Pharmacophore fingerprint-based approach to binding site subpocket similarity and its application to bioisostere replacement

Bioisosteres have been defined as structurally different molecules or substructures that can form comparable intermolecular interactions, and therefore, fragments that bind to similar protein structures exhibit a degree of bioisosterism. We present KRIPO (Key Representation of Interaction in POckets): a new method for quantifying the similarities of binding site subpockets based on pharmacophore fingerprints. The binding site fingerprints have been optimized to improve their performance for both intra- and interprotein family comparisons. A range of attributes of the fingerprints was considered in the optimization, including the placement of pharmacophore features, whether or not the fingerprints are fuzzified, and the resolution and complexity of the pharmacophore fingerprints (2-, 3-, and 4-point fingerprints). Fuzzy 3-point pharmacophore fingerprints were found to represent the optimal balance between computational resource requirements and the identification of potential replacements. The complete PDB was converted into a database comprising almost 300?000 optimized fingerprints of local binding sites together with their associated ligand fragments. The value of the approach is demonstrated by application to two crystal structures from the Protein Data Bank: (1) a MAP kinase P38 structure in complex with a pyridinylimidazole inhibitor ( 1A9U ) and (2) a complex of thrombin with melagatran ( 1K22 ). Potentially valuable bioisosteric replacements for all subpockets of the two studied protein are identified.     

Testing performance of the improved pinhole collimator and its application to small animals

Testing performance of the improved pinhole collimator of 1.5 mm aperture attached to the gamma camera was carried out with three kinds of radionuclides, 99mTc, 67Ga and 131I, using a hand-made phantom. The results obtained in this experiment were compared to those obtained with a human pinhole collimator of 4 mm aperture. Those were nearly understood by taking account of the effective aperture of a pinhole collimator for each effective photon energy. And all scintigrams obtained from rats with various scintigraphy showed high resolution images.     

Volatilities of codons and its application in similarity analysis of biological sequences

Volatilities of codons provide us a new way to characterize codons. In this article, we propose a new method measuring volatilities of codons base on the physics–chemical distances between amino acids and mutation frequencies between codons, then by which, we give a new graphical representation scheme for codon sequences. Finally, in order to show the effectiveness of our scheme, we analyze similarity among the coding codon sequences of exon 1 of beta-globin gene of human and those of other 10 species, find the result is consistent with those shown in the literature.     

Algorithm for accurate similarity measurements of peptide mass fingerprints and its application

We present a simple algorithm which allows accurate estimates of the similarity between peptide fingerprint mass spectra from matrix assisted laser desorption/ionization (MALDI) spectrometers. The algorithm, which is a combination of mass correlation and intensity rank correlation, was used to cluster similar spectra and to generate consensus spectra from a data store of more than 100,000 spectra. The resulting first spectra library of 1248 unambiguously identified different protein digests was used to search for missed cleavage patterns that have not been reported so far and to shed light on some peptide ionization characteristics. The findings of this study could be directly implemented in peptide mass fingerprint search algorithms to decrease the false positive error rate to <0.25%. Furthermore, the results contribute to the understanding of the peptide ionization process in MALDI experiments.     

Genetic analyzer-dependent DNA methylation detection and its application to existing age prediction models

DNA methylation is the most promising biomarker for estimating human age. There are various methods used for analyzing DNA methylation. Among those, the SNaPshot assay-based method provides a semi-quantitative measurement of DNA methylation using capillary electrophoresis on genetic analyzers. However, DNA methylation measures produced using different types of genetic analyzers have never been compared, although differences in methylation values can directly affect age estimates. To evaluate the differences between the results generated by different genetic analyzers, we analyzed the same blood, saliva, and control methylated DNA using three genetic analyzers—the Applied Biosystems 3130, 3500, and SeqStudio—and compared the methylation values at five CpG sites: ELOVL2, FHL2, KLF14, MIR29B2C, and TRIM59. The methylation value at each of the five CpG sites decreased in the order 3130, 3500, and SeqStudio. The differences in the results produced by the different genetic analyzers resulted in significant errors when applying the 3500 and SeqStudio data to a previous age estimation model constructed using the 3130 Genetic Analyzer data. Therefore, DNA methylation measurements from 3500 and SeqStudio were corrected using the regression functions obtained by plotting the DNA methylation data of one instrument versus the other to facilitate the application of DNA methylation data from one instrument to the age prediction model based on other instruments. The age prediction accuracy obtained by applying corrected 3500 and SeqStudio data to the existing age estimation model was as high as observed in the 3130 data.     

