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Protein destabilization is a common mechanism by which amino acid substitutions cause human diseases. Although several machine learning methods have been reported for predicting protein stability changes upon amino acid substitutions, the previous studies did not utilize relevant sequence features representing biological knowledge for classifier(More)
Many studies have shown that missense mutations might play an important role in carcinogenesis. However, the extent to which cancer mutations might affect biomolecular interactions remains unclear. Here, we map glioblastoma missense mutations on the human protein interactome, model the structures of affected protein complexes and decipher the effect of(More)
Understanding how genes are expressed specifically in particular tissues is a fundamental question in developmental biology. Many tissue-specific genes are involved in the pathogenesis of complex human diseases. However, experimental identification of tissue-specific genes is time consuming and difficult. The accurate predictions of tissue-specific gene(More)
A large set of three-dimensional structures of 264 protein-protein complexes with known nonsynonymous single nucleotide polymorphisms (nsSNPs) at the interface was built using homology-based methods. The nsSNPs were mapped on the proteins' structures and their effect on the binding energy was investigated with CHARMM force field and continuum electrostatic(More)
Applying in silico simulations and in vitro experiments, the amino acid proline was proved to have a profound influence on Streptomyces griseus trypsinogen, and the hydrogen bond between H(57) and D(102) was found to be crucial for trypsin activity. By introducing an artificial propeptide, IVEF, the titer of trypsin was increased 6.71-fold.
The Snyder-Robinson syndrome is caused by missense mutations in the spermine sythase gene that encodes a protein (SMS) of 529 amino acids. Here we investigate, in silico, the molecular effect of three missense mutations, c.267G>A (p.G56S), c.496T>G (p.V132G), and c.550T>C (p.I150T) in SMS that were clinically identified to cause the disease. Single-point(More)
Protein sumoylation is a post-translational modification that plays an important role in a wide range of cellular processes. Small ubiquitin-related modifier (SUMO) can be covalently and reversibly conjugated to the sumoylation sites of target proteins, many of which are implicated in various human genetic disorders. The accurate prediction of protein(More)
We report here the cloning and tissue distribution of the human B3GALT7 gene, a member of the β1,3-Glycosyltransferase family, structurally related to the β1,3-Galactosyltransferase family and β1,3-N-acetylglucosaminyltransferase family, isolated from a human lung cDNA library. B3GALT7 is mapped to chromosome 19q13.2 by browsing the UCSC genomic database.(More)
Bacterial leaf streak (BLS), caused by the pathogen Xanthomonas campestris pv. Oryzicola, is a major rice disease in tropical and subtropical regions of Asia. Rice proteins responsive to BLS are still not well characterized. We took a proteomics approach to identify the proteins that are up-regulated in rice leaves after infection. Approximately 1,500(More)
Protein sumoylation play essential roles in the eukaryotic cell and any alterations in this process may cause various human diseases. This paper describes a new machine learning approach for the sumoylation site prediction from protein sequence information. Random Forests (RFs), which can handle a large number of input variables and avoid model overfitting,(More)