Xingran Xue

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Stochastic context-free grammar (SCFG) has been successful in modeling biomolecular structures, typically RNA secondary structure, for statistical analysis and structure prediction. Context-free grammar rules specify parallel and nested co-occurren-ces of terminals, and thus are ideal for modeling nucleotide canonical base pairs that constitute the RNA(More)
Given the importance of non-coding RNAs to cellular regulatory functions and rapid growth of RNA transcripts, computational prediction of RNA tertiary structure remains highly demanded yet significantly challenging. Even for a short RNA sequence, the space of tertiary conformations is immense; existing methods to identify native-like conformations mostly(More)
UNLABELLED TRFolder-W is a web server capable of predicting core structures of telomerase RNA (TR) in yeast genomes. TRFolder is a command-line Python toolkit for TR-specific structure prediction. We developed a web-version built on the django web framework, leveraging the work done previously, to include enhancements to increase flexibility of usage. To(More)
MOTIVATION Given the importance of non-coding RNAs to cellular regulatory functions, it would be highly desirable to have accurate computational prediction of RNA 3D structure, a task which remains challenging. Even for a short RNA sequence, the space of tertiary conformations is immense; existing methods to identify native-like conformations mostly resort(More)
Protein fold classification is essential to recognition of protein tertiary structure. It is of particular interest to the structure analyses of proteins of low sequence identity with respect to proteins of known structures. We investigated the protein fold recognition problem with the Committee Support Vector Machine (CSVM) that proved efficient and(More)
Here we announce the launch of the Gly-Spec Webtool (www. glycam.org/gr) that automates a recently reported method for structure-based prediction of glycan specificity (Grant et al. 2016) (Figure 1). The Gly-Spec Webtool requires the user to upload a 3D structure of a protein co-complexed with a carbohydrate fragment; typically the minimal binding(More)
We prove that, for many parameterized problems in the class FPT, the existence of polynomial kernels implies the collapse of the Whierarchy (i.e., W[P] = FPT). The collapsing results are also extended to assumed exponential kernels for problems in the class FPT. In particular, we establish a close relationship between polynomial (and exponential)(More)
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