SENDBS computes average nucleotide substitutions within and between populations with standard errors of average nucleotide substitutions estimated with a bootstrap method by resampling sites. Also constructs a population tree with a neighbor-joining method.
expected5to3distance is a web server that computes the expected distance between the 5′ and 3′ ends of the Boltzmann ensemble of all secondary structures for a given RNA sequence
TMatch is a tool for comparing two rooted ordered labeled trees, which are represented in a preorder parenthesized form. The tool calculates the editing distance of the two trees and displays the edit operations (insertions, deletions and substitutions) needed to transform one tree to the other.
Jason T. L. Wang, Kaizhong Zhang, Karpjoo Jeong and Dennis Shasha,
“A System for Approximate Tree Matching,”
IEEE Transactions on Knowledge and Data Engineering, Vol. 6, No. 4, August 1994, pp. 559-571.
AlloPathFinder allows users to compute likely allosteric pathways in proteins. The underlying assumption is that residues participating in allosteric communication should be fairly conserved and that communication happens through residues that are close in space.The initial application for the code provided was to study the allosteric communication in myosin. Myosin is a well-studied molecular motor protein that walks along actin filaments to achieve cellular tasks such as movement of cargo proteins.It couples ATP hydrolysis to highly-coordinated conformational changes that result in a power-stroke motion, or ”walking” of myosin. Communication between a set of residues must link the three functional regions of myosin and transduce energy: the catalytic ATP binding region, the lever arm, and the actin-binding domain. We are investigating which residues are likely to participate in allosteric communication pathways.