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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
Tue Nov 16 2021
Journal Name
Eurasian Chemical Communications
The role of metalloendopeptidase (MEP) as a vital predictor of early diabetic nephropathy and its relationship to some other biochemical variables
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Metalloendo peptidase is a neutral endopeptidase that cleaves peptides at the amino side of hydrophobic residues and inactivates several peptide hormones, including atrial natriuretic factor, giucagon, enkephalin, substance p, neurotensin, oxytocin, and bradykinin. It is also a major enzyme for the degradation of beta-amyloid. This study aimed to measure enzyme activity and compare it with other biochemical changes in sera patients with diabetic nephropathy. The study included 35 pathological samples of people with diabetic nephropathy, 24 samples from males and 11 samples from females, as well as the same number of healthy people as a comparison group of 15 males, 20 females, with the ages of both groups of patients with diabetic nephropat

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Publication Date
Tue Jan 01 2019
Journal Name
Journal Of Global Pharma Technology
Study of the genetic diversity in three species belonging to family: Daphniidae (Crustaceae, Cladocera) collected from different regions in Baghdad Province/Iraq
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Publication Date
Fri Jun 01 2012
Journal Name
Journal Of The College Of Languages (jcl)
A Stylistic Study of English Aphorisms of “Life and Death”
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In this paper , some of lexical stylistic , syntactical stylistic  devices , and one phonetic stylistic device are going to be illustrated in the study of the aphorisms of “life and death” . These stylistic  devices are parallelism , hyperbole , alliteration , meiosis , irony , oxymoron , cliché , litotes , metalepsis , and loose sentences.  This paper aims at identifying the functions and the  frequencies of these devices. These stylistic devices make one speech and writing more interesting and help to get the attention of readers/ listeners

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Publication Date
Sat Jul 22 2023
Journal Name
Journal Of Engineering
Experimental Study of a Biomechanical Behaviour of Rat Patellar Tendon
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Tendon is important structure of the human body, since it can sustain tensile loading. The primary function of this tissue is to stabilize the joints they attached to it during daily activities. As well as, tendon has viscoelastic properties that can determine their response to loading and restrict the potential of injuries. One of the major points that this paper works with is the study of the biomechanical behaviour of tendon in response to tensile loading to describe their biological behaviour. Also, conclude the mathematical expression that may illustrate the tendon behaviour. All of the experiments were made in Physiology laboratories / Medical College/ Al- Nahrain University on ten rats "Rattus Norvegicus" of [108- 360] gm weight f

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Publication Date
Sat Nov 22 2025
Journal Name
Al–bahith Al–a'alami
The Role of Media Coverage of the Iraqi Satellite Channels in Shaping Public Attitudes towards Terrorism (a Field Study of a Sample of an Audience of the City of Baghdad)
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Violence is one of the most serious threats facing societies because it affects their internal structure and threatens the security and stability of society. It is classified as one of the types of security crises that are emerging in Arab and Islamic societies in particular, and in most countries of the world in general.

The threat of this crisis is increasing. Terrorism is considered as one of the most serious aspects of that all the countries of the world, currently, suffer from. The terrorism has begun to penetrate deep into society in one way or another starting from the Second World War, which led to the emergence of leftist movements in Western Europe, Japan, France, Italy and other countries as a result of emerging ideas

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Publication Date
Sat Nov 22 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation of antibacterial action of photosensitizer solution activated by diode lamp and three intracanal medicaments (in vitro study)
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Background: The elimination of the microorganisms from the root canal systems, an important step for the successful root canal treatment. This study was conducted to evaluate the antibacterial effectiveness of the photoactivated disinfection by using the toluidine blue O and a low- energy light emitting diode (LED) lamp . Materials and method: Sixty single rooted extracted teeth were decoronated, instrumented, irrigated, sealed at the apex and contaminated with endodontic anaerobic bacteria for 7 days to form biofilms in prepared root canals. Group I. Twelve teeth were medicated by photosensitizer (toluidine blue O) solution activated by diode lamp (FotoSan; CMS Dental, Copenhagen, Denmark).Group II. Twelve teeth were medicated by the tricr

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Publication Date
Mon Jan 01 2018
Journal Name
The Journal Of Contemporary Dental Practice
Assessment of Ions released from Three Types of Orthodontic Brackets immersed in Different Mouthwashes: An in vitro Study
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Publication Date
Thu May 01 2025
Journal Name
Process Safety And Environmental Protection
Electromembrane extraction of Cadmium (II) using a novel design of electrochemical cell with a flat sheet supported liquid membrane
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Publication Date
Wed Dec 27 2023
Journal Name
Journal Of Planner And Development
The dynamics of the oil industry in shaping land uses: a case study of the Zubair oil field
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The emergence of oil fields and subsequent changes in adjacent land use are known to affect settlements and communities. Everywhere the industry emerges, there is little understanding about the impact of oil fields on land use in the surrounding areas. The oil industry in Iraq is one of the most important industries and is almost the main industry in the Iraqi economic sector, and it is very clear that this industry is spread over large areas, and at the same time adjoins with population communities linked to it developmentally.

The rapid development and expansion of oil extraction activities in various regions has led to many challenges related to land-use planning and management. Here, the problem of research  arises on th

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Publication Date
Tue Dec 01 2015
Journal Name
Journal Of Engineering
Experimental Evaluation Use of Semifluidized Bed Adsorber for the Treatment of P-chlorophenol and O-cresol in Wastewater using Activated Carbon as Adsorbent
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In the present work the performance of semifluidized bed adsorber was evaluated for removal of phenolic compound from wastewater using commercial activated carbon as adsorbent. P-chlorophenol (4-Chlorophenol) and o-cresol (2-methylphenol) was selected as a phenolic compound for that purpose. The phenols percent removal, in term of breakthrough curves were studied as affected by hydrodynamics limitations which include minimum and maximum semifluidization velocities and packed bed formation in the column by varying various parameters such as inlet liquid superficial velocity (from Uminsf to 8Uminsf m/s), and retaining grid (sometimes referred to as adsorbent loading) to initial static bed height ratio (from 3-4.5). In

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