绑定机构
扫描成功 请在APP上操作
打开万方数据APP,点击右上角"扫一扫",扫描二维码即可将您登录的个人账号与机构账号绑定,绑定后您可在APP上享有机构权限,如需更换机构账号,可到个人中心解绑。
欢迎的朋友
万方知识发现服务平台
获取范围
  • 1 / 8
找到 142 条结果
摘要:An interest in the fluorescent protein asFP595 is due to unexplained puzzles in its photophysical behavior. We report the results of calculations of structures, absorption, and emission bands in asFP595 by considering model molecular clusters in the coordinate-locking scheme. Both trans and cis conformations of the anionic chromophore are considered. Equilibrium geometry coordinates on the ground potential energy surface were optimized in the density functional theory approaches by considering both large- and reduced-size clusters. The cluster size was reduced to locate positions of the minimum energy points on the excited-state potential surface by using the configuration interaction singles approach. Vertical excitation energies and oscillator strengths were computed by using the ZINDO method. We show that consideration of large clusters mimicking the protein-containing pocket is an essential issue to calculate positions of absorption and emission bands with the accuracy compatible to experiments....
摘要:DNA methyltransferases 1 (DNMT1) has been looked as crucial targets against various types of cancers. MD simulations have advanced to a point where the atomic level information of biological macromolecule (protein or DNA-protein or protein-protein) can easily be advantageous to predict the functionality. In this study we utilize xanthomicrol and galloyl compounds to investigate potential compounds for the inhibition of DNMT1, and the results of these two compounds are compared with drug decitabine. Xanthomicrol and galloyl are found to dock successfully within the active site of DNMT1. A comparison of the inhibitory potential of screened xanthomicrol inhibited DNMT1 approximately is identical with those of their corresponding drugs, decitabine. The stability of the DNMT1 with the best docked xanthomicrol, were further analysed in molecular dynamics (MD) simulation and compared with those of the respective drugs namely decitabine which revealed stabilization of these complexes within 300 ns of simulation with better stability of DNMT1....
摘要:A novel avian origin influenza H7N9 virus emerged in March 2013 in China and caused severe disease in humans. The high human death rate has caused public health concern and attracted global attention. The influenza viruses have two surface proteins: hemagglutinin (HA) and neuraminidase (NA), with HA facilitating viral entry into a host cell and NA helping new viral particles leave a host cell to infect more host cells. In a previous study published in May 2003, we applied computational analysis to the HA sequences of this new virus. Our findings suggested that the HA of this virus had avian type receptors as its primary binding and human types as secondary binding, which was verified by several subsequent wet lab experiments in later months of 2013. We also showed that the human H7N9 and avian H7N9 in China in 2013 shared the same HA receptor binding patterns. The NA protein of this new virus has a stalk deletion that is associated with virulence and host adaptation. In the present study, we wanted to understand the biological effects of this NA deletion on the HA receptor binding preference of this virus. However, the NA proteins of human H7N9 in China in 2013 all carry a stalk deletion so we lack the NA proteins with no stalk deletion as a control. In this study, we chose instead the NA proteins of avian H7N9 in China in 2013-14 and those of avian H7N7 in Netherlands in 2003 as some of them had a NA stalk deletion and some did not. We sought to employ a computational approach to revealing the impact of this NA stalk deletion on HA receptor binding preference of this virus. Our analysis implied that this deletion in the stalk region of NA enhanced the human receptor binding of avian H7N9 in China in 2013-14 and avian H7N7 in the Netherlands in 2003....
摘要: align="justify"> A spin-dependent quantum trajectory methodology is outlined which achieves electron exchangecorrelation on an ab initio basis. The methodology is intended to give workers in electronic structure the same computational capability which has been available for decades in classical dynamics.
...
摘要:A method for analyzing the protein site similarity was devised aiming at understanding selectivity of homologous proteins and guiding the design of new drugs. The method is based on calculating Cα distances between selected pocket residues and subsequent analysis by multivariate methods. Five closely related serine proteases, the coagulation factors II, VII, IX, X, and XI, were studied and their pocket similarity was illustrated by PCA clustering. OPLS-DA was then applied to identify the residues responsible for the variation. By combining these two multivariate methods, we could successfully cluster the different proteases according to class and identify the important residues responsible for the observed variation....
摘要: align="justify"> Each eukaryotic cell of multicellular organisms must be able to maintain its integrity by sensing both external and internal stimuli. The primary goal of the generated response mechanism is to drive back the system to the former or to a new homeostatic state. Moreover, the response has to provide an accurate survival-or-death decision to avoid any “misunderstanding” and its unwanted consequences. New data revealed that a systems-level crosstalk of molecular networks has an essential role in achieving the correct characteristic of the response. Although many molecular components of these processes already have been revealed, several elements and regulatory connections of crosstalk are still missing. These “gaps” of the complex control networks make hardly impossible to present comprehensive models. Therefore we approach the questions from a systems biology aspect by combining the experimental results with the special technique of mathematical modelling. In this short report we discuss some novel and preliminary data gained by this approach on the crosstalk between life and death decisions under cellular stress, to get a systems biological view of these networks.
