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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
Mon May 01 2017
Journal Name
Desalination And Water Treatment
Cadmium removal from simulated chloride wastewater using a novel flow-by fixed bed electrochemical reactor: Taguchi approach
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Publication Date
Mon Jan 01 2024
Journal Name
Russian Electronic Journal Of Radiology
COHORT COMPARATIVE STUDY OF COVID-19 VACCINATED AND NON-VACCINATED PATIENTS DEPENDING ON CT CHEST FINDINGS BETWEEN IRAQI AND JORDANIAN POPULATION
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Publication Date
Wed Dec 30 2020
Journal Name
Al-kindy College Medical Journal
Comparative Study between Nasal Endoscopic Findings and Nose and Paranasal Sinus Computerized Tomography in diagnosis of Nose and Paranasal Sinuses Diseases
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Background: Nasal obstruction is common in otorhinolaryngology outpatient visitors. The diagnosis of such compliant is by history, clinical examination and diagnostic procedures. Nasal endoscopy and computerized tomography scan are common diagnostic investigations. Nasal obstruction is either anterior or posterior (nasal septal deviations, hypertrophied turbinate pathological cyst, polyps, mass etc), or postnasal obstruction (hypertrophied turbinate, adenoid hypertrophy, nasopharyngeal cyst or nasopharyngeal tumors).

Aim of study: Prospective study to compare endoscopic finding and computerized tomography of nose, paranasal sinuses and postnasal space as diagnostic methods for nasal obstruction and other nose, p

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Publication Date
Sat Feb 22 2025
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
In vivo Brain Pharmacokinetics of Dolutegravir Sodium-Loaded Nanostructured Lipid Carrier in situ Gel: Comparative Study with an Intravenous Drug Solution
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Background: Dolutegravir sodium (DTG), used to treat HIV, faces challenges in delivering effective therapeutic concentrations to the brain due to the blood-brain barrier (BBB). Nanostructured lipid carriers (NLCs) combined with in situ gels present a promising strategy for enhancing brain drug delivery via the intranasal route. Objective: To compare brain pharmacokinetics of DTGs delivered via NLC-loaded in situ gel intranasal administration with the conventional intravenous (IV) drug solution. Methods: 80 Wistar rats, which were divided into three groups: two groups consisting of 39 animals each and a control group with 2 animals. Rats were administered with a dose of 1.0 mg/kg of DTGs IV, and DTGs NLC-loaded in situ gel were admin

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Publication Date
Mon Apr 03 2023
Journal Name
Journal Of Genetic And Environmental Resources Conservation, 2023, 11(1):53-59.
Comparative histomorphological and immunohistochemical study of parathyroid gland in two Iraqi mammals (Weasel, Herpestes javanicus and long-ear hedgehog, Hemiechinus auritus)
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The present study aimed to investigate the anatomy, histology, and immunohistochemistry of parathyroid gland in two Iraqi mammals (Weasel, Herpestes javanicus and Long-ear hedgehog, Hemiechinus auritus) as a comparative study. A total of (20) animal for each species were used in the present study. Animals collected were immediately anesthesia and dissected to get the parathyroid gland. Methods of Humason and Bancroft and Stevens were employed for histological techniques. Different stains were used (Hematoxylin- Eosin stain-(H & E), Periodic Acid Schiff stain-(PAS), Azan stain, and Methyl Blue stain-(MB)) for staining the histological sections. Anti-calcitonin, code140778 marker used for immune-histochemical study. Results of the present stu

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Publication Date
Wed May 01 2024
Journal Name
Journal Of International Society Of Preventive And Community Dentistry
Effect of Incorporating Chitosan to Resin Modified Glass Ionomer Cement on Shear Bond Strength to Dentin (An In vitro Comparative Study)
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A<sc>bstract</sc> <sec> <title>Aim:

Resin-modified glass ionomer cement tends to shrink due to polymerization of the resin component. Additionally, they are more prone to syneresis and imbibition during the setting process. This in vitro study evaluates the impact of chitosan, a biopolymer that is, both biomaterial and biocompatible, on the strength of dentin bonding and compares it with ACTIVA Bio-ACTIVE Restorative. The present study was aimed to assess the impact of including chitosan into Fuji II on the shear bond strength between. the restoration material and tooth dentin,

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Publication Date
Sun Jan 01 2017
Journal Name
International Journal Of Chem Tech Research
Synthesis of New Selective Electrodes for the Determination of Metronidazole Benzoate (MNZB) Based on a Molecularly Imprinted Polymer Combined With Poly Vinyl Chloride
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Publication Date
Sat Dec 31 2022
Journal Name
Al-kindy College Medical Journal
A Role of Therapy that Targets Immune Checkpoint Proteins for the Treatment of Melanoma Brain Metastasis, Liver, Breast, Pancreatic Cancer and Pancreatic Adenocarcinoma
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Checkpoint inhibitors are a type of immune therapy used to treat different types of cancers. These drugs block different checkpoint proteins, for example, CTLA-4, PD-1, and PD-L1 inhibitors.

They block proteins that stop the immune system from attacking the cancer cells.  Checkpoints are also described as a type of monoclonal antibody that antagonizes binding between B7 to CTLA-4 and PD-L1 to PD-1.

 Immune checkpoint inhibitors are used to treat BARCA mutated triple-negative breast cancer (TNBCS) in patients who do not respond to chemotherapy, and also in the treatment of highly mutated and solid tumors such as brain tumors, liver, and pancreatic cancers.

Immune checkpoint inhibitors exhibit an effect on solid tumo

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Publication Date
Sat Apr 01 2023
Journal Name
Baghdad Science Journal
Development and Validation of a Simple and Sensitive Reverse-Phase High Performance Liquid Chromatographic Method for the Determination of Ibuprofen in Pharmaceutical Suspensions
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The aim of this work was to develop and validate a rapid and low cost method for estimation of ibuprofen in pharmaceutical suspensions using Reverse-Phase High Performance Liquid Chromatography. The proposed method was conducted and validated according to International Conference on Harmonization (ICH) requirements. The chromatographic parameters were as follows: column of octyldecylsilyl C18 with dimensions (150 × 4.6) mm, mobile phase composed of acetonitrile with phosphoric acid with a ratio of 50 to 50 each using isocratic mode, flow rate of 1.5 mL/min and injection volume of 5 μL. The detection was carried out using UV detector at 220 nm. The method was validated and showed short retention time for ibuprofen peak at 7.651 min, wit

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Publication Date
Mon Feb 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Employment of critical success factors in achieving the strategy Entrepreneurship: A field research for my company Oil Products Distribution and Midland Refineries
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Abstract

        The critical success factors of the means of the most modern in determining the main directions for organizations to achieve competitive advantage. and can be a critical success factors in organizations that overlap in the functional areas of the organization. that successful organizations use these factors to get to the uniqueness and distinction. as the entrance of critical success factors with the capacity Evaluative phase correction because discovery increases the perception of managers of what is important to the organization and using them to get to the Strategic Entrepreneurship. as it begins in terms of permanence of success and

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