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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
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
Sun Oct 01 2023
Journal Name
Medical Journal Of Babylon
Prevalence of coronary artery disease in patients with left bundle branch block and its association with risk factors hypertension and diabetes mellitus
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Abstract<sec> <title>Background:

Left bundle branch block (LBBB) is a common finding in electrocardiography, there are many causes of LBBB.

Objectives:

The aim of this study is to discuss the true prevalence of coronary artery disease (CAD) in patients with LBBB and associated risk factors in the form of hypertension and diabetes mellitus.

Materials and Methods:

Patients with LBBB were admitted to the Iraqi heart center for cardiac disea

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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
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
Effect of Citrus aurantifolia Seed Extracts In Some Bacteria Isolated From Burns Infections: Suaad K. Ibrahim|Ilham S. Banno|Sawsan M. Abdella
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The present study was carried to evaluate antibacterial activity of Acetone, Alcholic (cold and hot) and Aqueaus(water) extracts of Citrus aurantifoliaseeds,against growth of some bacteria isolated from burns infections(Pseudomonas aeruginosa,Escherichia coli, Klebsiellapneumonia,Staphylococcusaureus)fromKindy HospitalIn Baghdad from March to June 2012.Antibiotic Sensitivity was done for all isolated bacteria used in this study.Results showed variation in antibacterial activity of different extracts against all tested bacteria by well diffusion technique in agar and measuring the diameter of inhibition zone, at concentration 250Mg-ml. Acetone extract had the greatest inhibitory effect followed by hot alcoholci extract, and then cold alcohol

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Publication Date
Tue Mar 08 2016
Journal Name
Ibn Al-haitham Jour. For Pure & Appl. Sci.
Synthesis, Characterization and Spectral Studies of Y(III), La(II) and Rh(III) Complexes with 2,4-dimethyl-6-(4-nitro-phenylazo)- Phenol
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Transition metal complexes of Y(III), La(III) and Rh(III) with azo dye 2,4-dimethyl-6- (4-nitro-phenylazo)-phenol derived from 4-nitroaniline and 2,4-dimethylphenol were synthesized. Characterization of these compounds has been done on the basis of elemental analysis, electronic data, FT-IR,UV-Vis and 1HNMR, as well as conductivity measurements. The nature of the complexes formed were studies following the mole ratio and continuous variation methods, Beer's law obeyed over a concentration range (1x10-4- 3x10-4). High molar absorbtivity of the complex solutions were observed. From the analytical data, the stoichiomerty of the complexes has been found to be 1:3 (Metal:ligand). On the basis of Physicochemical data octahedral geometries were as

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Publication Date
Sat Apr 01 2023
Journal Name
Baghdad Science Journal
Evaluation of Some Heavy Metals, Their Fate and Transportation in Water, Sediment, and Some Biota within AL-Musayyib River, Babylon Governorate, Iraq
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This study estimated seven heavy metals (Fe, Cu, Zn, Pb, Ni, Cd, Cr) in water (dissolved and particulate phase), sediments and some aquatic organisms including two species from aquatic plants (Ceratophyllum demersum&Phragmites australis); one species of clam (Psedontopeses euphratics) and two species from fish (Oreochromis aureus& Leuciscus vorax)in four sites within Mashroo AL- Musayyib channel project/ branch  of Euphrates river, Babylon , medial of Iraq . This aims to show the concentration of these elements, their fate and the mechanisms of their transmission through the food chain in this lotic aquatic system ; also in addition to examining  some physicochemical properties of ri

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Publication Date
Tue Jan 09 2018
Journal Name
Iraqi Journal Of Cancer And Medical Genetics
Photodynamic Action of low power He-Ne laser on photosensitized human Hep-2 and AMN3 cell lines with Hematoporphyrin derivative in vitro
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Photodynamic Action (PDA) by using appropriate wavelength of irradiation conjugated with porphyrin derivatives is a powerful mechanism of tumor destruction. Hematoporphyrin derivative has been shown to selectively localize in neoplastic cells and then cause destruction of them by generation of singlet oxygen when activated by low power He-Ne laser. Light which used in this study has been emitting from this laser has a wavelength equal to 632.8 nm (red light). Doses of laser had been varied from 3.6 J/cm2 to 14.4 J/cm2 . The beam of laser adjusted with a modified tissue culture plate. Cell lines had exposed to Hematoporphyrin D (HpD) for 24 hours before Laser exposure, their concentrations were varied from 5 µg/ml to 80 µg/ml. Resu

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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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