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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 Sep 02 2014
Journal Name
Arab J Sci Eng
Modeling of Trichloroethylene Migration in Three-Dimensional Saturated Sandy Soil
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Publication Date
Fri Sep 15 2023
Journal Name
Sumer 2
Response of Three Citrus Rootstocks to Organic and Biological Fertilizers
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This study was conducted in a lath house, Dept of Hort. and Landscape, College of Agricultural Engineering Sciences, Univ. During the 2021 growing season, Baghdad will investigate the influence of organic and Biological fertilizers on three Citrus rootstocks' growth and leaf mineral content. The first factor is the addition of liquid organic fertilizers Vit-Org (O) at three levels without addition (O0), soil addition at 10 ml.L-1 (O10) and soil addition at 20 ml.L-1 (O20). The second factor is the addition of nitrogen-fixing bacteria without addition (N1), add 30 ml.Transplant-1 of Azotobacter chroococcum (N2) and add 30 ml.Transplant-1 of Azospirillum brasilemse (N3). The third factor is three citrus rootstocks: sour orange (R1), R

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Publication Date
Tue Dec 30 2014
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Performance Evaluation of Three Phase Spray Direct Contact Heat Exchanger
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The present investigation deals with experimental study of three-phase direct-contact heat exchanger, for water-Freon R11 system, where water is the continuous phase (liquid) and Freon R11 (liquid-gas) is the dispersed phase. The test section consisted of a cylindrical Perspex column with inner diameter 8cm and 1.2m long, in which, water was to be confined. Liquid Freon R11 drops were injected into the hot water filled column, through a special design of distributors at the bottom of the column. The liquid Freon R11 drops rose on their way up and evaporated into two-phase bubbles at atmospheric pressure. The study was devoted to express the effect of process variables such as c

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Publication Date
Sun Mar 01 2020
Journal Name
Journal Of Engineering
Three-Dimensional Explicit Finite Element Simulation of Piled-Raft Foundation
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This paper aims to validate a proposed finite element model to be adopted in predicting displacement and soil stresses of a piled-raft foundation. The proposed model adopts the solid element to simulate the raft, piles, and soil mass. An explicit integration scheme has been used to simulate nonlinear static aspects of the piled-raft foundation and to avoid the computational difficulties associated with the implicit finite element analysis.

The validation process is based on comparing the results of the proposed finite element model with those of a scaled-down experimental work achieved by other researchers. Centrifuge apparatus has been used in the experimental work to generate the required stresses to simulate t

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Publication Date
Wed Feb 01 2023
Journal Name
Baghdad Science Journal
Antibacterial Activity of Three Algal Genera against some Pathogenic Bacteria
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In the current study, three types of algae namely Tetradesmus nygaardi (MZ801740), Scenedesmus quadricauda (MZ801741) and Coelastrella sp (MZ801742) were extracted by 95% ethanol and hexane against two types of gram positive and two types of gram negative bacteria by wells diffusion methods. Eleven concentrations from the extract of algae (2, 5, 10, 15, 20, 25, 30, 35, 40, 45 and 50 mg/ml) were utilized. It was noticed that ethanolic extraction was more effective than hexane in Scenedesmus quadricauda than the two other mentioned algal species against all pathogenic bacteria, Acintobacter baumanii (ATCC: 19606), Klebsiella pneumonia (ATCC: 13883) Enterococcus faecalis (ATCC: 29212) and Staphylococc

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Publication Date
Sun Jun 04 2017
Journal Name
Baghdad Science Journal
Effect of Ferocene Concentration on the Percent Conversion and Molecular Weight of Poly(Methyl Methacrylate) Homopolymers
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This research is addressing the effect of different ferrocene concentration (0.00, 2.15x10-3, 4.30x10-3, 8.60x10-3, and 12.9x10-3) on the bulk free radical polymerization of methyl methacrylate monomer in benzene using benzoyl peroxide as initiator. The polymerization was conducted at 60º C under free oxygen atmosphere. The resulting polymers were characterized by FTIR. The results were compared with the presence and absence of ferrocene at 10% conversion. The %conversion was 3.04% with no ferrocene present in the polymerization medium and its increase to 9.06 with a first lowest ferrocene concentration added, i.e. 2.15 x10-3mol/l. This was positively reflected on the poly(methyl methacrylate) molecular weight measured by viscosity techniq

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Publication Date
Sun Jul 17 2022
Journal Name
Al–bahith Al–a'alami
The Pocessing of Extremism’s Manifestations in the T.V Talk Shows : A Paper Extracted from A Masters Thesis
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This study aims to know how and what is the media processing presented by the television talk shows for the religious extremism topics in terms of topics, hosted personalities, and ways to address this global phenomenon.

The study is based on descriptive research, and the researcher used the analytical-survey method, analyzing the episodes of (Awkar Al Dhalam) T.V Show which was presented on Al-Iraqiya News Channel, and (Islam Hur) T.V Show which was presented on Al-Hurra in 2019 with 25 episodes from each Show, The sample and research community was chosen with the intent to cover the research problem and its

The study reached several conclusions, including:

  • The various dialogs in the episo

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Publication Date
Sat Nov 03 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
A study of Addictive Inpatients at Ibn-Rushd Psychiatric Teaching Hospital in Baghdad
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Objective :.
1-Find out the prevalence of alcohol and drugs addiction in two different years before and after the last
war i.e. in 2002 and in 200. 2-Study the association between the addiction
and some variables. 3-Identify the prescribed drugs and other substances that
have been abused
Methodology : A retrospective study has been conducted involving the in-patients at addiction unit-IbnRushd
psychiatric hospital in Baghdad by applying the semi-structured form based on ICD-10 criteria
of addiction and dependency with the confirmation of the specialist psychiatrist diagnosis of
dependency. Data concerning each patient admitted in the hospital was gathered to have an idea about
the problem of addiction (drugs an

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Publication Date
Tue Mar 31 2020
Journal Name
College Of Islamic Sciences
Ruling on conducting a marriage contract through modern means of communication Juristic study
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This research dealt with highlighting the images of marriage through the modern means of communication and the legal ruling for it. Dowry even be knotted on them; because they are then one of the parties to the contract and contracted in one contract, and this is prohibited by law and law and common sense.

It turns out that it is permissible to advertise marriage through the Internet in accordance with the rules and standards that preserve values ​​and morals and safeguard dignity and chastity. The acts in Islamic law are vested with intentions. If intentions are true, then the act is true, and Internet marriage is what falls under this order.<

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Publication Date
Sun Dec 30 2012
Journal Name
Al-kindy College Medical Journal
A typical clinical presentation of molluscum contagiosum in Iraqi patients;clinical descriptive study
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Background Molluscum contagiosum is skin disease caused by the molluscum contagiosum virus (MCV) usually causing one or more small dome shaped umbilicated papules with symptoms that maybe self-resolve. MCV was once a disease primarily of children, but it has evolved to become a sexually transmitted disease in adults. It is believed to be a member of the pox virus family. In addition to the classic presentation of the disease; it can also come in different clinical forms that simulate large number of dermatolological disease.
Objective: To study different clinical forms of Molluscum contagiosum presentation in different age groups of Iraqi patients.
Method:This clinical descriptive study was performed in the outpatient department of

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