水溶性InP/ZnS量子点的合成及其在指纹显现中的应用

以磷化锌、氯化铟为原料,以十二烷胺为溶剂,在150～200℃下合成了InP量子点,通过相转移和紫外光照得到了巯基乙酸修饰的水溶性InP/ZnS量子点.利用X射线衍射仪、透射电镜、高分辨透射电镜、荧光光谱仪等分析了不同温度下合成的量子点的粒径、形貌、荧光性能及指纹显现效果.结果表明,合成的InP和InP/ZnS量子点为球...     

New description of molecular chirality and its application to the prediction of the preferred enantiomer in stereoselective reactions

A new representation of molecular chirality as a fixed-length code is introduced. This code describes chiral carbon atoms using atomic properties and geometrical features independent of conformation and is able to distinguish between enantiomers. It was used as input to counterpropagation (CPG) neural networks in two different applications. In the case of a catalytic enantioselective reaction the CPG network established a correlation between the chirality codes of the catalysts and the major enantiomer obtained by the reaction. In the second application-enantioselective reduction of ketones by DIP-chloride-the series of major and minor enantiomers produced from different substrates were clustered by the CPG neural network into separate regions, one characteristic of the minor products and the other characteristic of the major products.     

Reformulated space-charge-limited current model and its application to disordered organic systems

We have reformulated a traditional model used to describe the current-voltage dependence of low mobility materials sandwiched between planar electrodes by using the quasi-electrochemical potential as the fundamental variable instead of the local electric field or the local charge carrier density. This allows the material density-of-states to enter explicitly in the equations and dispenses with the need to assume a particular type of contact. The diffusion current is included and as a consequence the current-voltage dependence obtained covers, with increasing bias, the diffusion limited current, the space-charge limited current, and the injection limited current regimes. The generalized Einstein relation and the field and density dependent mobility are naturally incorporated into the formalism; these two points being of particular relevance for disordered organic semiconductors. The reformulated model can be applied to any material where the carrier density and the mobility may be written as a function of the quasi-electrochemical potential. We applied it to the textbook example of a nondegenerate, constant mobility material and showed how a single dimensionless parameter determines the form of the I(V) curve. We obtained integral expressions for the carrier density and for the mobility as a function of the quasi-electrochemical potential for a Gaussianly disordered organic material and found the general form of the I(V) curve for such materials over the full range of bias, showing how the energetic disorder alone can give rise, in the space-charge limited current regime, to an I∝V(n) dependence with an exponent n larger than 2.     

Note on the application of the reduced graph model in conjunction with search trees to the enumeration ofKekulé structures

The reduced graph model, when used in conjunction with the search trees method, provides a novel combinatorial procedure for the enumeration and generation ofKekulé structures. The procedure is suited for large benzenoid hydrocarbons consisting of cata- and thin peri-condensed parts.

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Zur Anwendung des Reduced Graph Model im Zusammenhang mit Search Trees zur Ermittlung der Anzahl möglicherKekulé-Strukturen

Zusammenfassung Das Modell erlaubt mit der im Titel genannten Kombination eine neuartige Methode zur Ermittlung und Generierung vonKekulé-Strukturen. Das Verfahren ist für große benzoide Kohlenwasserstoffe geeignet, die aus cata- und (dünnen) peri-kondensierten Teilstrukturen bestehen.

     

Information theory for experiments with known conditional probabilities: Application to the prediction of branching ratios

Information theory is used, under conditions of incomplete data, to provide a maximally conservative prior expectation of a population distribution. This is done by systematically refining the estimates of the full distribution via the incorporation of fragmentary data in the form of conditional probabilities. The net effect is to reduce the available phase space volume of the distribution as more data are incorporated. The above refinements are then applied to calculate estimates of branching ratios for chemical reactions with more than one possible product. Two new branching ratio expressions are derived: one for the case where each product's internal state distribution is known for reactions originating from various specific reactant state?, and when the joint state-to-state reactive probability is known.     

