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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
Sun Dec 01 2019
Journal Name
Al-ustath Journal For Human And Social Sciences
Landscape as History: A Postcolonial Ecopoetic Study of the Poetry of Derek Walcott
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Abstract: As human history is implicated in landscape or the natural history, it can be stated that the origins of the Caribbean writers' conflict, in general, are the colonial history of West India. That history which tells the story behind not only their fragmented identity, but also the problems connected to their language as well. Building on the arguments of the prominent Postcolonial ecoccritics such as Elizabeth DeLoughrey, George Handley, Helen Tiffin, and Graham Huggan, this research analyzes selected poems by Derek Walcott's which are bounded in his volume, Collected Poems. It shows how the Caribbean history has been erased due to the brutality of colonization offering landscape as a reliable source which has recorded that history

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Publication Date
Thu Dec 15 2022
Journal Name
Engineering, Technology & Applied Science Research
Numerical Modeling of a Pile Group Subjected to Seismic Loading Using the Hypoplasticity Model
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Various simple and complicated models have been utilized to simulate the stress-strain behavior of the soil. These models are used in Finite Element Modeling (FEM) for geotechnical engineering applications and analysis of dynamic soil-structure interaction problems. These models either can't adequately describe some features, such as the strain-softening of dense sand, or they require several parameters that are difficult to gather by conventional laboratory testing. Furthermore, soils are not completely linearly elastic and perfectly plastic for the whole range of loads. Soil behavior is quite difficult to comprehend and exhibits a variety of behaviors under various circumstances. As a result, a more realistic constitutive model is

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Publication Date
Thu Dec 15 2022
Journal Name
Engineering, Technology & Applied Science Research (etasr)
Numerical Modeling of a Pile Group Subjected to Seismic Loading Using the Hypoplasticity Model
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Various simple and complicated models have been utilized to simulate the stress-strain behavior of the soil. These models are used in Finite Element Modeling (FEM) for geotechnical engineering applications and analysis of dynamic soil-structure interaction problems. These models either can't adequately describe some features, such as the strain-softening of dense sand, or they require several parameters that are difficult to gather by conventional laboratory testing. Furthermore, soils are not completely linearly elastic and perfectly plastic for the whole range of loads. Soil behavior is quite difficult to comprehend and exhibits a variety of behaviors under various circumstances. As a result, a more realistic constitutive model is

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Publication Date
Tue Sep 28 2021
Journal Name
Journal Of The College Of Education For Women
An Estimated Answer of a Condition between the Interpretive Structure and Surface Structure: Al-Qurtubi’s Tafseer as a Model: عمر عقلة خليف الدعجة
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This present work is concerned with one of the syntactic issues that has been researched by many linguists, grammarians, and specialists in Islamic studies, the estimated answer to a condition. However, this topic is researched this time by examining Imam Al-Qurtbi’s opinions in interpreting related ayas from the holly Quraan in his book (Collector of Quranic Rules) or its transliteration (Al-Jami’ Li Ahkam Al-Quran). Such a step involves commenting on, tracking what Al-Qurtbi said in this regard, discussing it from the points of view of other grammarians, and judging  it accordingly, taking into account the apparent surface structures of the examples collected. To achieve this objective, the inductive analytical approach has be

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Publication Date
Thu Apr 14 2016
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
Study The Effect of α-amylase Inhibitors Isolated from Plant Sources on Some Mold.: Study The Effect of α-amylase Inhibitors Isolated from Plant Sources on Some Mold.
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Activity test of the inhibitors purified from barley and broad beans crop proved the inhibition activity against 6 types of rots Pencillium ssp and Aspergellusflavus and Aspergillus niger and Fusarium solani and Fusarium semitectum and Mucor with three concentrations 0.1 and 0.2 and 0.3 mg/ml, where the inhibitor purified from the second peak of broad beans proved that it had a higher inhibition activity against the growth of test rots which were 53.75 and 62.5 and 78.5 and 76.25 and 84 and 18.8% respectively, at 0.3 mg/ ml followed by the first peak of the inhibitor purified from broad beans the inhibition activity were 43.75 and 50 and 62.96 and 75 and 80 and 12.5 then the inhibitor purified from barley in which the inhibition activity

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Publication Date
Thu Jun 30 2011
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A PARTICULAR SOLUTION OF THE TWO AND THREE DIMENSIONAL TRANSIENT DIFFUSION EQUATIONS
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A particular solution of the two and three dimensional unsteady state thermal or mass diffusion equation is obtained by introducing a combination of variables of the form,
η = (x+y) / √ct , and η = (x+y+z) / √ct, for two and three dimensional equations
respectively. And the corresponding solutions are,
θ (t,x,y) = θ0 erfc (x+y)/√8ct and θ( t,x,y,z) =θ0 erfc (x+y+z/√12ct)

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Publication Date
Thu Jun 04 2020
Journal Name
Fibers
A Comparative Study of the Performance of Slender Reinforced Concrete Columns with Different Cross-Sectional Shapes
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Most reinforced concrete (RC) structures are constructed with square/rectangular columns. The cross-section size of these types of columns is much larger than the thickness of their partitions. Therefore, parts of these columns are protruded out of the partitions. The emergence of columns edges out of the walls has some disadvantages. This limitation is difficult to be overcome with square or rectangular columns. To solve this problem, new types of RC columns called specially shaped reinforced concrete (SSRC) columns have been used as hidden columns. Besides, the use of SSRC columns provides many structural and architectural advantages as compared with rectangular columns. Therefore, this study was conducted to explain the structura

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Publication Date
Tue Feb 04 2020
Journal Name
International Journal Of Psychosocial Rehabilitation
A Comparative Study on the Probability of Diabetes and Psychosocial Deficiency of Badminton Players Youth Category
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Many people believe that diabetes appears after a psychological crisis, which is a misconception but it could be in them before having a crisis ore the crisis. But emotion increases the appearance of symptoms, and athletes are at risk of developing diabetes. Hypoglycemia is not unusual for athletes, and during physical activity the sugar level changes in the blood. Therefore, it is important to conduct tests for the measurement of sugar before and immediately after the activity, for the purpose of detecting the sharp drop in the sugar level and treating it, and the early detection is necessary to avoid the possibility of diabetes, the concept of psychological immunity in psychology is considered a positive concepts that maintain the balance

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Publication Date
Tue Jan 02 2024
Journal Name
Medical Oncology
COX 2-inhibitors; a thorough and updated survey into combinational therapies in cancers
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Publication Date
Wed Jun 18 2025
Journal Name
Al–bahith Al–a'alami
Preferences of the Iraqi Public towards Arab News Channels Programs and Materials (Al Jazeera, Al Arabiya, Al Ekhbariya Satellite Channels: a field Study)
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Broadcasting across satellites has become an important media phenomenon and largely available for watchers. As the receiver can see the events at the very moment and at any spot in the world. This study aims to discover the degree of the extent of exposure of Iraqi people to the news broadcasting satellites in Arabic language, (Al Jazeera, Al Arabiya, Al Ekhbariya Satellite Channels) as one of the media that serves the public; and to discover the range of these Satellite Channels in covering the local Iraqi situation in different sides and aspects; and to know the significance of the Iraqi people in watching those news programmers; and state the motives behind the Iraqi public's dependence on these channels.

The

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