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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
Thu Jan 23 2020
Journal Name
Oncology Letters
Overexpression of HURP mRNA in head and neck carcinoma and association with in�vitro response to vinorelbine
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Publication Date
Tue Mar 28 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Serum Levels of Total IgE, IL-12, IL-13 and IL-18 in Children Patients with Asthma
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T-cell activation and alteration of cytokine levels are involved in the pathogenesis of asthma. However, the profile of circulating T-lymphocyte subsets and related cytokines during asthmatic attacks is still unclear. We compared the serum concentrations of proinflammatory cytokines Interleukine-18( IL-18) and Interleukine-12(IL-12), T-helper 2 (Th2) cytokine Interleukine-13(IL-13 ) and Immunoglobuline-E ( IgE) in 27 asthmatic children and 21 sex and age matched healthy control subjects. Serum cytokines and IgE concentrations were measured by enzyme-linked immunosorbent assay. Serum IL-13 , IL-18 and IgE concentrations were significantly higher in asthmatic patients than normal control subjects ( IL-13: median 9.73 versus 4.43 pg/ml, P&l

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Publication Date
Mon Sep 30 2019
Journal Name
Pharmacy Practice
Pharmacist intervention to enhance postoperative fluid prescribing practice in an Iraqi hospital through implementation of NICE guideline
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Publication Date
Thu Mar 20 2025
Journal Name
Journal Of Applied And Natural Science
Isolation and identification of pathogenic bacteria from drinking tap water and Tigris River water sources in Baghdad
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Water is a resource and a crucial aspect of living and surviving. In Iraq, the Tigris River is one of the most critical water sources. The present study aimed to provide an insight analysis of some water quality parameters including the microbial content of drinkable tap water and river water. Ten Water samples (T1- T10) in triplicate were collected from sampling sites -Site I (Tap water) from home water taps, supplied by the Water Filtration Station/ Al Karama Project/ Al-Karkh> 10 from Site II (R1- R10)River water from Tigris River (around or near the Water Filtration Station/ Al Karama Project) every week (from September to half of November 2022), then were immediately placed in sterile bottles and transported to Microbiolo

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Publication Date
Mon Mar 15 2021
Journal Name
Egyptian Journal Of Chemistry
Antimicrobial Activity of New Synthesized Aza -Beta Lactam and Tetrazole Derivatives Bearing Imidazo[2,1-B]Benzothiazole Moiety
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Publication Date
Mon Jan 01 2024
Journal Name
International Journal Of Advanced Community Medicine
Knowledge and attitude of breast self-examination toward breast cancer among nonmedical female students at Diyala University
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Abstract Background: Women in developed and poor nations more often get breast cancer. BSE involves women frequently checking their breasts for lumps or swelling to seek medical assistance. BSE lets women know how their breasts appear and feel so they can notify their doctors of any changes. Objectives: To determine the knowledge and attitude of breast self-examination among nonmedical female student. Method: A descriptive cross-sectional research was conducted at Diyala University/Governorate-Iraq on fourth-grade non-medical female students. A 700-student online questionnaire was employed. We got official agreements. Fisher's exact or chi-square test was employed. Statistical significance was set at p<0.05. Results: The mean age of partici

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Publication Date
Fri Dec 01 2023
Journal Name
Case Studies In Chemical And Environmental Engineering
Treatment of petroleum refinery wastewater by an innovative electro-Fenton system: Performance and specific energy consumption evaluation
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Publication Date
Wed Mar 29 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Design and Synthesis of New Non-Steroidal Anti-inflammatory Agents with Expected Selectivity toward Cyclooxygenase-2 Inhibition
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This study includes design and synthesis of new non-steroidal anti-inflammatory agents (NSAIDs) with expected cyclooxygenase-2 (COX-2) selective inhibition to achieve better activity and low gastric side effects. Two series of compounds have been designed and synthesized as potential NSAIDs,these  are:     Salicylamide derivatives (compounds 3,4,5 ) and Diflunisal derivatives (compounds 10&11). In vivo acute anti-inflammatory effect of one of the synthesized agents (compound 3)  was evaluated in the rat using egg-white induced paw edema model of inflammation. Preliminary pharmacological study revealed that compound 3 exhibited less anti-inflammatory effect  compared to that of aspirin after

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Publication Date
Mon Feb 04 2019
Journal Name
Iraqi Journal Of Physics
Temperature effect on optical properties of nickel (ii) phthalocyanine tetrasulfonic acid tetrasodium salt (NiPcTs) organic thin films
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This study describe the effect of temperature on the optical
properties of nickel(ii) phthalocyanine tetrasulfonic acid tetrasodium
salt (NiPcTs) organic thin films which are prepared by spin coating
on indium tin oxide (ITO-glass). The optical absorption spectra of
these thin films are measured. Present studies reveal that the optical
band gap energies of NiPcTs thin films are dependent on the
annealing temperatures. The optical band gap decreases with increase
in annealing temperature, then increased when the temperature rising
to 473K. To enhance the results of Uv-Vis measurements and get
more accurate values of optical energy gaps; the Photoluminescence
spectra of as-deposited and annealed NiPcTs thin fi

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Publication Date
Sat Jul 08 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Estimation of Superoxide Dismutase, Matrix-metalloprotinase-9, and Interleukin -18 in Patients with Type Two Diabetes Mellitus
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Antioxidant status imbalance and inflammatory process are cooperative events involved in type 2 diabetes mellitus. This study aimed to investigate     superoxide dismutase as a potential biomarkers of antioxidant imbalance, matrix-metaloprotinase-9,   and interleukin -18  as biomarkers of inflammation in serum and to estimate  the effects of other confounding factors  gender, age and finally measuring the relation among the interested biomarkers.

This case - control study included 50 patients,   and   45 of  healthy subjects matched age –gender were also enrolled  in this study as a control group.    The   focused &nbsp

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