Different approaches toward an automatic structural alignment of drug molecules: Applications to sterol mimics,thrombin and thermolysin inhibitors

Summary A relative comparison of the binding properties of different drug molecules requires their mutual superposition with respect to various alignment criteria. In order to validate the results of different alignment methods, the crystallographically observed binding geometries of ligands in the pocket of a common protein receptor have been used. The alignment function in the program SEAL that calculates the mutual superposition of molecules has been optimized with respect to these references. Across the reference data set, alignments could be produced that show mean rms deviations of approximately 1 Å compared to the experimental situation. For structures with obvious skeletal similarities a multiple-flexible fit, linking common pharmacophoric groups by virtual springs, has been incorporated into the molecular mechanics program MOMO. In order to combine conformational searching with comparative alignments, the optimized SEAL approach has been applied to sets of conformers generated by MIMUMBA, a program for conformational analysis. Multiple-flexible fits have been calculated for inhibitors of ergosterol biosynthesis. Sets of different thrombin and thermolysin inhibitors have been conformationally analyzed and subsequently aligned by a combined MIMUMBA/SEAL approach. Since for these examples crystallographic data on their mutual alignment are available, an objective assessment of the computed results could be performed. Among the generated conformers, one geometry could be selected for the thrombin and thermolysin inhibitors that approached reasonably well the experimentally observed alignment.     

Optical Alignment of Organic Dopants in a Solid Gel Matrix: Dispersed and Grafted Rhodamine B Molecules

We study herein the rotational mobility of organic dye molecules and their ability to align on a strong optical electric field when they are encaged in the pores of an inorganic silica xerogel matrix. We compare the case of dye molecules simply dispersed in the pores of the gel—and possibly held by hydrogen bonds—to the case of molecules chemically grafted on the inner surface of these pores through covalent bonds. The study is led on hybrid silicon-zirconium based inorganic matrices doped with organic rhodamine B molecules. The stronger holding of the dopants when these are grafted to the matrix enhances the molecular alignment—and thus the induced anisotropy—as well as the remanence of this alignment. Furthermore, we show that submitting the samples to a supplementary drying at higher temperature tends to increase both the alignment anisotropy and its stability. We explain these results in terms of mobility of the molecules, in relation to their immediate environment.     

液晶光定向层材料

本文综述了近10年来液晶显示用光定向层材料领域的研究现状和进展情况，主要概述了光降解型、光致异构型、光交联型以及自组装等材料，并对目前报道的液晶光定向机理进行了总结和归纳。     

Aligning Text and Phonemes for Speech Technology Applications Using an EM-Like Algorithm

A common requirement in speech technology is to align two different symbolic representations of the same linguistic ‘message’. For instance, we often need to align letters of words listed in a dictionary with the corresponding phonemes specifying their pronunciation. As dictionaries become ever bigger, manual alignment becomes less and less tenable yet automatic alignment is a hard problem for a language like English. In this paper, we describe the use of a form of the expectation-maximization (EM) algorithm to learn alignments of English text and phonemes, starting from a variety of initializations. We use the British English Example Pronunciation (BEEP) dictionary of almost 200,000 words in this work. The quality of alignment is difficult to determine quantitatively since no ‘gold standard’ correct alignment exists. We evaluate the success of our algorithm indirectly from the performance of a pronunciation by analogy system using the aligned dictionary data as a knowledge base for inferring pronunciations. We find excellent performance—the best so far reported in the literature. There is very little dependence on the start point for alignment, indicating that the EM search space is strongly convex. Since the aligned BEEP dictionary is a potentially valuable resource, it is made freely available for research use.     

An evaluation of molecular models of the cytochrome P450 Streptomyces griseolus enzymes P450SU1 and P450SU2

Summary P450SU1 and P450SU2 are herbicide-inducible bacterial cytochrome P450 enzymes from Streptomyces griseolus. They have two of the highest sequence identities to camphor hydroxylase (P450cam from Pseudomonas putida), the cytochrome P450 with the first known crystal structure. We have built several models of these two proteins to investigate the variability in the structures that can occur from using different modeling protocols. We looked at variability due to alignment methods, backbone loop conformations and refinement methods. We have constructed two models for each protein using two alignment algorithms, and then an additional model using an identical alignment but different loop conformations for both buried and surface loops. The alignments used to build the models were created using the Needleman-Wunsch method, adapted for multiple sequences, and a manual method that utilized both a dotmatrix search matrix and the Needleman-Wunsch method. After constructing the initial models, several energy minimization methods were used to explore the variability in the final models caused by the choice of minimization techniques. Features of cytochrome P450cam and the cytochrome P450 superfamily, such as the ferredoxin binding site, the heme binding site and the substrate binding site were used to evaluate the validity of the models. Although the final structures were very similar between the models with different alignments, active-site residues were found to be dependent on the conformations of buried loops and early stages of energy minimization. We show which regions of the active site are the most dependent on the particular methods used, and which parts of the structures seem to be independent of the methods.     

