Interrogating HIV integrase for compounds that bind- a SAMPL challenge

Tremendous gains and novel methods are often developed when people are challenged to do something new or difficult. This process is enhanced when people compete against each other-this can be seen in sport as well as in science and technology (e.g. the space race). The SAMPL challenges, like the CASP challenges, aim to challenge modellers and software developers to develop new ways of looking at molecular interactions so the community as a whole can progress in the accurate prediction of these interactions. In order for this challenge to occur, data must be supplied so the prospective test can be done. We have supplied unpublished data related to a drug discovery program run several years ago on HIV integrase for the SAMPL4 challenge. This paper describes the methods used to obtain these data and the chemistry involved.     

Three-dimensional concentration field measurements in a mixing layer using magnetic resonance imaging

Magnetic resonance imaging (MRI) was used to measure the three-dimensional, time-averaged concentration distribution in a turbulent two-stream mixing layer. Test fluids and MRI scanning parameters were chosen to give good signal linearity, and a calibration/normalization procedure was developed to reduce the concentration measurement uncertainty. Plain deionized water mixing with a solution of 0.8% gadopentetate dimeglumine in deionized water were selected as test fluids. The concentration of the marked water was measured on an array of 220,000 0.69 mm³ voxels covering the entire flow apparatus. Planar laser-induced fluorescence experiments were performed on the flow centerplane to provide validation data. The uncertainty of a single voxel measurement was estimated to be less than 12% with the largest source of uncertainty being turbulent dephasing. Averaging two runs in which the marked water was switched between the two streams reduced the uncertainty to only 4%. The complete magnetic resonance concentration (MRC) procedure including the adjustment of scanning parameters, a background run, two reference/calibration runs, and multiple concentration measurement runs can be completed in 2–3 h. This work establishes MRC as a viable technique for studying the mixing in complex turbulent liquid flows.     

High-spin structure of yrast-band in 78Kr

Lifetime of levels up to 22⁺, have been measured in ⁷⁸Kr and an oblate shape is assigned to the ground state using the CSM and the configuration dependent shell correction calculations. Calculations further show that ⁷⁸Kr is highly γ-soft nucleus. The experimental Q _t values coupled with theoretical calculations indicate an oblate shape for ⁷⁸Kr at low spins and triaxial shape at higher spins     

Finite-bandwidth effects on the causal prediction of ultrasonic attenuation of the power-law form

Kramers-Kronig (K-K) relations exist as a consequence of causality, placing nonlocal constraints on the relationship between dispersion and absorption. The finite-bandwidth method of applying these relations is examined where the K-K integrals are restricted to the spectrum of the experimental data. These finite-bandwidth K-K relations are known to work with resonant-type data and here are applied to dispersion data consistent with a power-law attenuation coefficient (exponent from 1 to 2). Bandwidth-restricted forms of the zero and once-subtracted K-K relations are used to determine the attenuation coefficient from phase velocity. Analytically, it is shown that these transforms produce the proper power-law form of the attenuation coefficient as a stand-alone term summed with artifacts that are dependent on the integration limits. Calculations are performed to demonstrate how these finite-bandwidth artifacts affect the K-K predictions under a variety of conditions. The predictions are studied in a local context as a function of subtraction frequency, bandwidth, and power-law exponent. The K-K predictions of the power-law exponent within various decades of the spectrum are also examined. In general, the agreement between finite-bandwidth K-K predictions and exact values grows as the power-law exponent approaches 1 and with increasing bandwidth.