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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 Dec 31 2020
Journal Name
Political Sciences Journal
Effects of international variables on the principle of citizenship in Arab countries: "Kuwait as a Model"
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The principle of citizenship has international dimensions that affect the application of the principle, such as the structure of the international system, and the control of the concepts of globalization, international organizations which played an important role in the consolidation of this principle.

The problem of the study revolves around the effects of international variables on the principle of citizenship in Kuwait during the period 1991-2018.

The study used several indicators, such as: the rule of law, achieving the principle of separation of powers, the right to form parties, the application of the law of nationality, and racial discrimination, women's rights, and freedom of expression.

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Publication Date
Wed Oct 02 2024
Journal Name
International Development Planning Review
A COMPARATIVE STUDY OF THE AMOUNT OF FORCE EXERTED ON THE GROUND AND THE TIME OF PROPULSION IN THE VERTICAL AND HORIZONTAL JUMPING TESTS FROM STABILITY USING A FOOT SCAN DEVICE
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Publication Date
Sat May 16 2009
Journal Name
Journal Of Planner And Development
Support environmental programs using knowledge management
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The research deals with Environmental Management and how to develop its programs with the use of Knowledge Management, the environmental programs that integrate with processes can add strategic value to business through improving rates of resource utilization , efficiencies , reduce waste, use risk management, cut costs, avoid fines and reduce insurance. All these activities and processes can improve it through knowledge management, the optimal usage for all organizations information , employ it in high value and share it among all organizations members who involves in modify its strategy . Choosing suitable environmental management information system, develop it and modify it with organization processes, can greatly serve the en

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Publication Date
Thu Apr 01 2021
Journal Name
Journal Of Molecular Structure
Mixed-ligand complexes of ampicillin derived Schiff base ligand and Nicotinamide: Synthesis, physico-chemical studies, DFT calculation, antibacterial study and molecular docking analysis
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A novel series of mixed-ligand complexes of the type, [ML1(L2)3]Clx [M= Cr(III), Fe(III), Co(II),Ni(II), Cu(II), Cd(II) and Hg(II), n = 2, 3], was synthesized using Schiff base (HL1) as main ligand, nicotinamide (L2) as secondary ligand, and the corresponding metal ions in 1:3:1 molar ratio. The main ligand, HL1 was prepared by the interaction of ampicillin drug and 4-chlorobenzophenone. The synthesized mixed ligand complexes were characterized by elemental analysis, UV-Vis, FT-IR,1H-NMR,13C-NMR and TG/DTG studies. In the mixed-ligand complexes, the Schiff base ligand, HL1 showed coordination to the central metal ion in tridentate manner via azomethine nitrogen, β-lactam ring oxygen and deprotonated carboxylic oxygen atoms, whereas the sec

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Publication Date
Fri Feb 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
A Comparison of Parameters Estimation Methods for the Negative Binomial Regression Model under Multicollinearity Problem by Using Simulation
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This study discussed a biased estimator of the Negative Binomial Regression model known as (Liu Estimator), This estimate was used to reduce variance and overcome the problem Multicollinearity between explanatory variables, Some estimates were used such as Ridge Regression and Maximum Likelihood Estimators, This research aims at the theoretical comparisons between the new estimator (Liu Estimator) and the estimators

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Publication Date
Tue Nov 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Using Public and Private Cloud Computing in developing the Evaluation System of annual employees' performance at Iraqi Universities: A comparative study
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Abstract

Business organizations are using the technological innovations like cloud computing (CC) as a developmental platform in order to improve the performance of their information systems. In that context, our paper discusses know-how in employing the public and private CC to serve as platforms to develop the evaluation system of annual employees' performance (ESAEP) at Iraqi universities. Therefore, we ask the paper question which is Is it possible to adopt the innovative solutions of ICTs (Like: public and private CC) for finding the developmental vision about management information systems at business organizations?”. In addition, the paper aim

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Publication Date
Tue Oct 01 2024
Journal Name
Journal Of Engineering Science And Technology
NUMERICAL SIMULATION OF SHEET PILES AS A SEEPAGE CUTTER OFF: AL-KIFIL REGULATOR AS A CASE STUDY
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Sheet piles are necessary with hydraulic structures as seepage cut-off to reduce the seepage. In this research, the computational work methodology was followed by building a numerical model using Geo-Studio program to check the efficiency of using concrete sheet piles as a cut-off or reducer for seepage with time if the sheet piles facing the drawdown technique. Al-Kifil regulator was chosen as a case study, an accurate model was built with a help of observed reading of the measuring devices, which was satisfactory and helped in checking the sheet piles efficiency. Through the study, three scenarios were adopted (with and without) drawdown technique, it was found that at the short time there's no effect of the drawdown technique on

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Scopus
Publication Date
Tue Dec 12 2017
Journal Name
Al-khwarizmi Engineering Journal
Design a Vegetative Filter Strips Length Using VFSMOD_W Model for Reducing Sediments and Pesticides
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 Abstract 

The vegetative filter strips (VFS) are a useful tool used for reducing the movement of sediment and pesticide in therivers. The filter strip’s soil can help in reducing the runoff volume by infiltration. However, the characteristics of VFS (i.e., length) are not recently identified depending on the estimation of VFS modeling performance. The aim of this research is to study these characteristics and determine acorrelation between filter strip length and percent reduction (trapping efficiency) for sediment, water, and pesticide. Two proposed pesticides(one has organic carbon sorption coefficient, Koc, of 147 L/kg which is more moveable than XXXX, and another one

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Publication Date
Fri Dec 31 2010
Journal Name
Journal Of Legal Sciences
The Moment of Contract Formation under the United Nations Convention on Contracts for the International Sale of Goods (1980) – A Comparative Study
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There are two ways that the contract might be formed with (contracting between persons who are attended and contracting between absence persons).the need for determining the precise moment of the contract , is so clear because there is a specify period separate between the declaration of acceptance and the knowledge with it .and it is clear from the four theories known for jurisprudence (theory of the declaration of the acceptance, theory of exporting the acceptance , theory of the arrival of the acceptance , theory of the knowledge with the acceptance ) . It is difficult to promote one theory on another one if we look at each one and the justification of its supporters and what the opponents of each theory expose. Legal background and diff

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Publication Date
Sun Jun 30 2019
Journal Name
Journal Of The College Of Education For Women
Common Origin of Languages: A Comparative Study between the Holy Quran and the Heavenly Religions
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This research is a new reading of some of the words in the Holy Quran, which is very old. It is a human reading in which religions are intertwined by recognizing the relationship between man and his fellow man in the unity of existence and the unity of the source of religions and the unity of language. The importance of this research in comparing some of the Arabic words has been contained among books believed by followers that it is from the one God Sunday.

When words are spoken in one way in the form of one creature, from the beginning of creation to the present day, this indicates the single origin of the languages..

The research tools were books of heavenly religions, the Quran, dictionaries and interpretations.

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