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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 Nov 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
The role of compensation system in improving the quality of educational services (Halabja University as a model)
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          This study deals with the role of compensation system in improving the quality of educational services (University of Halabja as a Model) also our problem was the following question ; What is the role of compensation system in its different dimensions in improving the quality of educational services? And what is the relationship and impact of using the dimensions of the compensation system to improve the quality of educational services? The hypothesis of the research included the correlation and the impacts between the compensation system and its combined variables in the quality of educational services. This was proved through a field study and the distribution of questionn

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Publication Date
Sun Mar 15 2020
Journal Name
Journal Of The College Of Education For Women
The Use of English as Lingua Franca in the Classes of UKM: as A Case of Study
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           English has for long been one of the most widely used media of communication globally, especially in the Malaysian universities. It has been termed as a Lingua Franca because it is shared with other languages which are considered first languages by different speakers. For this reason, English as a Lingua Franca (ELF) has attracted a number of researchers to investigate its variety via other languages in various communities. The objective of this paper is therefore to establish the strategies which are employing by the international students at the National University of Malaysia/ UniversitiKebangsaan Malaysia (UKM) as an example of one of the Malaysian universities; when they e

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Publication Date
Fri Aug 01 2008
Journal Name
2008 First International Conference On The Applications Of Digital Information And Web Technologies (icadiwt)
Hybrid canonical genetic algorithm and steepest descent algorithm for optimizing likelihood estimators of ARMA (1, 1) model
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This paper presents a hybrid genetic algorithm (hGA) for optimizing the maximum likelihood function ln(L(phi(1),theta(1)))of the mixed model ARMA(1,1). The presented hybrid genetic algorithm (hGA) couples two processes: the canonical genetic algorithm (cGA) composed of three main steps: selection, local recombination and mutation, with the local search algorithm represent by steepest descent algorithm (sDA) which is defined by three basic parameters: frequency, probability, and number of local search iterations. The experimental design is based on simulating the cGA, hGA, and sDA algorithms with different values of model parameters, and sample size(n). The study contains comparison among these algorithms depending on MSE value. One can conc

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Publication Date
Wed Jan 01 2025
Journal Name
Lecture Notes In Networks And Systems
Diagnosis of Diabetes Using Artificial Intelligence Programs
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Scientific development has occupied a prominent place in the field of diagnosis, far from traditional procedures. Scientific progress and the development of cities have imposed diseases that have spread due to this development, perhaps the most prominent of which is diabetes for accurate diagnosis without examining blood samples and using image analysis by comparing two images of the affected person for no less than a period. Less than ten years ago they used artificial intelligence programs to analyze and prove the validity of this study by collecting samples of infected people and healthy people using one of the Python program libraries, which is (Open-CV) specialized in measuring changes to the human face, through which we can infer the

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Publication Date
Thu Oct 15 2020
Journal Name
International Journal Of Energy Research
Mixed-ligand complexes of ampicillin derived Schiffbase 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, [ML 1 (L 2 ) 3 ]Cl x [M = Cr(III), Fe(III), Co(II),Ni(II), Cu(II), Cd(II) and Hg(II), n = 2, 3], was synthesized using Schiffbase (HL 1 ) as main ligand, nicotinamide (L 2 ) as secondary ligand, and the corresponding metal ions in 1:3:1 molar ratio. The main ligand, HL 1 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, 1 H-NMR, 13 C-NMR and TG/DTG studies. In the mixed-ligand complexes, the Schiffbase ligand, HL 1 showed coordination to the central metal ion in tridentate manner via azomethine nitrogen, β-lactam ring oxygen and deprotonated carboxylic oxy- gen atom

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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
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
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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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
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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