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We describe a method for docking a ligand into a protein receptor while allowing flexibility of the protein binding site. The method employs a multistep procedure that begins with the generation of protein and ligand conformations. An initial placement of the ligand is then performed by computing binding site hotspots. This initial placement is followed by(More)
Programmable switching chips are becoming more commonplace , along with new packet processing languages to configure the forwarding behavior. Our paper explores the design of a compiler for such switching chips, in particular how to map logical lookup tables to physical tables , while meeting data and control dependencies in the program. We study the(More)
As datacenter speeds scale to 100 Gb/s and beyond, traditional congestion control algorithms like TCP and RCP converge slowly to steady sending rates, which leads to poorer and less predictable user performance. These reactive algorithms use congestion signals to perform gradient descent to approach ideal sending rates, causing poor convergence times. In(More)
Understanding the effects of mutation on pH-dependent protein binding affinity is important in protein design, especially in the area of protein therapeutics. We propose a novel method for fast in silico mutagenesis of protein-protein complexes to calculate the effect of mutation as a function of pH. The free energy differences between the wild type and(More)
The basic differences between the 20 natural amino acid residues are due to differences in their side-chain structures. This characteristic design of protein building blocks implies that side-chain-side-chain interactions play an important, even dominant role in 3D-structural realization of amino acid codes. Here we present the results of a comparative(More)
Human papillomaviruses (HPVs) infect epithelia and can lead to the development of lesions, some of which have malignant potential. HPV type 16 (HPV16) is the most oncogenic genotype and causes various types of cancer, including cervical, anal, and head and neck cancers. However, despite significant research, our understanding of the mechanism by which HPV16(More)
We report a very fast and accurate physics-based method to calculate pH-dependent electrostatic effects in protein molecules and to predict the pK values of individual sites of titration. In addition, a CHARMm-based algorithm is included to construct and refine the spatial coordinates of all hydrogen atoms at a given pH. The present method combines(More)
The renal 11beta-hydroxysteroid dehydrogenase (11beta-HSD) type 2 catalyzes the NAD(+)-dependent oxidation of the C11-alcohol on cortisol and corticosterone to yield inactive 11-ketosteroids. The lack of purified active enzyme complicates structure-function analyses of 11beta-HSD2. Here, we constructed a 3D-structural model of 11beta-HSD2, based on known(More)
According to experimental data, binding of the Cu(2+) ions destabilizes the native state of beta2-microglobulin (beta2m). The partial unfolding of the protein was generally considered an early step toward fibril formation in dialysis-related amyloidosis. Recent NMR studies have suggested that the destabilization of the protein might be achieved through(More)