Computational Design of Novel Allosteric Inhibitors for Plasmodium falciparum DegP

The serine protease, DegP exhibits proteolytic and chaperone activities, essential for cellular protein quality control and normal cell development in eukaryotes. The P. falciparum DegP is essential for the parasite survival and required to combat the oscillating thermal stress conditions during the infection, protein quality checks and protein homeostasis in the extra-cytoplasmic compartments, thereby establishing it as a potential target for drug development against malaria. Previous studies have shown that diisopropyl fluorophosphate (DFP) and the peptide SPMFKGV inhibit E. coli DegP protease activity. To identify novel potential inhibitors specific to PfDegP allosteric and the catalytic binding sites, we performed a high throughput in silico screening using Malaria Box, Pathogen Box, Maybridge library, ChEMBL library and the library of FDA approved compounds. The screening helped identify five best binders that showed high affinity to PfDegP allosteric (T0873, T2823, T2801, {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, CD00811) and the catalytic binding site (T0078L, T1524, T2328, BTB11534 and 552691). Further, molecular dynamics simulation analysis revealed {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, BTB11534 as the best hits forming a stable complex. WaterMap and electrostatic complementarity were used to evaluate the novel bio-isosteric chemotypes of {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, that led to the identification of 231 chemotypes that exhibited better binding affinity. Further analysis of the top 5 chemotypes, based on better binding affinity, revealed that the addition of electron donors like nitrogen and sulphur to the side chains of butanoate group are more favoured than the backbone of butanoate group. In a nutshell, the present study helps identify novel, potent and Plasmodium specific inhibitors, using high throughput in silico screening and bio-isosteric replacement, which may be experimentally validated.     

Current air quality analytics and monitoring: A review

This review summarizes the different tools and concepts that are commonly applied in air quality monitoring. The monitoring of atmosphere is extremely important as the air quality is an important problem for large communities. Main requirements for analytical devices used for monitoring include a long period of autonomic operation and portability. These instruments, however, are often characterized by poor analytical performance. Monitoring networks are the most common tools used for monitoring, so large-scale monitoring programmes are summarized here. Biomonitoring, as a cheap and convenient alternative to traditional sample collection, is becoming more and more popular, although its main drawback is the lack of standard procedures. Telemonitoring is another approach to air monitoring, which offers some interesting opportunities, such as ease of coverage of large or remote areas, constituting a complementary approach to traditional strategies; however, it requires huge costs.     

多小波子空间上的单小波表示

本文在较弱的条件下,建立了2重多小波子空间与单小波子空间的关系.即由2重多小波构造出单小波.一方面,这种单小波的平移伸缩与2重多小波的平移伸缩生成的子空间是完全相同的;另一方面,它具有插值性.因此通过构造出的单小波建立了多小波子空间上的Shannon型采样定理.     

Sets of sampling and interpolation in Bergman spaces

Properties of the unions of sampling and interpolation sets for Bergman spaces are discussed in conjunction with the examples given by Seip (1993). Their relationship to the classical interpolation sequences is explored. In addition, the role played by canonical divisors in the study of these sets is examined and an example of a sampling set is constructed in the disk.

     

一种改进的计算探测器校正因子的相关抽样方法

对于小尺寸探测器处于大块介质的情形, 在探测器的校正因子的Monte Carlo模拟中, 存在两个难题: 一是由于探测器尺寸很小粒子难以到达探测器并发生碰撞; 二是两个随机变量比值难以达到要求精度. 本文使用经过改进的粒子碰撞自动重要抽样方法, 再结合相关抽样方法, 解决了这两个难题, 并在MCNP-4C程序平台上加以实现. 除了粒子碰撞自动重要抽样以外, 还选用了其他3种方法: 直接模拟、区域分裂、强迫碰撞+Dxtran球分别与相关抽样方法结合, 对一个简化的探测器校正因子计算模型进行了计算. 实际计算结果表明, 相关抽样方法无论与哪种方法结合, 都起到了提高相关量计算效率的作用; 而它与粒子碰撞自动重要抽样结合, 比其他方法具有明显的优越性.     

Comment on “The Free Will Theorem”

In a recent paper Conway and Kochen, Found. Phys. 36, 2006, claim to have established that theories of the Ghirardi-Rimini-Weber (RW) type, i.e., of spontaneous wave function collapse, cannot be made relativistic. On the other hand, relativistic GRW-type theories have already been presented, in my recent paper, J. Stat. Phys. 125, 2006, and by Dowker and Henson, J. Stat. Phys. 115, 2004. Here, I elucidate why these are not excluded by the arguments of Conway and Kochen.      

Neutral Community Theory: How Stochasticity and Dispersal-Limitation Can Explain Species Coexistence

Neutral community theory explains biodiversity, i.e. the coexistence of several species, as the result of a stochastic balance between immigration and extinction on a local level, and between speciation and extinction on a regional level. The most popular model, presented by Hubbell in 2001, has seen many analytical developments in recent years, which can be used in model analysis, model testing and model comparison. We review these developments here, and present alternative derivations and shine previously unnoticed lights on them.     

The spectrum of BSA(v, 3, λ; α) with α = 2,3

In this article, a kind of auxiliary design BSA^* for constructing BSAs is introduced and studied. Two powerful recursive constructions on BSAs from 3‐IGDDs and BSA^*s are exploited. Finally, the necessary and sufficient conditions for the existence of a BSA(v, 3, λ; α) with α = 2, 3 are established. © 2006 Wiley Periodicals, Inc. J Combin Designs 15: 61–76, 2007     

Estimating tail probabilities of heavy tailed distributions with asymptotically zero relative error

Efficient estimation of tail probabilities involving heavy tailed random variables is amongst the most challenging problems in Monte-Carlo simulation. In the last few years, applied probabilists have achieved considerable success in developing efficient algorithms for some such simple but fundamental tail probabilities. Usually, unbiased importance sampling estimators of such tail probabilities are developed and it is proved that these estimators are asymptotically efficient or even possess the desirable bounded relative error property. In this paper, as an illustration, we consider a simple tail probability involving geometric sums of heavy tailed random variables. This is useful in estimating the probability of large delays in M/G/1 queues. In this setting we develop an unbiased estimator whose relative error decreases to zero asymptotically. The key idea is to decompose the probability of interest into a known dominant component and an unknown small component. Simulation then focuses on estimating the latter ‘residual’ probability. Here we show that the existing conditioning methods or importance sampling methods are not effective in estimating the residual probability while an appropriate combination of the two estimates it with bounded relative error. As a further illustration of the proposed ideas, we apply them to develop an estimator for the probability of large delays in stochastic activity networks that has an asymptotically zero relative error.      

Dual frames in connected with generalized sampling in shift-invariant spaces

The aim of this article is to derive stable generalized sampling in a shift-invariant space by using some special dual frames in L²(0,1). These sampling formulas involve samples of filtered versions of the functions in the shift-invariant space. The involved samples are expressed as the frame coefficients of an appropriate function in L²(0,1) with respect to some particular frame in L²(0,1). Since any shift-invariant space with stable generator is the image of L²(0,1) by means of a bounded invertible operator, our generalized sampling is derived from some dual frame expansions in L²(0,1).