Gene ontology (GO) is a standardized and controlled vocabulary of terms that describe the molecular functions, biological roles and cellular locations of proteins. GO terms and GO hierarchy are regularly updated as the accumulated biological knowledg...
BACKGROUND: In recent years, numerous computational methods predicted protein function based on the protein-protein interaction (PPI) network. These methods supposed that two proteins share the same function if they interact with each other. However,...
To improve the prediction accuracy of O-glycosylation sites, and analyze the structure of the O-glycosylation sites, factor analysis based prediction is proposed in this study. Our studies show that factor analysis strongly boosts machine learning al...
Journal of computer-aided molecular design
Sep 18, 2017
We present a novel optimization approach to train a free-shape distance-dependent protein-ligand scoring function called Convex-PL. We do not impose any functional form of the scoring function. Instead, we decompose it into a polynomial basis and ded...
We introduce a deep learning architecture for structure-based virtual screening that generates fixed-sized fingerprints of proteins and small molecules by applying learnable atom convolution and softmax operations to each molecule separately. These f...
Protein pupylation is a type of post-translation modification, which plays a crucial role in cellular function of bacterial organisms in prokaryotes. To have a better insight of the mechanisms underlying pupylation an initial, but important, step is ...
International journal for numerical methods in biomedical engineering
Aug 16, 2017
Protein-ligand binding is a fundamental biological process that is paramount to many other biological processes, such as signal transduction, metabolic pathways, enzyme construction, cell secretion, and gene expression. Accurate prediction of protein...
Glycosylation is one of the most complex post translation modification in eukaryotic cells. Almost 50% of the human proteome is glycosylated as glycosylation plays a vital role in various biological functions such as antigen's recognition, cell-cell ...
UNLABELLED: Hot spots are interfacial core areas of binding proteins, which have been applied as targets in drug design. Experimental methods are costly in both time and expense to locate hot spot areas. Recently, in-silicon computational methods hav...
Knowledge of subcellular locations of proteins is crucially important for in-depth understanding their functions in a cell. With the explosive growth of protein sequences generated in the postgenomic age, it is highly demanded to develop computationa...
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