Review of polymer oxidation and its relationship with materials performance and lifetime prediction

All polymers are intrinsically susceptible to oxidation, which is the underlying process for thermally driven materials degradation and of concern in various applications. There are many approaches for predicting oxidative polymer degradation. Aging studies usually are meant to accelerate oxidation chemistry for predictive purposes. Kinetic models attempt to describe reaction mechanisms and derive rate constants, whereas rapid qualification tests should provide confidence for extended performance during application, and similarly TGA tests are meant to provide rapid guidance for thermal degradation features. What are the underlying commonalities or diverging trends and complications when we approach thermo-oxidative aging of polymers in such different ways? This review presents a brief status report on the important aspects of polymer oxidation and focuses on the complexity of thermally accelerated polymer aging phenomena. Thermal aging and lifetime prediction, the importance of DLO, property correlations, kinetic models, TGA approaches, and a framework for predictive aging models are briefly discussed. An overall perspective is provided showing the challenges associated with our understanding of polymer oxidation as it relates to lifetime prediction requirements.     

An oxidized surface state model of vanadium oxides and its application to catalysis

The charge distribution around the VO bonds in V₂O₅, V₆O₁₃, and V₂O₄ was calculated by using an empirical formula. The same expression was also used to calculate the oxygen bond strengths on the surface. The surfaces of lower oxides were treated as though they were in an oxidized state which is believed to correspond to the conditions in oxidation and ammoxidation processes. The result is that O^2?, in the form of VO surface groups, is responsible for the catalytic oxidation of hydrocarbons. O^? is hindered by the formation of stable OH^? groups. The positions of lower valent oxygens are considered to be vacant because of a slow reoxidation rate. In V₂O₅ the VO groups are located on the (010) plane, while in V₆O₁₃ they are mainly located on the (001) surface plane. But in this case the (100) and (010) surface planes also have some VO groups. The catalytic activity of the rutile form of V₂O₄ is limited by sterical factors, but the (110) surface plane has oxygens pointing perpendicular out of the surface.     

Solid-State nuclear magnetic resonance: performance of point-charge distributions to model intermolecular effects in 19F chemical shifts

This contribution presents results from applying two different charge models to take into account intermolecular interactions to model the solid-state effects on the ¹⁹F NMR chemical-shift tensors. The density functional theory approach with the B3LYP gradient-corrected exchange correlation functional has been used because it includes electron correlation effects at a reasonable cost and is able to reproduce chemical shifts for a great variety of nuclei with reasonable accuracy. The results obtained with the charge models are compared with experimental data and with results obtained from employing the cluster model, which explicitly includes neighboring molecular fragments. The results show that the point-charge models offer similar accuracy to the cluster model with a lower cost. Received: 3 October 1999 / Accepted: 3 February 2000 / Published online: 5 June 2000     

Preparation of liquid crystal emulsion and its application performance study

The aim of this study was the formulation composition and characterization of the liquid crystal (LC) emulsion. First, influences of formulation composition on preparation of LC structure were studied, including the aliphatic alcohols with different carbon chain length, the liquid oils with different polarities, the sodium chloride, and the polygons. The results showed that fatty alcohols which is closer to the hydrophobic group of the emulsifier, little liquid oil, and little polyols were conducive to form LC structure. Then, the application performance of LC structure emulsion was studied. The results showed that compared with the conventional structure emulsion, the LC structure emulsion had more excellent moisturizing property, slow release effect, and the promoted penetration effect.     

Block-correlated coupled cluster theory: the general formulation and its application to the antiferromagnetic Heisenberg model

The general formalism of the block-correlated coupled cluster (BCCC) method, an alternative multireference coupled cluster method for calculating the ground-state electronic structures of molecular systems, has been presented. The BCCC theory is constructed in terms of a complete set of many-electron states of individual blocks, assumed that the whole system could be partitioned into a set of blocks. The reference state in the BCCC is selected as a tensor product of the most important many-electron state of each system block. By truncating the cluster operator to a certain n-block correlation level, an approximate but size-extensive BCCC method, denoted as BCCCn, is defined. For reducing the computational effort but without much loss of accuracy, the reduced density matrix is introduced to generate an optimal subset of many-electron states for each block. I have implemented the BCCCn (n=2,3) methods within the S=1/2 Heisenberg Hamiltonian, and applied them to calculate the ground-state energies of one-dimensional spin chains and quasi-one-dimensional two-leg spin ladders. The calculated results show that with the appropriate partition of the studied systems the BCCC3 method can yield quite satisfactory ground-state energies for these spin systems.