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MOTIVATION Disulfide bonds are primary covalent crosslinks between two cysteine residues in proteins that play critical roles in stabilizing the protein structures and are commonly found in extracy-toplasmatic or secreted proteins. In protein folding prediction, the localization of disulfide bonds can greatly reduce the search in conformational space.(More)
This paper describes our submission to the CoNLL 2014 shared task on grammatical error correction using a hybrid approach, which includes both a rule-based and an SMT system augmented by a large web-based language model. Furthermore, we demonstrate that correction type estimation can be used to remove unnecessary corrections, improving precision without(More)
BACKGROUND Protein tertiary structure can be partly characterized via each amino acid's contact number measuring how residues are spatially arranged. The contact number of a residue in a folded protein is a measure of its exposure to the local environment, and is defined as the number of Cbeta atoms in other residues within a sphere around the Cbeta atom of(More)
This paper describes our use of phrase-based statistical machine translation (PB-SMT) for the automatic correction of errors in learner text in our submission to the CoNLL 2013 Shared Task on Grammatical Error Correction. Since the limited training data provided for the task was insufficient for training an effective SMT system, we also explored alternative(More)
A new method has been developed for prediction of transmembrane helices using support vector machines. Different coding schemes of protein sequences were explored, and their performances were assessed by crossvalidation tests. The best performance method can predict the transmembrane helices with sensitivity of 93.4% and precision of 92.0%. For each(More)
MOTIVATION A major issue in cell biology today is how distinct intracellular regions of the cell, like the Golgi Apparatus, maintain their unique composition of proteins and lipids. The cell differentially separates Golgi resident proteins from proteins that move through the organelle to other subcellular destinations. We set out to determine if we could(More)
BACKGROUND RNA-protein interactions are important for a wide range of biological processes. Current computational methods to predict interacting residues in RNA-protein interfaces predominately rely on sequence data. It is, however, known that interface residue propensity is closely correlated with structural properties. In this paper we systematically(More)
Video retargeting (resolution adaptation) is a challenging problem for its highly subjective nature. In this paper, a nonlinear saliency fusing approach, that considers human perceptual characteristics for automatic video retargeting, is being proposed. First, we incorporate features from phase spectrum of quaternion Fourier Transform (PQFT) in spatial(More)
A Support Vector Machine learning system has been trained to predict protein solvent accessibility from the primary structure. Different kernel functions and sliding window sizes have been explored to find how they affect the prediction performance. Using a cut-off threshold of 15% that splits the dataset evenly (an equal number of exposed and buried(More)