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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
Wed Oct 02 2024
Journal Name
International Development Planning Review
COMPARISON OF THE PERFORMANCE OF THE FOREHANDKICK (STRAIGHT AND ACCOMPANIED BY FORWARD ROTATION) IN TERMS OF ACCURACY AND SPEED AMONG THE PLAYERS OF THE NATIONAL TEAM (ADVANCED CATEGORY) IN TENNIS
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Publication Date
Fri Jan 21 2022
Journal Name
International Journal Of Research In Social Sciences And Humanities
Managing Trading Decisions Using The True Strength Index –An Applied Study
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The purpose of this research is to test the ability of the true strength index To time and manage trading in the financial market to select the best stocks and achieve a higher return than the Simple buy and hold strategy. And To achieve the objectives of the research, it relied on the main hypothesis, which is By using the True Strength Index to manage trading decisions buying and selling, can be achieved higher returns than the buy and hold strategy . The research community has been identified with all stocks listed on the Iraq Stock Exchange. Implementing the financial research tests requires selecting a sample from the research community that fulfills the test requirements according to a number of conditions So (38) companies we

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Publication Date
Sun Oct 02 2016
Journal Name
Journal Of Educational And Psychological Researches
The Effect Of Flexible Grouping Strategy And Three Step Interview Strategy On Achievement Of The History Material Among Student Of The First Intermediate Class
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  The research aims to know The Effect Of Flexible Grouping Strategy  and Three Step Interview strategy on achievement of the history material among student of the first literary class, The Researcher used the experimental design of the two experimental groups and the control group and with post test, researcher group (a) represent the experimental group taught according the Flexible Grouping Strategy  , and Division (c) to represent the second experimental group which studied according Three Step Interview strategy and Division (b ) to represent the control group taught in the traditional method, the number of students (99) students of (33) female students in each division. T

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Publication Date
Tue Jun 01 2021
Journal Name
Minar International Journal Of Applied Sciences And Technology
STRUCTURAL AND ELECTRICAL PROPERTIES OF (CDO)1-X (V2O5)X PREPARED BY PULSE LASER DEPOSITION TECHNIQUE FOR SOLAR CELL APPLICATIONS
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In this work ,pure and doped(CdO)thin films with different concentration of V2O5x (0.0, 0.05, 0.1 ) wt.% have been prepared on glass substrate at room temperature using Pulse Laser Deposition technique(PLD).The focused Nd:YAG laser beam at 800 mJ with a frequency second radiation at 1064 nm (pulse width 9 ns) repetition frequency (6 Hz), for 500 laser pulses incident on the target surface At first ,The pellets of (CdO)1-x(V2O5)x at different V2O5 contents were sintered to a temperature of 773K for one hours.Then films of (CdO)1-x(V2O5)x have been prepared.The structure of the thin films was examined by using (XRD) analysis..Hall effect has been measured in orded to know the type of conductivity, Finally the solar cell and the effici

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Publication Date
Tue Jun 01 2021
Journal Name
Journal Of Optical Communications
Improving the optical link for UVLC using MIMO technique
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Abstract<p>This paper proposed a theoretical treatment to study underwater wireless optical communications (UWOC) system with different modulation schemes by multiple input-multiple output (MIMO) technology in coastal water. MIMO technology provides high-speed data rates with longer distance link. This technique employed to assess the system by BER, Q. factor and data rate under coastal water types. The reliability of the system is examined by the techniques of 1Tx/1Rx, 2Tx/2Rx, 3Tx/3Rx and 4Tx/4Rx. The results shows the proposed technique by MIMO can get the better performance compared with the other techniques in terms of BER. Theoretical results were obtained to compare between PIN and APD </p> ... Show More
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Publication Date
Fri Mar 06 2026
Journal Name
Tanmiat Al-rafidain
The Effect of the Strategic Lens in Enhancing Organizational Immunity: An Analytical Study of the Opinions of A Sample of Administrative Leaders in Some Private Banks in Baghdad
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Publication Date
Sat Apr 02 2022
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The structure of capital and its impact on the profitability of companies : is an analytical study of a sample of industrial companies listed on the Iraqi Stock Exchange
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This study aimed to know the impact of the capital structure measured by the ratio of financing to short-term capital and the ratio of financing to long-term capital on the profitability of companies, as measured by the rate of return on assets and the rate of return on equity. The study was applied to industrial sector companies listed in the Iraq Stock Exchange. The financial number of (14) companies, and (4) companies were selected that met the conditions for selecting the study sample. The study methodology relies on the analytical method as it is more appropriate to the nature, scope and objectives of the study, and the ready-made statistical program "SPSS" will be used to analyze the relationships and influence between the

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Publication Date
Thu Mar 30 2023
Journal Name
College Of Islamic Sciences
Ethics (stop harming, guarding the tongue, spreading peace and spending) in the hadiths of the Prophet, book (Faith) from Sahih Al-Bukhari / model - analytical study: : Ethics of restraining harm in the hadiths of the Prophet "Analytical study"
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(Social values) are of great importance in the lives of nations and peoples as they are the frame of reference that governs the relations of members of society to each other and regulates their life affairs.

And the Prophet of Islam (may God’s prayers and peace be upon him) has told about a group of (social values) such as: spreading peace, feeding food, being fair in dealing with others, and clarifying what a Muslim should have towards his Muslim brother from the safety of the chest and refraining from harming him with the tongue and hand, and so on. Ethics and behaviors that are directly and closely related to (social values).

The best book that abounds with these (social valu

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Publication Date
Wed Mar 01 2017
Journal Name
جامعة كرميان
The effect of a training program for chemistry teachers based on the strategy of both sides of the brain together on the thinking patterns of their students
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Publication Date
Mon Dec 25 2023
Journal Name
Optical Materials
Impact of a precise pH value change on the characteristics of deposited tin monosulphide films onto a flexible substrate
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The chemical bath deposition technique (CBD) is considered the cheapest and easiest compared with other deposition techniques. However, it is highly sensitive to effective parameter deposition values such as pH, temperature, and so on. The pH value of the reaction solution has a direct impact on both the nucleation and growth rate of the film. Consequently, this study presents a novel investigation into the effect of a precise change. in the pH reaction solution value on the structural, morphological, and photoresponse characteristics of tin monosulphide (SnS) films. The films were grown on a flexible polyester substrate with pH values of 7.1, 7.4, and 7.7. The X-ray diffraction patterns of the grown films at pH 7.1 and 7.4 confirmed

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