FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithm

The accurate prediction of protein–ligand binding is of great importance for rational drug design. We present herein a novel docking algorithm called as FIPSDock, which implements a variant of the Fully Informed Particle Swarm (FIPS) optimization method and adopts the newly developed energy function of AutoDock 4.20 suite for solving flexible protein–ligand docking problems. The search ability and docking accuracy of FIPSDock were first evaluated by multiple cognate docking experiments. In a benchmarking test for 77 protein/ligand complex structures derived from GOLD benchmark set, FIPSDock has obtained a successful predicting rate of 93.5% and outperformed a few docking programs including particle swarm optimization (PSO)@AutoDock, SODOCK, AutoDock, DOCK, Glide, GOLD, FlexX, Surflex, and MolDock. More importantly, FIPSDock was evaluated against PSO@AutoDock, SODOCK, and AutoDock 4.20 suite by cross‐docking experiments of 74 protein–ligand complexes among eight protein targets (CDK2, ESR1, F2, MAPK14, MMP8, MMP13, PDE4B, and PDE5A) derived from Sutherland‐crossdock‐set. Remarkably, FIPSDock is superior to PSO@AutoDock, SODOCK, and AutoDock in seven out of eight cross‐docking experiments. The results reveal that FIPS algorithm might be more suitable than the conventional genetic algorithm‐based algorithms in dealing with highly flexible docking problems. © 2012 Wiley Periodicals, Inc.     

Two‐dimensional replica‐exchange method for predicting protein–ligand binding structures

We have developed a two‐dimensional replica‐exchange method for the prediction of protein–ligand binding structures. The first dimension is the umbrella sampling along the reaction coordinate, which is the distance between a protein binding pocket and a ligand. The second dimension is the solute tempering, in which the interaction between a ligand and a protein and water is weakened. The second dimension is introduced to make a ligand follow the umbrella potential more easily and enhance the binding events, which should improve the sampling efficiency. As test cases, we applied our method to two protein‐ligand complex systems (MDM2 and HSP 90‐alpha). Starting from the configuration in which the protein and the ligand are far away from each other in each system, our method predicted the ligand binding structures in excellent agreement with the experimental data from Protein Data Bank much faster with the improved sampling efficiency than the replica‐exchange umbrella sampling method that we have previously developed. © 2013 Wiley Periodicals, Inc.     

Free‐energy differences between states with different conformational ensembles

Multiple conformations separated by high‐energy barriers represent a challenging problem in free‐energy calculations due to the difficulties in achieving adequate sampling. We present an application of thermodynamic integration (TI) in conjunction with the local elevation umbrella sampling (LE/US) method to improve convergence in alchemical free‐energy calculations. TI‐LE/US was applied to the guanosine triphosphate (GTP) to 8‐Br‐GTP perturbation, molecules that present high‐energy barriers between the anti and syn states and that have inverted preferences for those states. The convergence and reliability of TI‐LE/US was assessed by comparing with previous results using the enhanced‐sampling one‐step perturbation (OSP) method. A linear interpolation of the end‐state biasing potentials was sufficient to dramatically improve sampling along the chosen reaction coordinate. Conformational free‐energy differences were also computed for the syn and anti states and compared to experimental and theoretical results. Additionally, a coupled OSP with LE/US was carried out, allowing the calculation of conformational and alchemical free energies of GTP and 8‐substituted GTP analogs. © 2013 Wiley Periodicals, Inc.     

The Use of Various Chromatographic Techniques for the Determination of Phenylurea Herbicides and Their Corresponding Anilines in Environmental Samples,II. Applications

Abstract

In earlier work, various strategies have been developed for the trace-level determination of phenylurea herbicides and the anilines which are their main degradation products. They include catalytic hydrolysis of the phenylureas on silica, liquid chromatographic fractionation of complex mixtures of herbicides and anilines, derivatization of anilines and herbicides with electron-capture-sensitive reagents, and final analysis by means of capillary gas chromatography. In the present paper, the application of these principles to trace-level analysis of surface water, soil and crop samples is demonstrated.     

Application of the Combustion Method in a Closed Flask to the Lead Determination in Atmospheric Aerosols

Abstract

The destruction of the filter for metal determination in atmospheric aerosols is an important step in the analysis. Nowadays the decomposition of this kind of sample has not been completely solved, so it is interesting to study new methods for filter sample attack. In the present work the application of the combustion method in a closed flask for mixed cellulose esters filter decomposition for lead determination is proposed. For this purpose optimum operating conditions as stopper flask design, sample size, flask volume, shaking time and volume and concentration of absorbing solution are established, and accuracy and precision of the proposed method using AAS for the measurements is given. The results obtained by the closed flask combustion are compared with those found by wet attack with HNO₃. The method proposed is rapid, has low reagent contamination and no loss of lead by volatilization or by amalgamation occurs. This method shows an accuracy and a precision in good agreement with the standard method.     

