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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
Thu Feb 07 2019
Journal Name
Iraqi Journal Of Laser
Antibacterial Photodynamic Effect of 532 nm Diode-Pumped Solid State and 650 nm Diode Lasers on Methicillin Resistant Staphylococcus Aureus in Vitro
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The photodynamic inactivation against Methicillin-resistant Staphylococcus aureus using two different lasers, 532 nm diode pumped solid state laser (DPSS) in combination with safranin O and 650 nm diode laser in combination with methylene blue was investigated in the present work. A hundred swab samples were collected from patients with burn and wound infections admitted to two hospitals in Baghdad (Specialized Burns Hospital in Medical City and Al Imamein Al Jwadein Medical City Hospital) from December 2015 to February 2016 Antimicrobial susceptibility was performed by using Kirby- Bauer method. The irradiation experiments included four groups; a control group, a photosensitizer only group, a laser irradiation only group and a laser irr

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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
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 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 Jun 05 2023
Journal Name
Journal Of Engineering
Removal of Cu2+, Pb2+ , And Ni 2+ Ions From Simulated Waste Water By Ion Exchange Method On Zeolite And Purolite C105 Resin
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The removal of heavy metal ions from wastewater by ion exchange resins ( zeolite and purolite C105), was investigated. The adsorption process, which is pH dependent, shows maximum removal of metal ions at pH 6 and 7 for zeolite and purolite C105 for initial metal ion
concentrations of 50-250 mg/l, with resin dose of 0.25-3 g. The maximum ion exchange capacity was found to be 9.74, 9.23 and 9.71 mg/g for Cu2+, Pb2+, and Ni2+ on zeolite respectively, while on purolite C105 the maximum ion exchange capacity was found to be 9.64 ,8.73 and 9.39 for Cu2+, Pb2+, and Ni2+ respectively. The maximum removal was 97-98% for Cu2+ and Ni2+ and 92- 93% for Pb2+ on zeolite, while it was 93-94% for Cu2+, 96-97% for Ni2+, and 87-88% for Pb2+ on puroli

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Publication Date
Wed Aug 31 2022
Journal Name
Al-kindy College Medical Journal
Assessment of Awareness And Knowledge among Medical Students Regarding Radiation Exposure from Common Diagnostic Imaging Procedures: Radiation exposure awareness among medical students
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Objective: to assess the awareness and knowledge of our medical students regarding dose levels of imaging procedures and radiation safety issues, and to conclude how the curriculum of clinical radiology in the college medical program impacts such knowledge.

Subjects and methods:  this is a cross-sectional study conducted among 150 medical students in Alkindy College of Medicine between January 2021 to July 2021, regardless of their age or gender. The study included six grades according to the year 2020-2021. A questionnaire consisting of 12 multiple-choice questions was conducted via an online survey using Google Forms. The questions were divided into two parts

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Publication Date
Sun Oct 30 2022
Journal Name
Egyptian Journal Of Hospital Medicine
Antibiofilm Activity of Conocarpus erectus Leaves Extract and Assessment Its Effect on pelA and algD Genes on Multi-drug Resistant Pseudomonas aeruginosa
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Due to its various resistance mechanisms, Pseudomonas aeruginosa is the most prevalent opportunistic infection that kills hospitalized patients. Thus, therapeutic options become limited. Objective: The study aimed to estimate the antibiofilm effectiveness of Conocarpus erectus leaf extracts against MDR P. aeruginosa isolates and examines pelA and algD gene expression. Subjects and Methods: One hundred-fifty clinical samples were collected from five Baghdad hospitals between September 2021 and January 2022. Samples were grown on different mediums. Despite cetrimide agar's ability to detect P. aeruginosa, only 83 isolates developed at 42°C. VITEK 2 compact system identification followed. This study examined 83 of P. aeruginosa isolates for r

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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
Sun Oct 06 1996
Journal Name
Iraqi Journal Of Chemistry
Synthesis of new Schiff bases derived from [3-amino-3-C-cyano-3-deoxy-1,2:5,6-di-O-isopropylidene-α-D-allofuranose
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Aromatic Schiff-bases are known to have antibacterial activity, but most of these compounds are sparingly soluble in water. The present work describes the synthesis of new Schiff-bases derived from branched aminosugars. Treatment of 3-Amino-3-Cyano-3-Deoxy-1,2:5,6-Di-O-Isopropylene-α-D-Allofuranose (1) with the aldehydes (2) under reflux in methanol afforded the Schiff-bases (3) in good yields. The new Schiff-bases were in accord with their NMR, IR spectral data and elemental analysis.

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