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Protein is the major component of the organism. It has a unique three-dimensional structure determined by its amino acid sequence. A concave (pocket) on the surface of a protein is known to be the best target for a drug to react. We started analyzing how" drug ability" of proteins related to the location of amino acids in a pocket. For as tarter of the study, this paper presents a visualization...
A phosphorylatable short peptide(pSP) with the amino acid composition of ??LLLRRRDNEYFYVRRLL?? containing two potentially phosphorylatable tyrosine residues was chemically synthesized. This short peptide was characteristic with the isoelectric point of 10.88 and could be positively charged under physiological condition. The ??DNEYFYV?? motif in the pSP is the substrate of Jak2 kinase which was verified...
In this study, a QSAR model of neuraminidase (NA) type 1 (Nl) was elevated. This map contained two hydrogen bond acceptor features, one hydrogen bond donor features, and one positive ionizable feature. In the second step, we created the interaction maps in the active sites on the neuraminidase type2, and type7 (N2 and N7) protein structures. The structure-based pharmacophore map was showed the features...
Signal peptides are short regions of amino acid residues, which have become a crucial tool in finding new drugs or reprogramming cells for gene therapy. Owing to the rapidly increasing number of protein, it is highly demanded to develop the automated algorithm to identify the signal peptides. Recently, we had adopted a new alignment kernel function to identify secretory proteins. Compared with previous...
In our attempts to construct methods for automated structural prediction and annotation of proteins as well as automated drug design and discovery, the identification of structure and function from the primary structure of a protein is an important, but difficult problem. We extract features using biophysical properties of the different amino acids and using the patterns of poly-peptide sequences...
We report on the design and the implementation of ESCAPE 2.0, the parallel exhaustive conformational search system for peptides. We employed an exhaustive search method for conformational searches, so that ESCAPE 2.0 does not overlook any important conformations that may be overlooked by other systems. Although the previous version of ESCAPE can analyze short peptide segments, we added new functions...
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