...
摘要:The highly pathogenic avian H5N1 influenza virus could infect humans with high mortality rate, even though it has not yet become efficiently transmissible among humans. This proteomic study investigated the molecular basis of interspecies transmission and host range of this lethal virus in Asia, due to its potential pandemic threat. Although there are host markers located in previous research between general avian and human influenza viruses, the novelty of our work was to uncover host markers between highly pathogenic avian and human H5N1 viruses in Asia. Many host markers we found were not present in the previous general markers, thus expanding the current repertoire of host markers with these strain-specific host markers. Ranked by their order of importance, the top 10 host markers discovered in this report were PB2_627, HA_325, NS1_205, PB2_524, HA_86, NA_201, NP_373, NS1_7, HA_156, NA_74, confirming our current knowledge that PB2_627 is the most critical site for distinguishing avian and human H5N1. We also identified several naturally-occurred mutations in the HA protein that might shift the receptor binding preference of Asian avian H5N1, since early detection of mutations that might lead to emergence of a new pandemic virus is of prime importance. Finally, we analyzed the distinctive interaction patterns within and between proteins of avian and human H5N1 in Asia at protein level and individual residue level. From multiple viewpoints, our findings reinforced the experimental observation that multiple genes of Asian avian H5N1 are involved in its gradual adaptation to human hosts....
摘要:Interactions of anionic, cationic and metal phthalocyanine with adenosine deaminase were studied by molecular dynamics and docking simulation. Structural parameters such as solvent accessible surface area (SAS), mid-point of transition temperature (Tm), radial distribution function (RDF) and hydrogen bond, helix, coil, beta percentage and other physical parameters were obtained. The denaturation of adenosine deaminase (ADA) by heat, anionic and cationic phthalocyanines was compared. A series of 20 ns simulation performed at temperatures ranging from 275 to 450 K, starting from the ADA native structure. Results of radial distribution functions (RDFs) showed that metallic derivative at low concentration behaves the same as osmolytes that increases the beta form and increases the enzyme stability. Molecular docking studies have been carried out to confirm the simulation results. Investigation of binding site and free energy confirmed that the efficiency of interaction with adenosine deaminase depends on metal core. Binding energy of non-metallic form is more negative than metallic form and it significantly decreases for phthalocyanine. Self-aggregation of anionic phthalocyanine decreases in comparison with cationic derivative, therefore enzyme denaturation in the presence of anionic form is higher than the other. Furthermore, thermal stability of the enzyme also depends on temperature in presence of phthalocyanine. Binding site of phthalocyanine on the enzyme has been identified by docking analysis....
摘要:The amino acid biosynthesis and proteolytic system of Lactobacillus bulgaricus (L.Bulgaricus ) is important for its growth in niche-specific environments, as well as for flavour formation in the food industry. Comparative analyses of 4 completed sequences of the L.Bulgaricus strain genome on a genomic scale revealed that genes involved in amino acids synthesis were undergoing reductive evolution. However, the selected industrial strains, namely, L.Bulgaricus 2038 and L.Bulgaricus ND02, retained more complete genes in the amino acid synthesis and proteolytic system category than the laboratory strains, and have some unique genes and pathways for obtaining amino acids that enable these bacteria to adapt to their various environmental niches....
摘要:Researchers have been searching for molecular features that could make avian H5N1 influenza transmissible among people since the first report of human infections with this virus in 1997. A recent study surprisingly demonstrated that only five mutations, fewer than previously estimated, are needed to make avian H5N1 influenza transmissible between ferrets through the air, raising fears that a human pandemic is possible if this virus escapes from the lab. Of the five mutations found, four of them are located in the HA gene that is responsible for the viral entry into the host cells. A crucial step for avian influenza to go across the species boundary to infect humans is the switch of its receptor binding specificity from avian to human types. The first task of this study was to quantify the individual as well as the collective effect of the known HA mutations from the previous research on receptor binding selection. Our second task was to identify new combinations of HA mutations that could change the receptor binding preference of H5N1 from avian to human types. Our findings thus deepened our understanding of the previous research and also extended its results by discovering new combinations of mutations that could enhance the binding of avian H5N1 to human type receptors while reduce that to avian types....
