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51.
Alexey Sulimov Danil Kutov Ivan Ilin Yibei Xiao Sheng Jiang Vladimir Sulimov 《Molecules (Basel, Switzerland)》2022,27(9)
The COVID-19 pandemic is still affecting many people worldwide and causing a heavy burden to global health. To eliminate the disease, SARS-CoV-2, the virus responsible for the pandemic, can be targeted in several ways. One of them is to inhibit the 2′-O-methyltransferase (nsp16) enzyme that is crucial for effective translation of viral RNA and virus replication. For methylation of substrates, nsp16 utilizes S-adenosyl methionine (SAM). Binding of a small molecule in the protein site where SAM binds can disrupt the synthesis of viral proteins and, as a result, the replication of the virus. Here, we performed high-throughput docking into the SAM-binding site of nsp16 for almost 40 thousand structures, prepared for compounds from three libraries: Enamine Coronavirus Library, Enamine Nucleoside Mimetics Library, and Chemdiv Nucleoside Analogue Library. For the top scoring ligands, semi-empirical quantum-chemical calculations were performed, to better estimate protein–ligand binding enthalpy. Relying upon the calculated binding energies and predicted docking poses, we selected 21 compounds for experimental testing. 相似文献
52.
Vladimir R. Perovic 《Journal of mathematical chemistry》2013,51(8):2238-2255
The highly pathogenic avian influenza virus (HPAIV) A subtype H5N1 is causing threat to human health over the years. Phylogenetic analysis is an important tool for analyzing the evolution of influenza. A novel phylogenetic algorithm based on a new protein distance measure derived from the informational spectrum method (ISM) has been presented. The new phylogenetic approach allows assessment of functional evolution of protein sequences. The new ISM-based phylogenetic approach has been found to overcome some drawbacks of other phylogenetic approaches, particularly concerning sensitivity to a single mutation, deletion and the position of the mutation. The ISM-based approach applied to hemagglutinin subunit 1 protein (HA1) of HPAIV A subtype H5N1 viruses in Egypt between 2006 and 2011, revealed clear clustering in two groups, with one growing group of H5N1 viruses after 2009 with increased number of human infections with H5N1. Four group-specific mutations are identified which are important for increased human tropism and the pandemic potential. 相似文献
53.
The accuracy of using step-function approximations to the Arrhenius exponential in computing the wavespeed in combustion wave propagation is investigated. Gaseous and gasless combustion, and first- and second-order reactions are included in the study. The theoretical analysis is based on Melnikov theory from dynamical systems. The error is shown to be small in most instances. The analytical results are supported with numerical simulations. 相似文献
54.
We study processes with unstable particles in intermediate time-like states. It is shown that the amplitudes squared of such processes factor exactly in the framework of the model of unstable particles with continuous masses. Decay widths and cross sections can then be represented in a universal factorized form for an arbitrary set of interacting particles. This exact factorization is caused by specific structure of propagators in the model. We formulate the factorization method and perform a phenomenological analysis of the factorization effects. The factorization method considerably simplifies calculations while leading to compact and reasonable results. 相似文献
55.
Vladimir Ya Shevchenko 《Structural chemistry》2012,23(4):943-944
There is a special collection of contribution in the August 2012 issue of Structural Chemistry honoring the Swedish crystallographer Sten Andersson. This Encomium emphasizes the exemplary characteristics of his oeuvre. 相似文献
56.
Vladimir R. Rosenfeld Douglas J. Klein Josep M. Oliva 《Journal of mathematical chemistry》2012,50(7):2012-2022
Various sorts of isomer enumeration problems are addressed in the context of polycarboranes, with special illustrative focus on the case of dicarboranes, for which then various numerical results are given. A systematic and general Pólya-theoretic methodology is used to make the computations, including some new techniques being applicable to a wide range of nano-structures built from a framework of like local subunits. 相似文献
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