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101.
Gerhard Klebe Thomas Mietzner Frank Weber 《Journal of computer-aided molecular design》1994,8(6):751-778
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. 相似文献
102.
103.
1 INTRODUCTION In 1984, thiolate ligand was successfully introduced into molybdenum carbonyl compound by the reaction of Mo(CO)6 with [Et4N]SR( R = C6H5, But) in a moderate condition[1]. From then on, a series of dinuclear molybdenum(0) carbonyl thiolate compounds have been synthesized and characterized by using a variety of thiolate ligands in our research group. It was found that a planar Mo2S2 unit is in the compound [Et4N]2[Mo2(CO)8(SC6H4-CH_3-p)2][2] (2) and a "butterfly" t… 相似文献
104.
Investigation of carbon-13 nuclear magnetic resonance spectra-structure correlation based on novel atomic distance-edge (ADE) vector 总被引:1,自引:0,他引:1
A set of novel graph-theoretical parameters,called the atomic distance-edge (ADE) vector,was developed.Based on the connecting C-C bond number between central carbon atom and the other ones,various carbon atoms of alkanes were classified as four types,i.e.,type 1,2,3 and 4 for primary,secondary,ternary and quaternary carbon,respectively; and then four regression equations were obtained to link carbon-13 chemical shift (CS) of each type of atoms.Furthermore,these regression models were used to predict the carbon-13 nuclear magnetic resonance spectra of alkanes and it was found that the estimated CS were in agreement with the experimental results. 相似文献
105.
Gonzalo Cerruela García Irene Luque Ruiz Miguel Ángel Gómez-Nieto 《Journal of mathematical chemistry》2006,40(3):213-231
In this paper, we propose a new method for clustering of chemical databases based on the representation of measurements of structural similarity onto multidimensional spaces. The proposed method permits the tuning of the clustering process through the selection of the dimension of the projection space, the normal vectors and the sensibility of the projection process. The structural similarity of each element regarding to the database elements is projected onto the defined spaces generating clusters that represent the characteristics and diversity of the database and whose size and characteristics can be easily adjusted. 相似文献
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107.
Formylation is one of the newly discovered post-translational modifications in lysine residue which is responsible for different kinds of diseases. In this work, a novel predictor, named predForm-Site, has been developed to predict formylation sites with higher accuracy. We have integrated multiple sequence features for developing a more informative representation of formylation sites. Moreover, decision function of the underlying classifier have been optimized on skewed formylation dataset during prediction model training for prediction quality improvement. On the dataset used by LFPred and Formator predictor, predForm-Site achieved 99.5% sensitivity, 99.8% specificity and 99.8% overall accuracy with AUC of 0.999 in the jackknife test. In the independent test, it has also achieved more than 97% sensitivity and 99% specificity. Similarly, in benchmarking with recent method CKSAAP_FormSite, the proposed predictor significantly outperformed in all the measures, particularly sensitivity by around 20%, specificity by nearly 30% and overall accuracy by more than 22%. These experimental results show that the proposed predForm-Site can be used as a complementary tool for the fast exploration of formylation sites. For convenience of the scientific community, predForm-Site has been deployed as an online tool, accessible at http://103.99.176.239:8080/predForm-Site. 相似文献
108.
In the analysis of gene expression profiles, the number of tissue samples with genes expression levels available is usually small compared with the number of genes. This can lead either to possible overfitting or even to a complete failure in analysis of microarray data. The selection of genes that are really indicative of the tissue classification concerned is becoming one of the key steps in microarray studies. In the present paper, we have combined the modified discrete particle swarm optimization (PSO) and support vector machines (SVM) for tumor classification. The modified discrete PSO is applied to select genes, while SVM is used as the classifier or the evaluator. The proposed approach is used to the microarray data of 22 normal and 40 colon tumor tissues and showed good prediction performance. It has been demonstrated that the modified PSO is a useful tool for gene selection and mining high dimension data. 相似文献
109.
聚类是芯片数据分析中被广泛使用的方法。未知基因的功能通常通过其与已知基因在不同生物状态下具有表达相似性来进行预测。然而,还未有人就这种通过表达相似性来进行功能注释的方法的可靠性进行评估。本文利用Gene Ontology对表达相似性和基因功能相似性的相关关系进行了全面的研究。研究表明,尽管表达谱的相似性和基因功能相似性之间有一定的依赖关系,但相关性较弱。在Gene Ontology的三大类中,相对生物过程和分子功能,基因表达谱的相似性更有助于细胞组分的注释。本文的研究结果对于基因功能的预测有一定的指导意义。 相似文献
110.