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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
Sat Apr 01 2023
Journal Name
Baghdad Science Journal
Impact of Azadirachta indica Fruit Mucilage on particle size and swelling index in Central Composite Designed Acyclovir mucoadhesive microspheres
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The drive of this exploration is to investigate the mucoadhesive assets of A. indica (Azadirachta indica) fruit mucilage by incorporating it into mucoadhesive microspheres with Acyclovir (AVR) as a model drug. The study was performed to check the impact of the mucilage proportion on particle size and swelling index. Nine batches of AVR mucoadhesive microspheres were made with varying proportions of Polyacrylic acid 934P and A. indica fruit mucilage (AIFM). A central composite design with design expert software to check the impact of dependent variables (A. indica mucilage and Polyacrylic acid 934 P levels) on particle size and swelling index as a response. As part of congeniality studies, the batches w

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Publication Date
Fri Jun 30 2023
Journal Name
Azerbaijan Pharmaceutical And Pharmacotherapy J
Evaluation of Nurses’ Practices and Perceived Barriers Related to Pain Assessment in Critically Ill Patients at Baghdad Teaching Hospitals
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Introduction: Inadequate pain assessment and management is a problem in hospitalized patients that impairs their wellbeing. Intensive care unit nurses’ pain practices are affected by several barriers and enablers. Objectives: The objectives of this study were to determine the level of nurses’ practices and perceived barriers related to pain assessment in critically ill patients. Methodology: A cross-sectional design study was used. Purposive sampling technique was employed, including 100 nurses recruited from 8 intensive care units in Baghdad city, Iraq. The study was conducted from September 1st to October 20th, 2022. The pain assessment and management for critically ill patients survey was used to collect data. Descriptive sta

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Publication Date
Sat Jul 01 2017
Journal Name
Energy Procedia
Preparation and Physical Properties of Doped CdBa 2-x Sr x Ca 2 Cu 3 O 8+δ Compound
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Publication Date
Sun Jun 02 2024
Journal Name
Methods And Objects Of Chemical Analysis
Simultaneous Spectrophotometric Determination of Piroxicam, Naproxen, Diclofenac Sodium and Mefenamic Acid in Pharmaceutical Formulations by Partial Least Squares Method
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A chemometric method, partial least squares regression (PLS) was applied for the simultaneous determination of piroxicam (PIR), naproxen (NAP), diclofenac sodium (DIC), and mefenamic acid (MEF) in synthetic mixtures and commercial formulations. The proposed method is based on the use of spectrophotometric data coupled with PLS multivariate calibration. The Spectra of drugs were recorded at concentrations in the linear range of 1.0 - 10 μg mL-1 for NAP and from 1.0 - 20 μg mL-1 for PIR, DIC, and MEF. 34 sets of mixtures were used for calibration and 10 sets of mixtures were used for validation in the wavelength range of 200 to 400 nm with the wavelength interval λ = 1 nm in methanol. This method has been used successfully to quant

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Publication Date
Tue Jun 16 2020
Journal Name
Frontiers In Pharmacology
Administration of Δ9‐Tetrahydrocannabinol (THC) Post‐Staphylococcal Enterotoxin B Exposure Protects Mice From Acute Respiratory Distress Syndrome and Toxicity
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Publication Date
Mon Jan 01 2024
Journal Name
Revista Brasileira De Saúde Materno Infantil
Misoprostol and mid trimester termination of pregnancy in patients with two previous scars and more at Elwiya Maternity Teaching Hospital
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Abstract Objectives: to determine efficiency and safety of three misoprostol regimens for 2nd trimester pregnancy termination in individuals with two or more cesarean section scars. Methods: a cross-sectional study included 100 pregnant ladies at 13th-26th weeks gestation with previous two cesarean sections (CSs) who were scheduled for pregnancy termination using misoprostol. Patients were conveniently assigned to 100µg/3h, 200µg/3h or 400 µg/3h regimens. Primary outcome was time to abortion, secondary outcomes were side effect and complications. Results: a significant association was found between number previous CSs and longer time to abortion (p=0.01). A highly significant association was identified between earlier gestatio

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Publication Date
Wed Apr 01 2020
Journal Name
Indian Journal Of Public Health
Green and Efficient Composition and Diagnosis of Pentdentate Schiff Base Donative Metal Complexes: Antimicrobial, Antifungal, Antioxidant Screening and DNA Binding
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Background: Enforcement of sustainable and green chemistry protocols has seen colossal surge in recent times, the development of an effective, eco-friendly, simple and novel methodologies towards the synthesis of valuable synthetic scaffolds and drug intermediates. Recent advances in technology have now a more efficient means of heating reactions that made microwave energy. Efforts to synthesize novel heterocyclic molecules of biological importance are in continuation. Microwave irradiation is well known to promote the synthesis of a variety of organic and inorganic compounds. The aim of current study was to conceivea mild base mediated preparation of novel Schiff base of 2-Acetylpheno with trimethoprim drug (H2TPBD) and its complexes w

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Publication Date
Mon Mar 01 2021
Journal Name
Journal Of Physics: Conference Series
Structural, surface morphology and optical properties of annealing treated Copper Phthalocyanine doped Fullerene (CuPc: C<sub>60</sub>) thin films
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Abstract<p>The doping process with materials related to carbon has become a newly emerged approach for achieving an improvement in different physical properties for the obtained doped films. Thin films of CuPc: C<sub>60</sub> with doping ratio of (100:1) were spin-coated onto pre-cleaned glass substrates at room temperature. The prepared films were annealed at different temperatures of (373, 423 and 473) K. The structural studies, using a specific diffractometry of annealed and as deposited samples showed a polymorphism structure and dominated by CuPc with preferential orientation of the plane (100) of (2θ = 7) except at temperature of 423K which indicated a small peak around (2θ = 3</p> ... Show More
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Publication Date
Fri Dec 01 2023
Journal Name
Baghdad Science Journal
Heat Production Rate and Radiation Hazard Indices from Radioactive Elements in Different Types of Natural Water in Nineveh Governorate, Iraq.
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The current study sheds light on the measurement and estimation of the radioactivity of radionuclides (238U, 226Ra, 232Th, and 40k) in natural waters of different regions of Nineveh Governorate in Iraq.15 samples were collected from different sources of natural waters, where gamma-ray spectroscopy was used using NaI)TI) sodium iodide detector to determine the concentration of radioactivity in the samples. According to the results, the radioactivity concentration in the tested water sample were ​​ranged from 0.36 ± 0.04-1.57 ± 0.09with an average value of 0.69 ± 0.06 Bq/l for 238U, and 2.9 ± 0.02-0.88 ± 0.03 with an average value of 0.65 ± 0.03 Bq/l for 226Ra Bq/l

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Publication Date
Thu Aug 10 2017
Journal Name
Journal Of The College Of Basic Education
Detection of some major elements and protein in Fusarium wilt disease infected tomato(Lycopersicon esculentum) treated with Arbuscular mycorrhizal fung
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The present study was Conducted to evaluate the effect of amixture of three species of arbuscular mycorrhizal fungi ( Glomus etunicatum , G. leptotichum and Rhizophagus intraradices ) in Influence on the percentage of the components of NPK and protein of tomato leaves and roots infected with Fusarium oxysporum f.sp. Lycopersici wich cause Fusarial wilt disease , planted for 8 weeks in the presence of the organic matter ( peatmose) , using pot cultures in aplastic green house , Results indicated significant increase in the percentage of the elements of NK and protein of tomato leaves and roots In the control treatment (C), While the percentage of the element P was after infection with the pathogen 4 weaks after mycorrhizal colonization in al

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