摘要:?In recent years, the role of dietary phenolic compounds in the regulation of cellular metabolism in normal and pathological conditions has become increasingly important in cancer research. In most cases, the molecular mechanism of action related to the anticarcinogenic effect of phenolic compounds has been studied in vitro and in animal models, but these studies are still not complete. It is precisely here where in silico approaches can be an invaluable tool for complementing in vitro and in vivo research. In this paper, we adopt a tuple space-based modeling and simulation approach, and show how it can be applied to the simulation of complex interaction patterns of intracellular signaling pathways. Specifically, we are working to explore and to understand the molecular mechanism of action of dietary phenolic compounds on the inhibition of the PI3K/AKT anti-apoptotic pathway. As a first approximation, using the tuple spaces- based in silico approach, we model and simulate the anti-apoptotic PI3K/AKT pathway in the absence and presence of phenolic compounds, in order to determine the effectiveness of our platform, to employ it in future prediction of experimentally non visualized interactions between the pathway components and phenolic compounds....
摘要:A new class of enzyme was established that hydrolyze the ester bond between D-Tyr bound onto its cognate t-RNA. The enzyme is called D-Tyr-tRNA deacylase. The three dimensional structure of the D-Tyr-tRNA deacylase from industrially important microorganism Bacillus lichenformis DSM13 was predicted by comparative modeling approach. Since the protein acts as a dimer a dimeric model of the enzyme was constructed. The interactions responsible for dimerization were also predicted. With the help of docking and molecular dynamics simulations the favourable binding mode of the enzyme was predicted. The probable biochemical mechanism of the hydrolysis process was elucidated. This study provides a rational framework to interpret the molecular mechanistic details of the removal of toxic D-Tyr-tRNA from the cells of industrially important microorganism Bacillus lichenformis DSM13 using the enzyme D-Tyr-tRNA deacylase....
摘要:We analyzed DNA sequences using a new measure of entropy. The general aim was to analyze DNA sequences and find interesting sections of a genome using a new formulation of Shannon like entropy. We developed this new measure of entropy for any non-trivial graph or, more broadly, for any square matrix whose non-zero elements represent probabilistic weights assigned to connections or transitions between pairs of vertices. The new measure is called the graph entropy and it quantifies the aggregate indeterminacy effected by the variety of unique walks that exist between each pair of vertices. The new tool is shown to be uniquely capable of revealing CRISPR regions in bacterial genomes and to identify Tandem repeats and Direct repeats of genome. We have done experiment on 26 species and found many tandem repeats and direct repeats (CRISPR for bacteria or archaea). There are several existing separate CRISPR or Tandem finder tools but our entropy can find both of these features if present in genome....
摘要:Database is a repository of information. In today's world there are different types of databases available. In this present review the focus is on a few popular and most widely used biological databases that store protein sequence and structure information. The databases that are of utmost importance to do basic biological research work are PDB, SCOP, CATH and UniProt/SwissProt and GenBank. These databases have different utilities & they play important roles in different fields of biology and bioinformatics. PDB provides the structural information of proteins, protein-complexes and proteins complexed with other macromolecules. SCOP & CATH store various annotations of protein sequences and structures. UniProt is a central repository of protein sequences & functions created by joining the information contained in SwissProt, TrEMBL....
摘要:A DFT conformational and vibrational analysis of a single molecule of cisplatin (cis-[Pt(NH3)2Cl2]) was performed by means of PW91 functional and LANL08 ECP basis set for the Pt atom. 3-21G and 3-21G* Basis sets were used for the remaining atoms. All the initially chosen conformations were found to converge to the global minimum conformation of C2v symmetry with H atoms lying in the coordination plane and pointing to the Cl atoms. The computational results were compared with the newest experimental structural data and with the vibrational spectroscopic data for cisplatin, obtained by other workers. The chosen level of theory was found to describe satisfactory the molecular structure (r. m. s. of the relative deviations 6%) and the harmonic vibrational frequencies (r. m. s. of the relative deviations 5%) of cisplatin....
摘要:Analyzing gene network structure is an important way to discover and understand some unknown relevant functions and regulatory mechanisms of organism at the molecular level. In this work, mutual information networks and Boolean logic networks are constructed using the methods of reverse modeling based on gene expression profiles in lung tissues with and without cancer. The comparison of these network structures shows that average degree, the proportion of non-isolated nodes, average betweenness and average coreness can distinguish the networks corresponding to the lung tissues with and without cancer. According to the difference of degree, betweenness and coreness of each gene in these networks, nine structural key genes are obtained. Seven of them which are related to lung cancer are supported by literatures. The remaining two genes AKT1 and RBL may have important roles in the formation, development and metastasis of lung cancer. Furthermore, the contrast of these logic networks suggests that the distributions of logic types are obviously different. The structural differences can help us to understand the mechanism of formation and development of lung cancer....
摘要:

