Comparison of topological, shape, and docking methods in virtual screening

Virtual screening benchmarking studies were carried out on 11 targets to evaluate the performance of three commonly used approaches: 2D ligand similarity (Daylight, TOPOSIM), 3D ligand similarity (SQW, ROCS), and protein structure-based docking (FLOG, FRED, Glide). Active and decoy compound sets were assembled from both the MDDR and the Merck compound databases. Averaged over multiple targets, ligand-based methods outperformed docking algorithms. This was true for 3D ligand-based methods only when chemical typing was included. Using mean enrichment factor as a performance metric, Glide appears to be the best docking method among the three with FRED a close second. Results for all virtual screening methods are database dependent and can vary greatly for particular targets.     

Modeling Very Oscillating Signals. Application to Image Processing

This article is a companion paper of a previous work where we have developed the numerical analysis of a variational model first introduced by Rudin et al. and revisited by Meyer for removing the noise and capturing textures in an image. The basic idea in this model is to decompose an image f into two components (u + v) and then to search for (u,v) as a minimizer of an energy functional. The first component u belongs to BV and contains geometrical information, while the second one v is sought in a space G which contains signals with large oscillations, i.e. noise and textures. In Meyer carried out his study in the whole ² and his approach is rather built on harmonic analysis tools. We place ourselves in the case of a bounded set of ² which is the proper setting for image processing and our approach is based upon functional analysis arguments. We define in this context the space G, give some of its properties, and then study in this continuous setting the energy functional which allows us to recover the components u and v. We present some numerical experiments to show the relevance of the model for image decomposition and for image denoising.     

Structure Analysis of PVC Nanocomposites

In this paper poly(vinyl chloride)/clay nanocomposites were prepared by melt intercalation using a single screw extruder. Problems with thermal stability of these nanocomposites during compounding were largely eliminated by pre-treatment of the organoclay with plasticizer (dioctyl phthalate), which created a barrier between polymer and quaternary amine. These nanocomposite materials were analyzed with respect to their morphology. The intercalation, exfoliation, nano-phase dispersion and orientation were investigated using Transmission Electron Microscopy (TEM), Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM) and X-ray diffraction (XRD). Moreover, different types of sample preparation for these techniques were tested as well. It was found that partially intercalated and disordered structure arose in poly (vinyl chloride) composites containing sodium type of montmorillonite, while a fine dispersion of partial to nearly full exfoliation of individual montmorillonite layers in poly (vinyl chloride) matrix was observed when this clay was organically modified. Finally, the influence of different mixing time (in extruder) on nano-phase morphology was surveyed.     

Purification and characterization of acetate kinase from Clostridium thermocellum

Acetate kinase (EC 2.7.2.1), an enzyme involved in the wasteful production of acetate during conversion of cellulose to ethanol by Clostridium thermocellum, was purified 144-fold. The enzyme has an Mr of 84 kD by non-denaturing gradient gel electrophoresis, and an Mr of 46 kD when estimated with a denaturing gel; thus it appears to be a homodimer. Optimum enzyme activity occurs at 50°C and between pH 7.2 and 8.0. Acetate kinase is stable to temperatures up to 60°C, but is completely inactivated at 80°C after two h. The enzyme is stable between pH 7.0 and 9.0 when incubated at 50°C for two h. Optimum acetate kinase activity occurs at a MgCl₂:ATP ratio of 2:1, which indicates an interaction between Mg²⁺ and ATP and that between Mg²⁺ and acetate kinase. Enzyme activity is partially inhibited by KCl, an inorganic salt frequently used in chromatography and fermentation media, losing 60% activity in the presence of 0.2 M KCl. Sigmoidal enzyme kinetics were observed from the velocity plot of acetate kinase when either the acetate (S_0.5 = 285 mM) or ATP (S_0.5 = 11 mM) concentration was varied, suggesting cooperative binding of the two substrates.     

A biotechnological process involving filamentous fungi to produce natural crystalline vanillin from maize bran

A new process involving the filamentous fungi Aspergillus niger and Pycnoporus cinnabarinus has been designed for the release of ferulic acid by enzymic degradation of a cheap and natural agricultural byproduct (autoclaved maize bran) and its biotransformation into vanillic acid and/or vanillin with a limited number of steps. On the one hand, the potentialities of A. niger I-1472 to produce high levels of polysaccharide-degrading enzymes including feruloyl esterases and to transform ferulic acid into vanillic acid were successfully combined for the release of free ferulic acid from autoclaved maize bran. Then vanillic acid was recovered and efficiently transformed into vanillin by P. cinnabarinus MUCL 39533, since 767 mg/L of biotechnologic vanillin could be produced in the presence of cellobiose and XAD-2 resin. On the other hand, 3-d-old high-density cultures of P. cinnabarinus MUCL39533 could be fed with the autoclaved fraction of maize bran as a ferulic acid source and a. niger I-1472 culture filtrate as an extracellular enzyme source. Under these conditions, P. cinnabarinus MUCL39533 was shown to directly biotransform free ferulic acid released from the autoclaved maize bran by A. niger I-1472 enzymes into 584 mg/L of vanillin. These processes, involving physical, enzymic, and fungal treatments, permitted us to produce crystallin vanillin from autoclaved maize bran without any purification step.     

