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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
Mon Apr 01 2019
Journal Name
Journal Of Engineering
Removal of Methyl Orange from Aqueous Solutions by Adsorption Using Corn Leaves as Adsorbent Material
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A comparative study was done on the adsorption of methyl orange dye (MO) using non-activated and activated corn leaves with hydrochloric acid as an adsorbent material. Scanning electron microscopy (SEM) and Fourier Transform Infrared spectroscopy (FTIR) were utilized to specify the properties of adsorbent material. The effect of several variables (pH, initial dye concentration, temperature, amount of adsorbent and contact time) on the removal efficiency was studied and the results indicated that the adsorption efficiency increases with the increase in the concentration of dye, adsorbent dosage and contact time, while inversely proportional to the increase in pH and temperature for both the treated and untreated corn leav

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Publication Date
Mon Apr 01 2019
Journal Name
Journal Of Engineering
Removal of Methyl Orange from Aqueous Solutions by Adsorption Using Corn Leaves as Adsorbent Material
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A comparative study was done on the adsorption of methyl orange dye (MO) using non-activated and activated corn leaves with hydrochloric acid as an adsorbent material. Scanning electron microscopy (SEM) and Fourier Transform Infrared spectroscopy (FTIR) were utilized to specify the properties of adsorbent material. The effect of several variables (pH, initial dye concentration, temperature, amount of adsorbent and contact time) on the removal efficiency was studied and the results indicated that the adsorption efficiency increases with the increase in the concentration of dye, adsorbent dosage and contact time, while inversely proportional to the increase in pH and temperature for both the treated and untreated corn leaves. The equi

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Publication Date
Tue Nov 25 2025
Journal Name
Journal Of Physical Education
The Effect of Constructive Learning Model on Cognitive Achievement and Learning dribbling Skill in Soccer for Secondary School Students
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The research aimed at identifying the effect of using constructive learning model on academic achievement and learning soccer dribbling Skill in 2nd grade secondary school students. The researcher used the experimental method on (30) secondary school students; 10 selected for pilot study, 20 were divided into two groups. The experimental group followed constructive learning model while the controlling group followed the traditional method. The experimental program lasted for eight weeks with two teaching sessions per week for each group. The data was collected and treated using SPSS to conclude the positive effect of using constructive learning model on developing academic achievement and learning soccer dribbling Skill in 2nd grade seconda

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Publication Date
Sun Mar 01 2009
Journal Name
Journal Of Economics And Administrative Sciences
Calculate the sum of squares for parts (vehicles) SSE in 2n global trials with total integration In a suggested manne
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In order to serve the field of knowledge in the field of design and analysis of experiments by adopting formulas and methods that are easy and simple in arithmetic work, especially in experiments that require many calculations for squares, including tests of type
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Publication Date
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
Evaluation for the Effect of Heat Stable Enterotoxin (a) Produced by Enterotoxigenic Escherichia coli on Different Cancer Cells In Vitro
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This study was conducted for evaluating the cytotoxic effect of heat stable enterotoxin a (STa) produced by enterotoxigenic Escherichia coli on the proliferation of primary cancer cell cultures, obtained from tumor samples that were collected from (13) cancer patients and as follows: (five colon cancer patients, two bladder cancer patients, two breast cancer patients, two stomach cancer patients and two lung cancer patients), and on normal cell line (rat embryonic fibroblast / REF) (in vitro) with the use of different concentrations starting from (1) mg/ml and ending with (0.0002) mg/ml by making two fold serial dilutions by using the 96- well microtiter plate, and in comparison with negative (PBS) and positive (MMC, at concentration

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Publication Date
Fri Jul 14 2023
Journal Name
International Journal Of Information Technology & Decision Making
A Decision Modeling Approach for Data Acquisition Systems of the Vehicle Industry Based on Interval-Valued Linear Diophantine Fuzzy Set
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Modeling data acquisition systems (DASs) can support the vehicle industry in the development and design of sophisticated driver assistance systems. Modeling DASs on the basis of multiple criteria is considered as a multicriteria decision-making (MCDM) problem. Although literature reviews have provided models for DASs, the issue of imprecise, unclear, and ambiguous information remains unresolved. Compared with existing MCDM methods, the robustness of the fuzzy decision by opinion score method II (FDOSM II) and fuzzy weighted with zero inconsistency II (FWZIC II) is demonstrated for modeling the DASs. However, these methods are implemented in an intuitionistic fuzzy set environment that restricts the ability of experts to provide mem

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Publication Date
Tue Jan 29 2019
Journal Name
Journal Of The College Of Education For Women
Impact Media to take off and when the special gifts in Baghdad for a period of 555-656h / 1160-1258
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The dislocation and gifts at special is the aspect of social life they reflect us how rich and influential class of society, a special category of the ruling category of the caliph and his family and his ministers and his generals and senior statesmen, a powerful and wealth and power and study here dealing with the effect the media for the distribution of dislocations and gifts to the special category both internally and for employers the state and its men or externally represented foreign relations with princes in the state and the regions and include the definition of the concepts above with surrounding contents and events distributed as the some of which were distributed in certain occasions fixed times while others did not have a spe

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Publication Date
Thu Jul 01 2021
Journal Name
University Of Northampton Pue
Validating a Proposed Data Mining Approach (SLDM) for Motion Wearable Sensors to Detect the Early Signs of Lameness in Sheep
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Publication Date
Wed Jan 01 2020
Journal Name
Proceedings Of The 2020 2nd International Conference On Sustainable Manufacturing, Materials And Technologies
The impact of toxicant on the food chain ecological model
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Publication Date
Sun Sep 04 2016
Journal Name
Baghdad Science Journal
Comparative Study of Grains, Flours and Baking Quality of Wheat Cultivar (Uruq) with Other Wheat Cultivars (Triticumaestivum L.) in Iraq
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The grain hardness, wet and dry gluten contents, protein and ash contents are determined in grains from different cultivars of wheat which are important in food products, either which are present in raw materials or in final products. Wheat is also a very important food raw material, and flour as the final product of milling. The importance of knowing the physical and chemical properties of wheat and flour is due to the determination of quality and kind of flour which is produced after the milling process. In this work, some physical and chemical properties of different wheat cultivars are determined and the comparisons of these characteristics are performed in both wheat and flour. Uruq Wheat sample (W5) has the highest results when compar

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