HoPLLS (Hierarchy of protein loop-lock structures) (http://leah.haifa.ac.il/~skogan/Apache/mydata1/main.html) is a web server that identifies closed loops-a structural basis for protein domain hierarchy. The server is based on the loop-and-lock theory for structural organisation of natural proteins. We describe this web server, the algorithms for the decomposition of a 3D protein into loops and the results of scientific investigations into a structural “alphabet” of loops and locks.

...
摘要:Short Retraction Notice The paper does not meet the standards of "Computational Molecular Bioscience". This article has been retracted to straighten the academic record. In making this decision the Editorial Board follows COPE's href="http://publicationethics.org/files/retraction%20guidelines.pdf" target="_blank">Retraction Guidelines. The aim is to promote the circulation of scientific research by offering an ideal research publication platform with due consideration of internationally accepted standards on publication ethics. The Editorial Board would like to extend its sincere apologies for any inconvenience this retraction may have caused. Editor guiding this retraction: Dr. Christo Z. Christov (EiC of CMB) The full retraction notice in PDF is preceding the original paper, which is marked "RETRACTED"....
摘要:?The goal of this work is the development of novel peptides with high efficacy of inhibiting activity of CDK6/CyclinD complex. The peptides were derived from primary sequence of P16 protein and its homologues. The interactions between CDK6 and P16/INK4a-derived peptides are studied with molecular dynamics simulation employing umbrella sampling method. The SASA implicit solvent model was used for simulation, which was accelerated using NVIDIA GPUs....
摘要:We build a model of storage of well-defined positional information in probabilistic sequence patterns. Once a pattern is defined, it is possible to judge the effect of any mutation in it. We show that the frequency of beneficial mutations can be high in general and the same mutation can be either advantageous or deleterious depending on the pattern's context. The model allows to treat positional information as a physical quantity, formulate its conservation law and to model its continuous evolution in a whole genome, with meaningful applications of basic physical principles such as optimal efficiency and channel capacity. A plausible example of optimal solution analytically describes phase transitions-like behavior. The model shows that, in principle, it is possible to store error-free information on sequences with arbitrary low conservation. The described theoretical framework allows one to approach from novel general perspectives such long-standing paradoxes as excessive junk DNA in large genomes or the corresponding G- and C-values paradoxes. We also expect it to have an effect on a number of fundamental concepts in population genetics including the neutral theory, cost-of-selection dilemma, error catastrophe and others....
公   告

北京万方数据股份有限公司在天猫、京东开具唯一官方授权的直营店铺:

1、天猫--万方数据教育专营店

2、京东--万方数据官方旗舰店

敬请广大用户关注、支持!查看详情

手机版

万方数据知识服务平台 扫码关注微信公众号

万方选题

学术圈
实名学术社交
订阅
收藏
快速查看收藏过的文献
客服
服务
回到
顶部