Random walks on finite volume homogeneous spaces

Extending previous results by A. Eskin and G. Margulis, and answering their conjectures, we prove that a random walk on a finite volume homogeneous space is always recurrent as soon as the transition probability has finite exponential moments and its support generates a subgroup whose Zariski closure is semisimple.     

TOF-GISANS investigation of polymer infiltration in mesoporous TiO2 films for photovoltaic applications

The structure of porous TiO₂ films and TiO₂:poly(N-vinylcarbazole) (PVK) composite films is investigated with time-of-flight grazing incidence small-angle neutron scattering (TOF-GISANS). The TiO₂ films have been prepared by application of a sol–gel process with a diblock copolymer as structure directing agent, and the conductive polymer PVK is infiltrated in the porous network by spin coating and solution casting. The films show a hierarchical pore structure with mesopores 52 nm in size and additional large macropores with a diameter of about 180 nm. By matching the scattering contrast of the TiO₂ with the polymer information about the penetration of the polymer in the pores is determined. Whereas in the PVK film prepared by solution casting the pores are filled to a high degree; in the spin coated film, PVK wets only the TiO₂ pore walls and forms a solid overlying layer. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 1628–1635, 2010     

HIV-1 integrase inhibition of biscoumarin analogues

Nineteen biscoumarins bearing free and modified hydroxyl substituents at benzoyloxyphenyl linker have been synthesized by multiple step synthesis. Among these biscoumarins, thirteen were found to be active molecules against HIV-1 integrase (HIV-1 IN). The structure-activity relationship of the nineteen compounds on HIV IN may be useful for the design of potent therapeutic agents.     

Iodoplumbate mit polymeren Anionen – Synthese und Kristallstrukturen von [Na3(OCMe2)12][Pb4I11(OCMe2)], (Ph4P)2[Pb5I12] und (Ph4P)4[Pb15I34(dmf)6]

Iodoplumbates with Polymeric Anions – Synthesis and Crystal Structures of [Na₃(OCMe₂)₁₂][Pb₄I₁₁(OCMe₂)], (Ph₄P)₂[Pb₅I₁₂], and (Ph₄P)₄[Pb₁₅I₃₄(dmf)₆] Reactions of PbI₂ with NaI in polar organic solvents followed by crystallization with large cations yield iodoplumbate complexes with various compositions and structures. [Na₃(OCMe₂)₁₂][Pb₄I₁₁(OCMe₂)] 3 , (Ph₄P)₂[Pb₅I₁₂] 4 and (Ph₄P)₄[Pb₁₅I₃₄(dmf)₆] 7 contain one-dimensional infinite anionic chains of face- or edge-sharing PbI₆ or PbI₅L (L = acetone, DMF) octahedra. [Na₃(OCMe₂)₁₂][Pb₄I₁₁(OCMe₂)] 3 : Space group P1 (No. 1), a = 1120.3(5), b = 1265.3(6), c = 1608.3(8) pm, α = 74.64(4), β = 70.40(4), γ = 85.24(4)°, V = 2071(2) · 10⁶ pm³; (Ph₄P)₂[Pb₅I₁₂] 4 : Space group C2/c (No. 15), a = 787.00(10), b = 2812.0(5), c = 3115.9(5) pm, β = 96.240(13)°, V = 6885(2) · 10⁶ pm³; (Ph₄P)₄[Pb₁₅I₃₄(dmf)₆] 7 : Space group P2₁/n (No. 14), a = 2278.8(4), b = 1782.6(3), c = 2616.8(4) pm, β = 114.432(13)°, V = 9678(3) · 10⁶ pm³.     

Fast and Exact Simulation of Complex-Valued Stationary Gaussian Processes Through Embedding Circulant Matrix

This article is concerned with the study of the embedding circulant matrix method to simulate stationary complex-valued Gaussian sequences. The method is, in particular, shown to be well-suited to generate circularly symmetric stationary Gaussian processes. We provide simple conditions on the complex covariance function ensuring the theoretical validity of the minimal embedding circulant matrix method. We show that these conditions are satisfied by many examples and illustrate the simulation algorithm. In particular, we present a simulation study involving the circularly symmetric fractional Gaussian noise, a model introduced in this article. Supplementary material for this article is available online.