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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 01 2023
Journal Name
Journal Of Medicinal And Chemical Sciences
Synthesis, Characterization, and Biological Activity of New Metal Ion Complexes with Schiff Base (Z)-3((E)-2-Hydroxybenzylidene) Hydrazineylidene) Indolin-2-One
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The study involved preparing a new compound by combining between 2-hydroxybenzaldehyde and (Z)-3-hydrazineylideneindolin-2-one resulting in Schiff bases and metal ions: Mn(II), Co(II), Ni(II), Cu(II), and Zn(II) forming stable minerals-based-Schiff complexes. The formation of resulting Schiff bases is detected spectrally using LC-Mss which gave corresponding results with theoretical results, 1H-NMR proves the founding of N=CH signal, FT-IR indicates the occurrence of imine band and UV-VIs mean is proved the ligand formation. On the other hand, minerals-based-Schiff was characterized using the same spectral means that relied with ligand (Schiff bases). Those means gave satisfactory results and proved the suggested distinguishable geometries.

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Publication Date
Sat Dec 24 2022
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Neuroprotective Effect of Vinpocetine against Lead Acetate-Instigated Neurotoxicity in Rats by Evaluation Tumor Necrosis Factor-Alpha, Interleukin-1Beta and Interleukin-10
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Lead toxicity elicits neurological damage which is a well-known disorder that has been considered to be a major cause for multiple condition such as behavioral defect; mental retardation; and nerve insufficient activity.

This research is designed to estimate potential protective effect of vinpocetine on neurotoxicity stimulated by lead acetate in rats.

Eighteen adult rats of both sexes were randomly enrolled into three groups. Each group includes 6 rats as followings: Group I- Rats were given 0.3ml normal saline solution orally; then intraperitoneal injection of 100μl of the normal saline was given 1h later; this group was considered as control. Group II- Rats were given an intraperitoneal injection of 20mg/kg lead acetate

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Publication Date
Sun Sep 28 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Enamel defect of primary and permanent teeth in relation to nutrients daily intake among Down's syndrome children in comparison to normal children
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Background: Any child with Down's syndrome does not develop in the same manner as normal child. Therefore, the child should not be viewed as being like everyone else. Developmental enamel defects in primary teeth have been found at least twice as frequently in disabled children as in control children. Down's syndrome consumed protein more than the recommended daily allowance compared to other disabled groups. Therefore, the aim of this study was to investigate developmental defects of enamel and their relations to nutrient intake among Down's syndrome children in comparison to normal children. Materials and Methods: A sample consisted of fifty institutionalized Down's syndrome children (study group) and 50 normal children (control group)

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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
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 May 01 2021
Journal Name
Journal Of Physics: Conference Series
Metal Complexes of Multidentate N<sub>2</sub>S<sub>2</sub> Heterocyclic Schiff-base Ligands;Formation, Structural Characterisation and Biological Activity
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Abstract<p>The synthesis of ligands with N<sub>2</sub>S<sub>2</sub> donor sets that include imine, an amide, thioether, thiolate moieties and their metal complexes were achieved. The new Schiff-base ligands; N-(2-((2,4-diphenyl-3-azabicyclo[3.3.1]nonan-9-ylidene)amino)ethyl)-2-((2-mercaptoethyl)thio)-acetamide (H<sub>2</sub>L<sup>1</sup>) and N-(2-((2,4-di-p-tolyl-3-azabicyclo[3.3.1]nonan-9-ylidene)amino)ethyl)-2-((2-mercaptoethyl)thio) acetamide (H2L<sup>2</sup>) were obtained from the reaction of amine precursors with 1,4-dithian-2-one in the presence of triethylamine as a base in the CHCl3 medium. Complexes of the general formula K<sub>2<</sub></p> ... Show More
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Publication Date
Wed Apr 01 2020
Journal Name
Biochemical & Cellular Archives
INVESTIGATION OF VITAMIN D, ESTRADIOL AND C-REACTIVE PROTEIN LEVELS IN PRE AND POST-MENOPAUSAL IRAQI TYPE 2 DIABETES MELLITUS IN WOMEN.
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Diabetes mellitus is a metabolic chronic disease, with global estimation increase in patient (around 100 million in 2030).The aim of the current study is to investigate vitamin D, C-reactive protein and estradiol levels in pre and postmenopausal Iraqi women with type 2 diabetes (T2MD).A total of 176 female distributed into two groups: the first included 90 women withT2MD (43 pre and 47 post-menopausal); the second group included 86 healthy subjects (41 pre and 45 postmenopausal) considered as control. This study has shown that women in premenopausal (20-40 years) had highly significant difference in the estradiol and vitamin D levels in diabetes subjects (62.192 ± 17.643pg/ml, 10.522 ± 1.958ng/ml) compared with healthy (131.793 ± 1

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Publication Date
Tue Sep 03 2019
Journal Name
Rawal Medical Journal
Evaluation of Radial Nerve Injury Associated with Closed Humeral Shaft Fracture by Early Pre-operative Ultrasonic Evaluation and Correlation with Surgical Exploration
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Traumatic radial nerve injury in humeral shaft fracture is the most common traumatic nerve injury in long-bone fracture, with overall prevalence 2-18%, ranging from traction to complete transection. Spontaneous recovery may reach 88%. The aim of the study is to assess the sensitivity & specificity of the ultrasound to detect the radial nerve injury and to see if this can be used as a diagnostic test. This is a prospective study on 17 adult patients with a closed fracture of the humeral shaft, dividing into two groups, the first group of 7 patients had signs and symptoms of radial nerve palsy at presentation and the second group of 10 patients had intact radial nerve function was considered as a control group. All these patients had at leas

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Publication Date
Thu Sep 01 2022
Journal Name
Archives Of Razi Institute
Effects of Avena sativa and Glycyrrhiza glabra Leaves Extracts on Immune Responses in Serum Cytokine and Liver Enzyme Levels in NIH Mice
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In addition to their high quantities of active chemicals, medicinal plants are well-known for their pharmacological qualities, which include immunological modulation. T Consequently, this study aimed to examine the effects of Avena sativa and Glycyrrhiza glabra leaf extracts on immunological responses as measured by blood cytokine and liver enzyme levels. The phytochemical analysis of Avena sativa crude leaf extracts revealed the presence of alkaloids,flavonoids, tannins, phenolic compounds, and saponins but the absence of resins and violet oils. On the other hand, violet oils, flavonoids, tannins, saponins, and glycosides were detected in significant concentration in Glycyrrhiza glabra ethanolic extract, although resins and phenolic compou

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Publication Date
Tue Sep 28 2021
Journal Name
Journal Of Physical Education
Youth and Sports Forums’ Administration and Their Relationship with Baghdad’s Youth and Sport Directorates Forum Organizational Culture from Workers’ Point of View
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The study aimed at identifying youth and sport forums from planning and leadership point of view and their relation with organizational culture. The researchers used the descriptive method on (140) worker in Baghdad youth and sport forums. A scale was designed for measuring planning and leadership in youth and sport forums as well as designing a scale for measuring organizational culture. After the application of the main experiment, the results showed that both youth and sport forum administration scale and organizational culture scale are appropriate to the study community. Finally the researchers recommended using these scales by workers in youth and sport forums and involving administration mangers in periodical training courses

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