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We have calculated the binding free energies of a series of benzamidine-like inhibitors to trypsin with a polarizable force field using both explicit and implicit solvent approaches. Free energy perturbation has been performed for the ligands in bulk water and in protein complex with molecular dynamics simulations. The binding free energies calculated from(More)
An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids,(More)
Development of the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Simulation) force field for proteins is presented. The current version (AMOEBA-2013) utilizes permanent electrostatic multipole moments through the quadrupole at each atom, and explicitly treats polarization effects in various chemical and physical environments. The atomic(More)
As the second most abundant cation in human body, zinc is vital for the structures and functions of many proteins. Zinc-containing matrix metalloproteinases (MMPs) have been widely investigated as potential drug targets in a range of diseases ranging from cardiovascular disorders to cancers. However, it remains a challenge in theoretical studies to treat(More)
A depsipeptide is a chemical structure consisting of both ester and amide bonds. Quantum mechanics calculations have been performed to investigate the conformational properties of a depsidipeptide in the gas and solution phases. Similar to an alanine dipeptide, the depsidipeptide exhibits a strong preference for the polyproline II (PPII) helical(More)
Hyperglycemia may be associated with worse functional outcomes in patients with primary intracerebral hemorrhage. We performed a systematic review and meta-analysis to investigate the relationship between hyperglycemia and mortality risk in patients with primary intracerebral hemorrhage. We searched PubMed and Embase databases for studies investigating the(More)
—RFID security and RFID anti-collision are research hotspots of RFID technology in the internet of things, most of the existing studies took them as separated parts and researched them individually. This paper attempts to deal with them as a whole, with a strategy integrating lightweight random key double-authentication and dynamic slot-ALOHA protocol. The(More)
—Inspired by the idea of the S-Tree Coding (STC) and by extending the popular Gouraud shading approach, in this paper, we propose a new image representation method using the Nonoverlapping Non-symmetry and Anti-packing Model (NNAM) for medical images, which is called the NNAM method. Also, a raster-first strategy for searching a rectangle subpattern in the(More)
There are always some crosscutting behaviors and features in the software architecture model described by conventional architecture description languages. They tangle and scatter in different design elements of software architecture and thus lead to difficulties in comprehension, evolution and reusability of software architecture model. Aiming at these(More)
The aspect-oriented software architectural weaving mechanism, to integrate aspectual components that encapsulate crosscutting behaviors and features into components and connectors constituting software architecture (SA), contributes to analyze and verify overall behaviors and quality attributes of SA. This paper proposes a new kind of weaving process and(More)