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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
Wed Aug 31 2022
Journal Name
Al-kindy College Medical Journal
Assessment of Awareness And Knowledge among Medical Students Regarding Radiation Exposure from Common Diagnostic Imaging Procedures: Radiation exposure awareness among medical students
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Objective: to assess the awareness and knowledge of our medical students regarding dose levels of imaging procedures and radiation safety issues, and to conclude how the curriculum of clinical radiology in the college medical program impacts such knowledge.

Subjects and methods:  this is a cross-sectional study conducted among 150 medical students in Alkindy College of Medicine between January 2021 to July 2021, regardless of their age or gender. The study included six grades according to the year 2020-2021. A questionnaire consisting of 12 multiple-choice questions was conducted via an online survey using Google Forms. The questions were divided into two parts

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Publication Date
Sun Oct 30 2022
Journal Name
Egyptian Journal Of Hospital Medicine
Antibiofilm Activity of Conocarpus erectus Leaves Extract and Assessment Its Effect on pelA and algD Genes on Multi-drug Resistant Pseudomonas aeruginosa
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Due to its various resistance mechanisms, Pseudomonas aeruginosa is the most prevalent opportunistic infection that kills hospitalized patients. Thus, therapeutic options become limited. Objective: The study aimed to estimate the antibiofilm effectiveness of Conocarpus erectus leaf extracts against MDR P. aeruginosa isolates and examines pelA and algD gene expression. Subjects and Methods: One hundred-fifty clinical samples were collected from five Baghdad hospitals between September 2021 and January 2022. Samples were grown on different mediums. Despite cetrimide agar's ability to detect P. aeruginosa, only 83 isolates developed at 42°C. VITEK 2 compact system identification followed. This study examined 83 of P. aeruginosa isolates for r

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Publication Date
Sun May 03 2015
Journal Name
Lasers In Medical Science
Investigations of radicular dentin permeability and ultrastructural changes after irradiation with Er,Cr:YSGG laser and dual wavelength (2780 and 940 nm) laser
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Publication Date
Sun Oct 06 1996
Journal Name
Iraqi Journal Of Chemistry
Synthesis of new Schiff bases derived from [3-amino-3-C-cyano-3-deoxy-1,2:5,6-di-O-isopropylidene-α-D-allofuranose
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Aromatic Schiff-bases are known to have antibacterial activity, but most of these compounds are sparingly soluble in water. The present work describes the synthesis of new Schiff-bases derived from branched aminosugars. Treatment of 3-Amino-3-Cyano-3-Deoxy-1,2:5,6-Di-O-Isopropylene-α-D-Allofuranose (1) with the aldehydes (2) under reflux in methanol afforded the Schiff-bases (3) in good yields. The new Schiff-bases were in accord with their NMR, IR spectral data and elemental analysis.

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Publication Date
Sun Sep 27 2020
Journal Name
Iraqi National Journal Of Nursing Specialties
Effectiveness of an Education Program on Nursing Staffs' Knowledge about Infection Control Measures at Intensive Care Unit in Al-Diwaniya Teaching Hospital
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Objectives: To determine the effectiveness of the educational program on nursing staff knowledge about infection control measures at the Intensive Care Unit in Al-Diwaniya Teaching Hospital.

Methodology: A pre-experimental design (one group design: pre-test and post-test) was used. This study was conducted in Al-Diwaniya Teaching Hospital for the period from ( 20th February to 5th March, 2020) on a non-probability (purposive) sample consisting of (25 nurses) working in ICU. A questionnaire was built as a data collection tool and consisted of two parts:

First part: The demographic characteristics of the nursing staff (age, gender, level of education, years of experien

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Publication Date
Wed Apr 22 2026
Journal Name
Environmental Earth Sciences
Transboundary hydrogeology and controlling factors of euphrates water chemistry: Insights from hydrochemistry, stable isotopes, and residence times in Syria and Western Iraq
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Arid and semi-arid climates are critical for water security in sustainable river systems. The Euphrates River in western Iraq has been increasingly stressed by both geogenic and anthropogenic factors. This study analyzed hydro-geochemical processes, recharge dynamics, and groundwater flow modeling in western Iraq. Additionally, stable isotope tracing (δ¹⁸O, Cl⁻) integrated with hydro-chemical parameters was used to assess water quality and river-aquifer connectivity in both Syria and western Iraq. A total of 144 groundwater samples were collected annually across 12 stations in western Iraq. Surface water and groundwater data were collected from previous studies at 13 stations in Syria. Results revealed slightly alkaline freshwater con

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Publication Date
Tue Jul 08 2014
Journal Name
African Journal Of Traditional, Complementary And Alternative Medicines
Hepatoprotective Effect Of <i>Cymbopogon Citratus</i> Aqueous Extract Against Hydrogen Peroxide-Induced Liver Injury In Male Rats
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Publication Date
Sat Jun 01 2024
Journal Name
Innovative Food Science & Emerging Technologies
Non-thermal pasteurization of milk by elongated electrode moderate electrical field: Chemical and sensory analysis during cold storage and shelf-life determination
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Publication Date
Mon Aug 19 2024
Journal Name
Chemical Papers
In vitro and in silico evaluation of 4'-hydroxy-[1,1'-biphenyl]-4-carbohydrazide Schiff base and oxadiazole derivatives targeting EGFR allosteric site
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Publication Date
Tue Nov 25 2025
Journal Name
Inorganic Chemistry Communications
Synthesis, spectroscopic and single-crystal analysis, and DFT studies of N₂O₂ diamine coordination complexes: solvent-driven geometry switching and NLO properties
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The design of coordination compounds with solvent-responsive optical properties remains a central challenge in molecular photonics. Here, we describe the synthesis and full characterisation of a symmetrical tetradentate diamine ligand, 3,3′-((1,2-phenylenebis(azanediyl))- bis(methanylylidene))bis(pentane-2,4-dione) (H₂L), and its neutral square-planar complexes [M(L)] (M(II) = Co, Ni, Cu). The Cu(II) complex crystallised as [Cu(L)]⋅0.5 (pyrazine), adopting a nearly square-planar geometry (τ₄ = 0.06) in the solid state, as confirmed by single-crystal X-ray diffraction. In DMSO solution, UV–Vis spectra revealed reversible axial coordination of two solvent molecules, driving a transformation to a distorted octahedral geometry. Struc

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