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MHC molecule plays a key role in immunology, and the molecule binding reaction with peptide is an important prerequisite for T cell immunity induced. MHC II molecules do not have conserved residues, so they appear as open grooves. As a consequence, this will increase the difficulty in predicting MHC II molecules binding peptides. In this paper, we aim to propose a novel prediction method for MHC II molecules binding peptides. First, we calculate sequence similarity and structural similarity between different MHC II molecules. Then, we reorder pseudosequences according to descending similarity values and use a weight calculation formula to calculate new pocket profiles. Finally, we use three scoring functions to predict binding cores and evaluate the accuracy of prediction to judge performance of each scoring function. In the experiment, we set a parameter α in the weight formula. By changing α value, we can observe different performances of each scoring function. We compare our method with the best function to some popular prediction methods and ultimately find that our method outperforms them in identifying binding cores of HLA-DR molecules. [ABSTRACT FROM AUTHOR]

The aim of the present study was to investigate the antiosteoclastogenic effects of black rice (Oryza sativa L.) fermented with Lactobacillus casei (LAB) in RANKL-induced RAW macrophage cells and its antiosteoporosis activity against ovariectomy-induced osteoporosis in rats. LAB extract (LABE) treatment attenuated receptor activator of nuclear factor-kappa B (NF-κB) ligand-induced osteoclastic differentiation in RAW cells by inhibiting intercellular reactive oxygen species generation and downregulating the activation of mitogen-activated protein kinases and NF-κB, leading to the downregulation of c-Fos and expression of nuclear factor of activated T cells c1. This consequently suppressed the expression of osteoclast-specific genes including those for cathepsin K, tartrate-resistant acid phosphatase, calcitonin receptor, and integrin β3. Oral administration of LABE protected against ovariectomy-induced bone loss by significantly inhibiting bone architecture alterations and improving serum bone turnover markers in ovariectomized rats. The findings suggest that the antiosteoporotic activity of LABE may be derived from its antiosteoclastic and anti-bone-resorptive activities. LABE has potential as a promising functional material or substrate to prepare protective agents for osteoporosis and osteoclast-mediated bone diseases. [ABSTRACT FROM AUTHOR]