Determination of zinc in marine/lacustrine sediments by graphite furnace atomic absorption spectrometry using Pd/Mg chemical modifier and slurry sampling

Effectiveness of Pd/Mg chemical modifier for the accurate direct determination of zinc in marine/lacustrine sediments by graphite furnace atomic absorption spectrometry (GF-AAS) using slurry samples was evaluated. A calibration curve prepared by aqueous zinc standard solution with addition of Pd/Mg chemical modifier is used to determine the zinc concentration in the sediment. The accuracy of the proposed method was confirmed using Certified Reference Materials, NMIJ CRM 7303-a (lacustrine sediment) from National Metrology Institute of Japan, National Institute of Advanced Industrial Science and Technology, Japan, and MESS-3 (marine sediment) and PACS-2 (marine sediment) from National Research Council, Canada. The analytical results obtained by employing Pd/Mg modifier are in good agreement with the certified values of all the reference sediment materials. Although for NRC MESS-3 an accurate determination of zinc is achieved even without the chemical modifier, the use of Pd/Mg chemical modifier is recommended as it leads to establishment of a reliable and accurate direct analytical method. One quantitative analysis takes less than 15 minutes after we obtain dried sediment samples, which is several tens of times faster than conventional analytical methods using acid digested sample solutions. The detection limits are 0.13?µg?g^?1 (213.9?nm) and 16?µg?g^?1 (307.6?nm), respectively, in sediment samples, when 40?mg of dried powdered samples are suspended in 20?mL of 0.1?mol?L^?1 nitric acid and a 10?µl portion of the slurry sample is measured. The precision of the proposed method is 8–15% (RSD).     

Volatile organic compounds in an urban environment: a comparison among Belgium,Vietnam and Ethiopia

The effects of urban and indoor air pollution on human health are a major environmental concern for all, but not much has been researched in the developing world. Specifically, quantitative data on the occurrence of volatile organic compounds (VOCs) – main contributors to air pollution – in Asia and Africa are scarce compared to the availability of data in the developed world. This paper presents one of the first studies focusing on the analysis and occurrence of VOCs in Vietnam and Ethiopia, which constitutes part of the novelty of this work. A spectrum of 34 VOCs was measured at eight different urban sites in Ghent (Belgium), Hanoi (Vietnam), Jimma and Addis Ababa (Ethiopia) during three sampling campaigns from September 2008 to September 2010. Sampling was done in an active way by means of sorbent tubes filled with Tenax TA. The analysis was done by TD-GC-MS using internal standard calibration. Data were interpreted and compared in terms of (i) individual, subgroup and total VOCs concentration (TVOCs), (ii) indoor-to-outdoor (I/O) concentration ratios, (iii) source identification by diagnostic ratio and/or correlation coefficients, and (iv) ozone formation potential (OFP) at outdoor sites based on up-to-date maximum incremental reactivity (MIR). I/O concentration ratios varied between 0.2 and 30, with big differences noticed with respect to the type of VOC(s) considered and the type of outdoor sampling location. The highest TVOC concentrations were measured in street samples with maximum values of 54?µg/m³ in Ghent, 507?µg/m³ in Hanoi and 318?µg/m³ in Addis Ababa illustrating the large difference in ambient air quality levels. This is also reflected in the arithmetic mean OFP values (µg/m³) of 82, 1308 and 596 in Ghent, Hanoi and Addis Ababa, respectively. Results of this study could be helpful to support formulation of national policy with regard to ambient air quality.     

基于HMM的机载设备状态健康评估方法研究

针对机载设备的状态健康评估问题,采用隐马尔科夫模型(HMM)对其进行性能退化程度的评估。首先引入状态条件概率矢量对HMM进行不确定性改进,并推导了其表达式;其次以状态条件概率比值为基础,给出了机载设备状态等级量化分值的计算方法,并据此设计了机载设备状态健康评估流程。最后以飞机发动机温控放大器为例进行仿真验证,结果表明上述方法能够给出直观、准确的状态评估结果。     

Fitting formula for the injection volume of a gas chromatograph for radio‐xenon sampling in the lower troposphere

GC is usually used for xenon concentration and radon removal in the International Monitoring System of the Comprehensive Nuclear‐Test‐Ban Treaty. In a gas chromatograph, the injection volume is defined to calculate the column capacity. In this paper, the injection volume was investigated and a fitting formula for the injection volume was derived and discussed subsequently. As a consequence, the xenon injection volume exponentially decreased with the column temperature increased, but exponentially increased as the flow rate increased.     

Optimization of sampling frequency for routine river water quality monitoring

Sampling frequency is an important factor to be considered during the design of a water monitoring network,and the cost-effective selection of possible ways and means for the optimization of sampling frequency is still needed.This paper introduces water pollution index deviation ratio comparison(WPI DRC),a procedure for the optimization of sampling frequency for a routine river water quality monitoring system.Sampling frequency optimized using WPI DRC at monitoring station X5 in the mainstream of Xiangjiang River is compared with that established using the traditional Statistical Algorithm method.The result of comparison indicates that WPI DRC is more feasible than the traditional one.And then,the sampling frequencies for other 16 monitoring stations also have been optimized,and the results show the sampling frequencies of all the stations except that X4 are reduced,and there is no unacceptable difference between water quality evaluation results at 17 stations before and after the optimization.Therefore,it is concluded that WPI DRC is an effective optimization process with operable results,which can be used to fulfill the requirement of practical monitoring work.