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The systematic design of functional peptides has technological and therapeutic applications. However, there is a need for pattern-based search engines that help locate desired functional motifs in primary sequences regardless of their evolutionary conservation. Existing databases such as The Protein Secondary Structure database (PSS) no longer serves the community, while the Dictionary of Protein Secondary Structure (DSSP) annotates the secondary structures when tertiary structures of proteins are provided. Here, we extract 1.7 million helices from the PDB and compile them into a database (Therapeutic Peptide Design database; TP-DB) that allows queries of compounded patterns to facilitate the identification of sequence motifs of helical structures. We show how TP-DB helps us identify a known purification-tag-specific antibody that can be repurposed into a diagnostic kit for Helicobacter pylori. We also show how the database can be used to design a new antimicrobial peptide that shows better Candida albicans clearance and lower hemolysis than its template homologs. Finally, we demonstrate how TP-DB can suggest point mutations in helical peptide blockers to prevent a targeted tumorigenic protein-protein interaction. TP-DB is made available at http://dyn.life.nthu.edu.tw/design/., Here, we present TP-DB; a pattern-based search engine based on 1.67 million helices from the Protein Database (PDB). We demonstrate the utility of TP-DB in identifying microbe-specific antigens, as well as the design of antimicrobial peptides and Protein-protein interaction blockers.

In Taiwan, e-tailers have formed partnerships with third-party logistics providers (3PLs) and convenience stores so that the service of shopping on-line in an electronic store and picking up goods at a convenience store could be quite common and popular these days. This study observes that the e-tailers have more bargaining power at its disposal comparing to its counterparts, 3PLs, in the sense of partnership. The study applies the methodology of “Fuzzy cognitive maps” to model and explore the operation dynamics for 3PLs. The results show that the improvement on “Relationship with e-tailers” and “Logistics performance” could significantly facilitate 3PLs in expanding the market shares, total profits and somewhat mitigating the problems 3PLs would have encountered.

A finite difference method is developed for computing the two-dimensional transient potential flow generated by an impulse on the free surface. Both the dynamic and kinematic free surface conditions are considered in nonlinear version. the primary features of the present paper include the use of special coordinates transformations so that the geometry of the flow field is transformed into a time-invariant region, presents an iteration process, by which the velocity potential is computed as the solution of a Poisson equation, the application of fast Fourier transform (FFT) technique results in a tri-diagonal system of equations which can be readily solved by the Thomas algorithm, the computing time is significantly reduced. Thus an efficient technique for handling the transient potential problems is well justified. The feasibility of the present method has been verified by two examples including different initial disturbances respectively.