Hydrophobic Molecular Similarity from MST Fractional Contributions to the Octanol/water Partition Coefficient

Summary The use of a recently proposed hydrophobic similarity index for the alignment of molecules and the prediction of their differences in biological activity is described. The hydrophobic similarity index exploits atomic contributions to the octanol/water transfer free energy, which are evaluated by means of the fractional partitioning scheme developed within the framework of the Miertus-Scrocco-Tomasi continuum model. Those contributions are used to define global and local measures of hydrophobic similarity. The suitability of this computational strategy is examined for two series of compounds (ACAT inhibitors and 5-HT₃ receptor agonists), which are aligned to maximize the global hydrophobic similarity using a Monte Carlo-simulated protocol. Indeed, the concept of local hydrophobic similarity is used to explore structure–activity relationships in a series of COX-2 inhibitors. Inspection of the 3D distribution of hydrophobic/hydrophilic contributions in the aligned molecules is valuable to identify regions of very similar hydrophobicity, which can define pharmacophoric recognition patterns. Moreover, low similar regions permit to identify structural elements that modulate the differences in activity between molecules. Finally, the quantitative relationships found between the pharmacological activity and the hydrophobic similarity index points out that not only the global hydrophobicity, but its 3D distribution, is important to gain insight into the activity of molecules. J.M.M. and S.P. have contributed equally to this study.     

Thermocapillary Alignment of Gas Bubbles Induced by Convective Transport

The effect of a weak convective heat transfer on the thermocapillary interaction of two bubbles with an arbitrary orientation relative to an externally imposed temperature gradient is examined. Asymptotic analysis of the case of large separation distances, Z, suggests that the corrections to the bubbles' velocities are of (Pe/Z²), rather than (Pe²) previously found for an isolated bubble. Equal-sized bubbles are known to move with the same velocities, as if they were isolated, when heat conduction is the only transport mechanism. However, the convective transport results in a relative motion of the bubbles. The tendency of equal bubbles to line up in a plane perpendicular to the applied thermal gradient is shown analytically in the weakly nonlinear limit of small Pe numbers, and an interesting interaction behavior in the case of unequal bubbles is discussed.     

New liquid‐crystal alignment agents based on fluorinated polyimides with trifluoromethyl‐substituted benzene or diphenylether in the side chain

Fluorinated copolyimides derived from 4,4′‐oxydiphthalic anhydride (ODPA) with 4,4′‐oxydianline (ODA) and trifluoromethyl‐containing aromatic diamines have been synthesized and characterized. The trifluoromethyl‐containing diamines include 2,4‐diamino‐3′‐trifluoromethylazobenzene, 2,4‐diamino‐1‐[(4′‐trifluoromethylphenoxy) phenyl] aniline, 3,5‐diamino‐1‐[(4′‐trifluoromethylphenoxy) phenyl] benzamide, 3,5‐diamino‐1‐[(3′‐trifluoromethyl) phenyl] benzamide, 1,4‐bis(4′‐aminophenoxy)‐2‐(3′‐trifluoromethylphenyl) benzene, 3,5‐diaminobenzenetrifluoride, 4,4′‐diamino‐4″‐(p‐trifluoromethyl phenoxy) triphenylamine, and 4‐[(4′‐trifluoromethylphenoxy) phenyl]‐2,6‐bis(4″‐aminophenyl)pyridine. Strong and flexible copolyimide films, produced by casting the polyamic acid solution followed by thermal imidization, exhibited great thermal stability and high mechanical properties. The polyimides had an ultraviolet–visible absorption cutoff at 330–340 nm and pretilt angles as high as 20° for nematic liquid crystals, making them great potential candidates for advanced liquid‐crystal display applications. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 1583–1593, 2002     

神光-Ⅱ装置三倍频实验中靶场单元技术的改进

 主要介绍为了满足神光-Ⅱ高功率激光装置三倍频光（351nm，3ω）的物理实验要求，靶场三倍频模拟光源和瞄准监视系统两个主要单元技术的改进，即三倍频模拟光源由基频光（1 053nm，3ω）通过腔外的KTP+BBO晶体倍频获得，再经八路分光系统和主激光耦合；瞄准监视系统由透射式光学系统改进为反射式光学系统，避免原系统存在较大的色差，提高瞄准精度。     

An Extensive Assessment of Network Embedding in PPI Network Alignment

Network alignment is a fundamental task in network analysis. In the biological field, where the protein–protein interaction (PPI) is represented as a graph, network alignment allowed the discovery of underlying biological knowledge such as conserved evolutionary pathways and functionally conserved proteins throughout different species. A recent trend in network science concerns network embedding, i.e., the modelling of nodes in a network as a low-dimensional feature vector. In this survey, we present an overview of current PPI network embedding alignment methods, a comparison among them, and a comparison to classical PPI network alignment algorithms. The results of this comparison highlight that: (i) only five network embeddings for network alignment algorithms have been applied in the biological context, whereas the literature presents several classical network alignment algorithms; (ii) there is a need for developing an evaluation framework that may enable a unified comparison between different algorithms; (iii) the majority of the proposed algorithms perform network embedding through matrix factorization-based techniques; (iv) three out of five algorithms leverage external biological resources, while the remaining two are designed for domain agnostic network alignment and tested on PPI networks; (v) two algorithms out of three are stated to perform multi-network alignment, while the remaining perform pairwise network alignment.