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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 May 30 2024
Journal Name
Iraqi Journal Of Science
Single Nucleotide Polymorphism of Interleukin-28β Subunit Genes Predict Host Susceptibility to Hepatitis C virus (HCV) Infection among Iraqi Patients
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Hepatitis C virus (HCV) is a liver disease that affects14 million people. Feasible research was conducted for identifying the genotypes and allele frequency of some single nucleotide polymorphisms (SNPs) of the IL-28β genes and their predictive role in disease incidence in Iraqi patients. The SNPs (rs28416813, rs4803219, rs11881222, and rs8103142) of IL-28β have been associated with susceptibility to several diseases. Ninety eight (98) HCV patients were included in this research; with average age ± SE (42.28 ± 3.44) years. Also, 80 healthy people (with average age ± SE (29.40 ± 2.84) years) were included as a control group. The SNPs were detected by allele-specific PCR (polymerase chain reaction) using specific primers. The re

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Publication Date
Sat Jul 01 2017
Journal Name
Journal Of Physical Education
Special Exercises According to Refereeing and It's Effect on Developing Some Physical Abilities Of First Class Basketball Referees in Baghdad
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Basketball is one of the most popular and popular games that have a large audience both globally and locally because of the magic it contains in terms of performance. For this sport to be a success, fundamental factors must exist and these factors is the referee. The referee plays a large and important role in the success of the game and the establishment and application of rules.The research aimed at identifying the effect of special on the development of referee's physical abilities. The researcher used the experimental method. The subjects were (12) first class basketball referees. The researcher recommended using special exercises due to their great role in developing the physical abilities of first class basketball referees

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Publication Date
Wed Aug 10 2016
Journal Name
Fourth International Conference On Genetics And Scientific Environment. Cairo / Arab Republic Of Egypt For The Period From July 23 To 30
Efficacy of Arbuscular mycorrhiza (AM) in inducing non-enzymatic antioxidants in tomato leaves infected with Fusarium oxysporum f. sp. Lycopersici.
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Publication Date
Fri Nov 01 2024
Journal Name
Heliyon
Strength and Deformation of Encased Concrete Columns by I- Section Steel and I- Section GFRP Subjected to Different Load Conditions
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Publication Date
Mon Jul 01 2024
Journal Name
Journal Of Food Process Engineering
Artificial intelligence‐based modeling of novel non‐thermal milk pasteurization to achieve desirable color and predict quality parameters during storage
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Abstract<sec><label></label><p>This study proposed using color components as artificial intelligence (AI) input to predict milk moisture and fat contents. In this sense, an adaptive neuro‐fuzzy inference system (ANFIS) was applied to milk processed by moderate electrical field‐based non‐thermal (NP) and conventional pasteurization (CP). The differences between predicted and experimental data were not significant (<italic>p</italic> > 0.05) for lightness (<italic>L</italic>*), redness‐greenness (<italic>a</italic>*), yellowness‐blueness (<italic>b</italic>*), total color differences (∆<italic>E</italic>), hue angle (<italic>h</italic></p></sec> ... Show More
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Publication Date
Sat Apr 01 2023
Journal Name
Iop Conference Series: Earth And Environmental Science
Effect of Irrigation Systems, Bio-Fertilizers and Polymers on some Growth Characteristics and Potato Production in Desert Soils, Karbala Governorate
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Two field experiments were conducted during the spring season 2020 in Karbala governorate to study the effect of irrigation systems, irrigation intervals, biofertilizers and polymers on some characteristics of vegetative growth and potato production. The results showed that there were significant differences in the values of the average plant height due to the effect of the double interference between the irrigation system and the improvers, The height of potato plant under any irrigation system was superior when adding conditioners compared to the control treatment, as it reached 48.56, 58.00 and 64.33cm when adding polymer, biofertilizer, and polymers+ biofertilizers, respectively compared with the control treatment of 44.64cm in the surf

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Publication Date
Sat Aug 05 2017
Journal Name
Oriental Journal Of Chemistry
Adsorption of 4-Chlorophenol from Aqueous Solution onto Iraqi Bauxite and Surfactant–modified Iraqi Bauxite: Equilibrium, Kinetic, and Thermodynamic Studies
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Natural Bauxite (BXT) mineral clay was modified with a cationic surfactant (hexadecy ltrimethy lammonium bromide (BXT-HDTMA)) and characterized with different techniques: FTIR spectroscopy, X-ray powder diffraction (XRD) and scanning electron microscopy (SEM). The modified and natural bauxite (BXT) were used as adsorbents for the adsorption of 4- Chlorophenol (4-CP) from aqueous solutions. The adsorption study was carried out at different conditions and parameters: contact time, pH value, adsorbent dosage and ionic strength. The adsorption kinetic (described by a pseudo-first order and a pseudo-second order), equilibrium experimental data (analyzed by Langmuir, Freundlich and Temkin isotherm models) and thermodynamic parameters (change in s

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Publication Date
Mon Jan 01 2024
Journal Name
Clinical Laboratory
Histopathological Tracing of HPV Genotypes 6 and 11 in Pediatric Patients in Medical City with Chronic Palatine and Pharyngeal Tonsillitis
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Publication Date
Sun Jan 02 2022
Journal Name
Journal Of The College Of Languages (jcl)
Pragmatics and Speech Act- History, Importance and Stages of Development: הפרגמטיקה ופעולת־הדיבור- התולדות, החשיבות ושלבי ההתפתחות (יישמוים בלשון העברית)
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      The present study stresses two of the most significant aspects of linguistic approach: Pragmatics” and the “Speech Act Theory”, revealing its importance and the stages and levels of development through Hebrew language’s speech acts analysis including (political speech, the Holy Bible, Hebrew stories).

       Chronologically, Pragmatics has always been the center of linguists’ interests due to its importance in linguistic decryptions, particularly, through “Speech Act Theory” that has been initiated and developed by the most prominent philosophers and linguistics.

        The prese

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Publication Date
Fri Jan 01 2010
Journal Name
Diala, Journal
Synthesis and characterization of ( L- proline ) amino acid with (Mn+2 , Fe+2 , Co+2 , Zn+2 and Cd+2 )
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