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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
Fri Sep 01 2023
Journal Name
Journal Of Molecular Structure
Synthesis, spectral studies, DFT, biological evaluation, molecular docking and dyeing performance of 1-(4-((2-amino-5-methoxy)diazenyl)phenyl) ethanone complexes with some metallic ions
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Publication Date
Fri Sep 01 2023
Journal Name
Journal Of Molecular Structure
Synthesis, spectral studies, DFT, biological evaluation, molecular docking and dyeing performance of 1-(4-((2-amino-5-methoxy)diazenyl)phenyl) ethanone complexes with some metallic ions
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Four Co(II), (C1); Ni(II), (C2); Cu(II), (C3) and Zn(II), (C4) chelates have been synthesized with 1-(4-((2-amino- 5‑methoxy)diazenyl)phenyl)ethanone ligand (L). The produced compounds have been identified by using spectral studies, elemental analysis (C.H.N.O), conductivity and magnetic properties. The produced metal chelates were studied using molar ratio as well as sequences contrast types. Rate of concentration (1 ×10􀀀 4 - 3 ×10􀀀 4 Mol/L) sequence Beer’s law. Compound solutions have been noticed height molar absorptivity. The free of ligand and metal chelates had been applied as disperse dyes on cotton fabrics. Furthermore, the antibacterial activity of the produced compounds against various bacteria had been investigated. F

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Scopus (50)
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Publication Date
Fri May 05 2023
Journal Name
Journal Of Molecular Structure
Synthesis, spectral studies, DFT, biological evaluation, molecular docking and dyeing performance of 1-(4-((2-amino-5-methoxy)diazenyl)phenyl) ethanone complexes with some metallic ions
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Four Co(II), (C1); Ni(II), (C2); Cu(II), (C3) and Zn(II), (C4) chelates have been synthesized with 1-(4-((2-amino- 5‑methoxy)diazenyl)phenyl)ethanone ligand (L). The produced compounds have been identified by using spectral studies, elemental analysis (C.H.N.O), conductivity and magnetic properties. The produced metal chelates were studied using molar ratio as well as sequences contrast types. Rate of concentration (1 ×10􀀀 4 - 3 ×10􀀀 4 Mol/L) sequence Beer’s law. Compound solutions have been noticed height molar absorptivity. The free of ligand and metal chelates had been applied as disperse dyes on cotton fabrics. Furthermore, the antibacterial activity of the produced compounds against various bacteria had been investigated. F

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Publication Date
Sat Sep 23 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
A Study of using Mesocyclops hyalinus and Cyclops agilis as A biological Control of Anophles larvae
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The fresh water ecosystem constitute an essential and very important for human life, for this reason it should be kept away from all the chemical pollutants including the pesticides The best way for Fighting harmful insects.(such as Anophles larvae) is by the biological control.

 

In the present study two species of Cyclopoida: Copepod, Mesocyclops hyalinus and Cyclops agilis Ø¢ were used as predators for Anophles larvae.

 

The data showed that the percentages of predation were 65% and 56%

forM. hyalinus and C. agilis respectively

 

and the means of predation were 1.3 larvae/ female and 1.1

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Publication Date
Sat Jul 01 2023
Journal Name
Heliyon
Effect of plasma surface treatment of three different CAD/CAM materials on the micro shear bond strength with resin cement (A comparative in vitro study)
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Objectives: This study aimed to evaluate and compare the effect of plasma treatment versus conventional treatment on the micro shear bond strength (μSBS), surface roughness, and wettability of three different CAD/CAM materials. Materials and methods: Sixty cylindrical specimens (5 mm diameter ×3 mm height) were prepared from three different CAD/CAM materials: Group A: Zirconia, Group B: Lithium disilicate, and Group C: Resin nano-ceramic. Each group was subdivided into two subgroups according to surface treatment used: Subgroup I: Conventional treatment, zirconia was sandblasted with Al2O3, while lithium disilicate and resin nano-ceramic were etched with hydrofluoric acid. Subgroup II: Plasma treatment, the surface of each material was tr

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Publication Date
Tue Jun 10 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Immunohistochemical expression of ICAM-1 and Cortactin as cell adhesive molecule and invasive markers in Hodgkin’s and non-Hodgkin’s lymphoma of the head and neck region (A comparative study)
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Background: Lymphomas are a group of diseases caused by malignant lymphocytes that accumulate in lymph nodes and cause the characteristic clinical features of lymphadenopathy. Intercellular adhesion molecule-1 (ICAM-1) (CD54) is a transmembrane glycoprotein belonging to the immunoglobulin superfamily of adhesion molecules. Cortactin was first identified as one of the major substrates for src kinase. because it localized to Cortical actin structures, The aims of this study was to evaluate and compare the immunohistochemical of ICAM-1 expression as cell adhesion molecule marker and Cortactin expression as invasive marker. Material and Methods: This study was performed on (68) formalin-fixed, paraffin-embedded blocks, histopathologically diagn

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Publication Date
Tue Jun 10 2025
Journal Name
Journal Of Physical Education
A Comparative Study According to Angiotensin Genetic Diversity As Indicator for 30m Freestyle Swimming in Youth aged (15 – 16) Year Old
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Publication Date
Wed Jun 01 2016
Journal Name
Journal Of Engineering
Accuracy Evaluation of Digital Elevation Model Created Using Handheld Global Positioning System Receivers
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This study aims to assess the accuracy of digital elevation model (DEM) created with utilization of handheld Global Positioning System (GPS) and comparing with Advanced Spaceborne Thermal Emission and Reflection Radiometer Global Digital Elevation Model (ASTER GDEM), version 2. It is known that the quality of the DEM is affected by both of accuracy of elevation at each pixel (absolute accuracy) and accuracy of presented morphology (relative accuracy). The University of Baghdad, Al Jadriya campus was selected as a study area to create and analysis the resulting DEM. Additionally, Geographic Information System (GIS) was used to visualize, analyses and interpolate GPS track points (elevation data) of the study area. In this

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Publication Date
Sun Dec 31 2017
Journal Name
College Of Islamic Sciences
Stylistic phenomena in the Quranic referral: (Pronouns of backbiting as a model)
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Research summary

Backbiting pronouns have gained great importance in contemporary textual linguistic studies, as they play a coordinating function in the text and link its parts.

Interpreters did not overlook the role of backbiting pronouns in achieving the function of consistency and coherence in the Qur’anic text, as they referred to this, including Ibn Ashour, who had many analytical practices related to referral issues and their complexities. The Qur'anic reference to the pronouns of backbiting, so the researcher traced these phenomena and their evidence in the Holy Qur'an, aiming to clarify their role in enriching the significance and in the coherence and harmony

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Publication Date
Tue Jun 01 2021
Journal Name
Political Sciences Journal
The European Union and the Extremist Right Phenomenon: Brexit as a Model
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The European Unit has never been affected by a serious phenomena as the phenomena of the advancing of the far right parties. Though these parties vary in their impact in their original countries, they agree on one important issue which is the deconstruction of the European unit and limiting its supernational powers. These increasing popular parties aim at more national independence in decision making away from the decisions taken by Brussels. Moreover, they criticize the financial and administrative corruption accompanied many of the rescuing procedures directed for example towards countries like Greece and Spain during the international economic crisis. This failure nourishes many of the negative feelings against the European unit which

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