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...
Detecting the protein complexes is an important task in analyzing the protein interaction networks. Although many algorithms predict protein complexes in different ways, surveys on the interaction networks indicate that about 50% of detected interact...
MHC class II molecules play a fundamental role in the cellular immune system: they load short peptide fragments derived from extracellular proteins and present them on the cell surface. It is currently thought that the peptide binds lying more or les...