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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 Jul 20 2024
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Polyacrylonitrile Nanofiber Composites as Efficient Removal of Pollutants for Wastewater: A Review Article
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Polyacrylonitrile nanofiber (PANFS), a well-known polymers, has been extensively employed in the manufacturing of carbon nanofibers (CNFS), which have recently gained substantial attention due to their excellent features, such as spinnability, environmental friendliness, and commercial feasibility. Because of their high carbon yield and versatility in tailoring the final CNFS structure, In addition to the simple formation of ladder structures through nitrile polymerization to yield stable products, CNFS and PAN have been the focus of extensive research as potential production precursors. For instance, the development of biomedical and high-performance composites has now become achievable. PAN homopolymer or PAN-based precursor copolymer can

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Publication Date
Mon Jun 19 2023
Journal Name
Journal Of Polymer Research
Design, and synthesis of a plasticizer- Schiff’s bases complexes as additive for polystyrene
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This work involved the successful synthesis of three new Schiff base complexes, including Ni(II), Mn(II), and Cu(II) complexes. The Schiff base ligand was created by reacting the malonyldihydrazide molecule with naphthaldehyde, and the final step involved reacting the ligand with the corresponding metallic chloride yielding pure target complexes. FTIR, 1 H NMR, 13 C NMR, mass, and UV/Vis spectroscopies were used to comprehensively characterize the produced complexes. These substances have been employed in this study to photo-stabilize polystyrene (PS) and lessen the photo-degradation of its polymeric chains. Several methods, including FTIR, weight loss, viscosity average molecular weight, light and atomic force microscopy, and energy disper

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Publication Date
Mon Sep 04 2017
Journal Name
International Journal Of Environmental Science And Technology
A review of permeable reactive barrier as passive sustainable technology for groundwater remediation
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Publication Date
Thu Dec 01 2022
Journal Name
Journal Of Engineering
The Effectiveness of a Simulation Model of Thermal Insulation in Building Materials Using Cellulose Extracted from Agricultural Waste in Baghdad
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This study found that one of the constructive, necessary, beneficial, most effective, and cost-effective ways to meet the great challenge of rising energy prices is to develop and improve energy quality and efficiency. The process of improving the quality of energy and its means has been carried out in many buildings and around the world. It was found that the thermal insulation process in buildings and educational facilities has become the primary tool for improving energy efficiency, enabling us to improve and develop the internal thermal environment quality processes recommended for users (student - teacher). An excellent and essential empirical study has been conducted to calculate the fundamental values ​​of the

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Publication Date
Mon Jun 14 2021
Journal Name
Biosense Dementia 2017 - International Workshop On Biosensors For Dementia From 13 – 14 June 2017 – Plymouth University, Plymouth, Uk
Changes in the Electroencephalogram as a Biomarker of Alzheimer’s Disease
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The rapid increase in the number of older people with Alzheimer’s disease (AD) and other forms of dementia represents one of the major challenges to the health and social care systems because of a large number of people affected. Early detection of AD makes it possible for patients to access appropriate services and to benefit from new treatments and therapies, as and when they become available, and to plan for the future. The onset of AD starts many years before the clinical symptoms become clear. A biomarker that can measure the brain changes in this period would be useful for early diagnosis of AD. Potentially, the electroencephalogram (EEG) can play a valuable role in early detection of AD. Damage caused to the brain due to AD leads t

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Publication Date
Thu May 25 2023
Journal Name
Results In Chemistry
Synthesis and characterization of (E)-4-(((4-(5-mercapto-1, 3, 4-oxadiazol-2-yl) phenyl) amino) methyl)-2-methoxyphenol as a novel corrosion inhibitor for mild-steel in acidic medium
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Metal corrosion is a destructive process for many industrial operations, including oil well acidizing and acid pickling. Therefore, numerous efforts made by many researchers to control the steel corrosion. In the present work, A (E)-4-(((4-(5-mercapto-1,3,4-oxadiazol-2-yl) phenyl) amino) methyl)-2-methoxyphenol (MOPM) has been synthesized and characterized as a new corrosion inhibitor for mild steel in 0.1 M hydrochloric acid. FTIR and 1 HNMR were used in the diagnosis of MOPM, while electrochemical polarization technique was employed to test the performance of inhibitor at various temperatures and inhibitor concentrations. Electrochemical studies showed that MOPM acts as a mixed-type inhibitor with a maximum inhibition efficiency of

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Publication Date
Sun Jan 01 2023
Journal Name
Results In Chemistry
Synthesis and characterization of (E)-4-(((4-(5-mercapto-1, 3, 4-oxadiazol-2-yl) phenyl) amino) methyl)-2-methoxyphenol as a novel corrosion inhibitor for mild-steel in acidic medium
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Publication Date
Sun Mar 26 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Spectrophotometric Determination of Nitrofurantoin Drug in its Pharmaceutical Formulations Using MBTH as a Coupling Reagent
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A direct, sensitive and efficient spectrophotometric method for the determination of nitrofurantoin
drug (NIT) in pure as well as in dosage form (capsules) was described. The suggested method was
based on reduction NIT drug using Zn/HCl and then coupling with 3-methyl-2-benzothiazolinone
hydrazone hydrochloride (MBTH) in the presence of ammonium ceric sulfate. Spectrophotometric
measurement was established by recording the absorbance of the green colored product at 610 nm.
Using the optimized reaction conditions, beer’s law was obeyed in the range of 0.5-30 μg/mL, with
good correlation coefficient of 0.9998 and limits of detection and quantitation of 0.163 and 0.544
μg/mL, respectively. The accuracy and

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Publication Date
Sat Jul 01 2023
Journal Name
Journal Of Engineering
Performance of Solar Adsorption Cooling System Using Methanol and Activated Carbon as a Working Pair
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The need for renewable energy sources is higher than ever due to rising global warming, climate change, and ozone depletion. For refrigeration and air conditioning applications, adsorption refrigeration systems are viable alternatives cooling techniques. This study is a topic and part of the M.Sc. thesis. A field solar-powered ice maker unit was created, studied, tested, and evaluated on the 13th and 30th of May, 2022. Activated carbon and methanol pair was used to set up a refrigeration system in Baghdad (Al Dora). Experimental tests were carried out outdoors to determine the coefficient of performance COP and specific cooling power SCP of the system. The results showed that the lowest temperature

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Publication Date
Sat Apr 01 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Clinical Evaluation of a Formulated Econazol Nitrate as A Topical Solution
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Econazole nitrate (EN) is considered as the most effective agent for the treatment of all forms of dermatomycosis caused by dernatophytes. It was formulated as a topical solution in our laboratories. This study was designed to evaluate the effectiveness of Econazol Nitrate in the prepared formula and compared with that of commercial brand, Pevaryl®. A total of 104 patient suffering from dermatomycoses were involved in this investigation. Both formula were applied to the affected skin region in the morning and evening from week to 16 weeks with light massage until complete healing effect was achieved. The data revealed that the percentage of cured patient treated with the prepared formula and reference formula of Ecanozol Nitrate 1% so

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