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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
Sat Feb 02 2019
Journal Name
Journal Of The College Of Education For Women
Meaning of Added Verbs A New Approach: Meaning of Added Verbs A New Approach
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Summary
The subject ( meaning of added verbs) is one of the main subjects
which study in morphology since in Arabic language. It is include the meaning
of each format, and the increased meaning occurred by this increment in the
verbs.
The (strain) is one of very important meaning in this subject, it takes a
wide area of morphology studies, and interesting of scientists and
researchists.
There are two famous formats for this meaning; (infa la انفع
ل ), and (ifta
la افتع
ل ). Also There are another formats for the same meaning, but less than
the first two in use, they are; (taf ala تفعّ
ل ), (tafa ala تفاع
ل ), (taf lala ) ,(تفعل
ل
ifanlala افعنلل ), (ifanla .(

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Publication Date
Wed Dec 01 2010
Journal Name
Iraqi Journal Of Physics
An Improved Method for the Determination of Airplane Radial Velocity Using Doppler Shift
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In this research velocity of moving airplane from its recorded digital sound is introduced. The data of sound file is sliced into several frames using overlapping partitions. Then the array of each frame is transformed from time domain to frequency domain using Fourier Transform (FT). To determine the characteristic frequency of the sound, a moving window mechanics is used, the size of that window is made linearly proportional with the value of the tracked frequency. This proportionality is due to the existing linear relationship between the frequency and its Doppler shift. An algorithm was introduced to select the characteristic frequencies, this algorithm allocates the frequencies which satisfy the Doppler relation, beside that the tra

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Publication Date
Sat Oct 08 2022
Journal Name
Journal Of Computational Design And Engineering
Twisted-fin parametric study to enhance the solidification performance of phase-change material in a shell-and-tube latent heat thermal energy storage system
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Abstract<p>Phase change material (PCM) is considered as one of the most effective thermal energy storage (TES) systems to balance energy supply and demand. A key challenge in designing efficient PCM-based TES systems lies in the enhancement of heat transmission during phase transition. This study numerically examines the privilege of employing twisted-fin arrays inside a shell-and-tube latent heat storage unit to improve the solidification performance. The presence of twisted fins contributes to the dominating role of heat conduction by their curved shapes, which restricts the role of natural convection but largely aids the overall heat-transfer process during solidification. The heat-discharge </p> ... Show More
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Publication Date
Fri Dec 01 2017
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Job enrichment, knowledge capital and its impact on strategic success: exploratory study at a sample of the Iraqi government and Private Colleges on Baghdad
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The problem of research was the lack of research that dealt with issue of the job design approach that is more suitable for knowledge work, therefore, the research aims to determine the impact of job enrichment,  and knowledge capitalon strategic success, starting from the hypothesis that there significant impact of job enrichment and knowledge capital on strategic success, to achieve this goal the researchers from the theoretical literature and  related studies conclude to the construction of the scheme shows the hypothetical relationship between the variables, which was adopted job enrichment as independent variable while knowledge capital plays two roles, the first as an independent variable and the second as an intermediate

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Publication Date
Fri Mar 01 2019
Journal Name
Al-khwarizmi Engineering Journal
Comparison Study of Electromyography Using Wavelet and Neural Network
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In this paper we present a method to analyze five types with fifteen wavelet families for eighteen different EMG signals. A comparison study is also given to show performance of various families after modifying the results with back propagation Neural Network. This is actually will help the researchers with the first step of EMG analysis. Huge sets of results (more than 100 sets) are proposed and then classified to be discussed and reach the final.

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Publication Date
Sun Dec 15 2019
Journal Name
Al-academy
Artistic Integration of Aesthetic Manifestations in the Andalusian Islamic Style into the Interior Architecture (Mansour Laalaj's Door / Meknes a Case Study): شهريار عبد القادر محمود -سعد جرجيس
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The Islamic architectural heritage constitutes a civilized fortune that has to be preserved and protected and work should be done to maintain its development to be more convenient for the circumstances of the age and the civilization transformations. Due to the fact that architecture represents the civilization pot and cultural identity, its originality has to be preserved and work has to be done to prevent the strange architectural invasion that changes its character and make it lose the identity and the character and detached from its roots and environment.    

Decoration, in the interior design, as a concept is connected to ornamentation process of interior spaces, which is a process of adding certain items

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Publication Date
Wed Mar 18 2020
Journal Name
Baghdad Science Journal
Synthesis of Six and Seven-membered Heterocyclic Molecules Containing an Adamantyl Fragment and an X-ray Crystal Structure of (E)-N-(adamantan-1-yl)-1-(3-nitrophenyl)methanimine
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       Our work included a synthesis of three new imine derivatives—1,3-thiazinan-4-one, 1,3-oxazinan-6-one and 1,3-oxazepin-4,7-dione—which contained an adamantyl fragment. These were produced via the condensation of the Schiff`s base (E)-N-(adamantan-1-yl)-1-(3-aryl)methanimine with 3-mercaptopropanoic acid; 3-chloropropanoic acid; and maleic, citraconic anhydride, respectively. These new imines were prepared via the condensation of adamantan-1-ylamine and 3-nitro-, 3-bromobenzaldehyde in n-BuOH. We obtained a good yield of products. FTIR, 1H NMR spectroscopy and C.H.N.S analysis were used to diagnostic the products. The molecular structure of (E)-N-(adamantan-1-yl

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Publication Date
Sun Mar 03 2013
Journal Name
Baghdad Science Journal
Study the effects of bromothymol blue material on the optical properties for polystyrene (PS).
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Films of pure polystyrene (ps) and doped by bromothymol blue material with percentages(4%) prepared by using casting technique in room temperature , the absorption and transmission spectra has been recorded in the wavelength rang (200-900)nm and calculated refractive index , reflectivity, real and imaginary parts of dielectric constant and extinction coefficient . this study has been done by recording the absorption and transmission spectra by using spectrophotometer .

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Publication Date
Tue Dec 01 2020
Journal Name
Baghdad Science Journal
A Modified Support Vector Machine Classifiers Using Stochastic Gradient Descent with Application to Leukemia Cancer Type Dataset
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Support vector machines (SVMs) are supervised learning models that analyze data for classification or regression. For classification, SVM is widely used by selecting an optimal hyperplane that separates two classes. SVM has very good accuracy and extremally robust comparing with some other classification methods such as logistics linear regression, random forest, k-nearest neighbor and naïve model. However, working with large datasets can cause many problems such as time-consuming and inefficient results. In this paper, the SVM has been modified by using a stochastic Gradient descent process. The modified method, stochastic gradient descent SVM (SGD-SVM), checked by using two simulation datasets. Since the classification of different ca

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Publication Date
Wed Feb 01 2023
Journal Name
Chemical Engineering Research And Design
Nickel removal from simulated wastewater using a novel bio-electrochemical cell with packed bed rotating cylinder cathode
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