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A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
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Flexible molecular docking is a computational method of structure-based drug design to evaluate binding interactions between receptor and ligand and identify the ligand conformation within the receptor pocket. Currently, various molecular docking programs are extensively applied; therefore, realizing accuracy and performance of the various docking programs could have a significant value. In this comparative study, the performance and accuracy of three widely used non-commercial docking software (AutoDock Vina, 1-Click Docking, and UCSF DOCK) was evaluated through investigations of the predicted binding affinity and binding conformation of the same set of small molecules (HIV-1 protease inhibitors) and a protein target HIV-1 protease enzyme. The tested sets are composed of eight receptor-ligand complexes with high resolution crystal structures downloaded from Protein Data Bank website. Molecular dockings were applied between approved HIV-1 protease inhibitors and the HIV-1 protease using AutoDock Vina, 1-Click Docking, and DOCK6. Then, docking poses of the top-ranked solution was realized using UCSF Chimera. Furthermore, Pearson correlation coefficient (r) and coefficient of determination (r2) between the experimental results and the top scored docking results of each program were calculated using Graphpad prism V9.2. After comparing saquinavir top scored binding poses of each docking program with the crystal structure, various conformational changes were observed. Moreover, according to the relative comparison between the top ranked calculated ?Gbinding values against the experimental results, r2 value of AutoDock Vina, 1-Click Docking, and DOCK6 were 0.65, 0.41, and 0.005, respectively. The outcome of this study shows that the top scored binding free energy could not produce the best pose prediction. In addition, AutoDock Vina results have the highest correlation with the experimental results.

 

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Publication Date
Thu Apr 01 2021
Journal Name
Iop Conference Series: Earth And Environmental Science
Groundwater Quality Study Based on the Existence of Escherichia coli as Bioindicator
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Abstract<p>The research aim was to observe the distribution pattern of <italic>Escherichia coli</italic> as groundwater pollution indicator in the most populous area, Matraman Sub-District Area in Jakarta, Indonesia (106°49’35” EL and 06°10’37” SL) consists of six (6) Urban Villages. The existence of <italic>Escherichia coli</italic> was measured with Most Probable Number (MPN) method as mentioned in Indonesian Standard Number 01-2332.1-2006. This research was also measure pollution parameter of Dissolved Oxygen (DO) and pH, and topography analyses used as well to determine groundwater flow direction. Groundwater sampling was conducted in several housings that have </p> ... Show More
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Publication Date
Thu May 01 2025
Journal Name
Process Safety And Environmental Protection
Electromembrane extraction of Cadmium (II) using a novel design of electrochemical cell with a flat sheet supported liquid membrane
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Publication Date
Mon Sep 13 2021
Journal Name
Eureka: Physics And Engineering
A numerical study to improve the position and angle of the producer gas injector inside the intake manifold to minimize emissions and efficiency enhancement of a bi engine
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To develop a petrol engine so that it works under the bi-engine pattern (producer gas-petrol) without any additional engine modifications, a single-point injection method inside the intake manifold is a simple and inexpensive method. Still, it leads to poor mixing performance between the air and producer gas. This deficiency can cause unsatisfactory engine performance and high exhaust emissions. In order to improve the mixing inside the intake manifold, nine separate cases were modelled to evaluate the impact of the position and angle orientation inside the intake manifold on the uniformity and spread of the mixture under AFR=2.07. A petrol engine (1.6 L), the maximum engine speed (8000 rpm), and bi-engine mode (petrol-producer ga

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Publication Date
Tue Oct 01 2019
Journal Name
Biochem. Cell. Arch
MORPHOLOGICAL COMPARATIVE STUDY OF THE STOMACH IN THE FELIS CATUS (DOMESTIC CAT) AND SCIURUS CAROLINESIS (EASTERN GRAY SQURRIEL)
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Publication Date
Thu Jun 28 2018
Journal Name
2018 4th International Conference On Computer And Technology Applications (iccta)
Improving accuracy of CADx system by hybrid PCA and backpropagation
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—Medical images have recently played a significant role in the diagnosis and detection of various diseases. Medical imaging can provide a means of direct visualization to observe through the human body and notice the small anatomical change and biological processes associated by different biological and physical parameters. To achieve a more accurate and reliable diagnosis, nowadays, varieties of computer aided detection (CAD) and computer-aided diagnosis (CADx) approaches have been established to help interpretation of the medical images. The CAD has become among the many major research subjects in diagnostic radiology and medical imaging. In this work we study the improvement in accuracy of detection of CAD system when comb

