Learn More
Inspired by previous preprocessing approaches to SMT, this paper proposes a novel, probabilistic approach to reordering which combines the merits of syntax and phrase-based SMT. Given a source sentence and its parse tree, our method generates, by tree operations, an n-best list of reordered inputs, which are then fed to standard phrase-based decoder to(More)
Kinesin-microtubule (MT) binding plays a critical role in facilitating and regulating the motor function of kinesins. To obtain a detailed structural and energetic picture of kinesin-MT binding, we performed large-scale computational alanine-scanning mutagenesis based on long-time molecular dynamics (MD) simulations of the kinesin-MT complex in both ADP and(More)
MOTIVATION We are motivated by the fast-growing number of protein structures in the Protein Data Bank with necessary information for prediction of protein-protein interaction sites to develop methods for identification of residues participating in protein-protein interactions. We would like to compare conditional random fields (CRFs)-based method with(More)
In this study, we have performed a comprehensive structural investigation of three major biochemical states of a kinesin complexed with microtubule under the constraint of high-quality cryo-electron-microscopy (EM) maps. In addition to the ADP and ATP state which were captured by X-ray crystallography, we have also modeled the nucleotide-free or APO state(More)
The crucial prerequisite for proper biological function is the protein's ability to establish highly selective interactions with macromolecular partners. A missense mutation that alters the protein binding affinity may cause significant perturbations or complete abolishment of the function, potentially leading to diseases. The availability of computational(More)
BACKGROUND The secreted protein acidic and rich in cysteine (SPARC) plays a pivotal role in regulating cell-matrix interactions and tumor angiogenesis, proliferation, and migration. Detection of SPARC gene methylation may be useful as a tumorigenesis marker for early detection of pancreatic cancer. METHODS Methylation of the SPARC gene transcriptional(More)
Partially supervised text classification has received great research attention since it only uses positive and unlabeled examples as training data. This problem can be solved by automatically labeling some negative (and more positive) examples from unlabeled examples before training a text classifier. But it is difficult to guarantee both high quality and(More)