SPRITE) and amino acid pattern search for substructures and motifs (ASSAM) are graph theoretical programs that can search for 3D amino side chain matches in protein structures, by representing the amino acid side chains as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. Both programs require the input file to be in the PDB format. The objective of using SPRITE is to identify matches of side chains in a query structure to patterns with characterized function. In contrast, a 3D pattern of interest can be searched for existing occurrences in available PDB structures using ASSAM. Both programs are freely accessible without any login requirement. SPRITE is available at http://mfrlab.org/grafss/sprite/while ASSAM can be accessed at http://mfrlab.org/grafss/assam/