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Publication Date
Thu Dec 01 2011
Journal Name
Iraqi Journal Of Physics
Design of Achromatic Combined Quadrupole Lens Using the Modified Bell-Shaped Field Distribution Model
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The optimization calculations are made to find the optimum properties of combined quadrupole lens consist of electrostatic and magnetic lenses to produce achromatic lens. The modified bell-shaped model is used and the calculation is made by solving the equation of motion and finding the transfer matrices in convergence and divergence planes, these matrices are used to find the properties of lens as the magnification and aberrations coefficients. To find the optimum values of chromatic and spherical aberrations coefficients, the effect of both the excitation parameter of the lens (n) and the effective length of the lens into account as effective parameters in the optimization processing

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Publication Date
Sat Jul 22 2023
Journal Name
Journal Of Engineering
Experimental Study of a Biomechanical Behaviour of Rat Patellar Tendon
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Tendon is important structure of the human body, since it can sustain tensile loading. The primary function of this tissue is to stabilize the joints they attached to it during daily activities. As well as, tendon has viscoelastic properties that can determine their response to loading and restrict the potential of injuries. One of the major points that this paper works with is the study of the biomechanical behaviour of tendon in response to tensile loading to describe their biological behaviour. Also, conclude the mathematical expression that may illustrate the tendon behaviour. All of the experiments were made in Physiology laboratories / Medical College/ Al- Nahrain University on ten rats "Rattus Norvegicus" of [108- 360] gm weight f

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Publication Date
Fri Jun 01 2012
Journal Name
Journal Of The College Of Languages (jcl)
A Stylistic Study of English Aphorisms of “Life and Death”
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In this paper , some of lexical stylistic , syntactical stylistic  devices , and one phonetic stylistic device are going to be illustrated in the study of the aphorisms of “life and death” . These stylistic  devices are parallelism , hyperbole , alliteration , meiosis , irony , oxymoron , cliché , litotes , metalepsis , and loose sentences.  This paper aims at identifying the functions and the  frequencies of these devices. These stylistic devices make one speech and writing more interesting and help to get the attention of readers/ listeners

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Publication Date
Wed Mar 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
The Influence of Organizational Power on the Achievement of Entrepreneurship for Business Organizations An Analytical Study of the Views of a Sample of Managers in the Iraqi Ministry of Education
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This research aims to study the influence of organizational power on the achievement of entrepreneurship for business organizations. It is an analytical study of the views of a sample of managers in the Iraqi Ministry of Education. The research highlights the contribution that can be made from the knowledge of the theory of business organizations in achieving organizational success. The organizational power of the organization contributes to achieving entrepreneurship in the business environment and achieving a competitive position in the work environment. The research dealt with two variables: the first is the independent variable, the organizational power in its dimensions (Expend Power, Structural Power, Prestige Power). And t

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Publication Date
Tue Nov 16 2021
Journal Name
Eurasian Chemical Communications
The role of metalloendopeptidase (MEP) as a vital predictor of early diabetic nephropathy and its relationship to some other biochemical variables
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Metalloendo peptidase is a neutral endopeptidase that cleaves peptides at the amino side of hydrophobic residues and inactivates several peptide hormones, including atrial natriuretic factor, giucagon, enkephalin, substance p, neurotensin, oxytocin, and bradykinin. It is also a major enzyme for the degradation of beta-amyloid. This study aimed to measure enzyme activity and compare it with other biochemical changes in sera patients with diabetic nephropathy. The study included 35 pathological samples of people with diabetic nephropathy, 24 samples from males and 11 samples from females, as well as the same number of healthy people as a comparison group of 15 males, 20 females, with the ages of both groups of patients with diabetic nephropat

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