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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
Wed Nov 01 2017
Journal Name
Research Journal Of Pharmaceutical, Biological And Chemical Sciences
Preparation, Spectral studies and Biological Efficiency of Metal (II) Mixed Ligand Complexes Schiff Base derived from (Benzaldehyde and OAminoaniline) with 8-Hydroxyquinoline
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fication of benzaldehyde (C6H5CHO) and O- amino aniline O-C6H4(NH2)2 in ethanol with 8- Hydroxyquinoline (8HQ) . Formed compounds were acquired of 1:1:2 molar proportion reactions for metal ions and ligands (L) and 2(8HQ) during reaction for MCl2 .nH2O salt products complexes conformable into the forms [M(L)(8HQ)2] ,where M = Mn(II),Co(II) and Ni(II). Whole the compounds were identified during the basis of their; FT-IR and U.V spectrum, melting point, molar conduct, identify of the percentage from the metal at the complexes via flame (AAS), C, H and N content of the Schiff base (L) and metal complexes were analysis and magnetic susceptibility menstruations. A hexagonal coordinated metal complexes were proposed to the separated complexes of

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Publication Date
Sun May 03 2015
Journal Name
Lasers In Medical Science
Investigations of radicular dentin permeability and ultrastructural changes after irradiation with Er,Cr:YSGG laser and dual wavelength (2780 and 940 nm) laser
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Publication Date
Tue Sep 08 2020
Journal Name
Baghdad Science Journal
Improved throughput of Elliptic Curve Digital Signature Algorithm (ECDSA) processor implementation over Koblitz curve k-163 on Field Programmable Gate Array (FPGA)
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            The widespread use of the Internet of things (IoT) in different aspects of an individual’s life like banking, wireless intelligent devices and smartphones has led to new security and performance challenges under restricted resources. The Elliptic Curve Digital Signature Algorithm (ECDSA) is the most suitable choice for the environments due to the smaller size of the encryption key and changeable security related parameters. However, major performance metrics such as area, power, latency and throughput are still customisable and based on the design requirements of the device.

The present paper puts forward an enhancement for the throughput performance metric by p

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Publication Date
Mon Mar 15 2021
Journal Name
Iraqi National Journal Of Nursing Specialties
Effectiveness of an Educational Program on Female Students’ Knowledge toward Premenstrual Syndrome in Secondary Schools in Third Al- Rusafa Education Directorate, Iraq
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Objective: To evaluate the effectiveness of educational program on female students’ knowledge toward premenstrual syndrome.
Methodology: A quasi-experimental design study conducing on (140) student purposely in four secondary schools at Al-sadder city (70) student for study group and (70) for control group. The prevalence of PMS selected through American College of Obstetricians and Gynecologists (ACOG) (2015) criterias to select PMS students before program. The education program were set in four steps, the first step (pre-test) is to assess the knowledge , before the implementation of the program, the second step is implementing the program, following two steps post-test I and II between each test two weeks. Validity is determined

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Publication Date
Tue Jan 26 2021
Journal Name
Journal Of Antimicrobial Agents
Antifungal Activity Evaluation of Co(II), Ni(II), Cu(II), Zn(II) and Fe(III) Mixed Ligand Complexes with Different Schiff Bases
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Publication Date
Mon Jul 21 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 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
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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