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bijps-1604
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
Sun Jul 07 2019
Journal Name
Open Access Macedonian Journal Of Medical Sciences
Chromogenic in Situ Hybridization Technique versus Immunohistochemistry in Assessment of HER2/neu Status in 448 Iraqi Patients with Invasive Breast Carcinoma
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BACKGROUND: The rapidly growing knowledge regarding factors controlling tumour growth, with the new modalities of therapy acting on the biological activity of the tumours draw the attention of most cancer researches nowadays and represent a major focus for clinical oncology practice. For the detection of HER2/neu protein overexpression and gene amplification, immunohistochemistry (IHC) and in-situ hybridisation (ISH) is the recommended techniques, respectively, with high concordance between the two techniques. The current United Kingdom recommendations for HER2/neu testing are either for a two-tier system using IHC with reflex ISH testing in equivocal positive cases, or a one-tier ISH strategy. AIM: To compare the results of HER2/neu gene s

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Publication Date
Sun Mar 26 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Measurement of Serum Trace Elements (Zinc, Copper, Magnesium and Iron) Concentrations in Pediatric Patients with Otitis Media with Effusion in Iraq
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Otitis media with effusion (OME) is a common disease especially among young children (before school age) and it is one of the common causes of acquired hearing loss in childhood. Pediatric patients with OME are usually undernourished. The purpose of this study is to determine whether the serum levels of trace elements (zinc, copper, magnesium, iron) have a role in the development of OME in children. This study carried out on 55 children and subdivided them into two groups. Group 1 (patient group) consist of 30 children suffering from OME and group 2 (control group) included 25 apparently healthy children. Serum levels of zinc, copper, magnesium and iron were measured for both groups. Comparison the results between the two groups showed t

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Publication Date
Sun Jun 04 2017
Journal Name
Baghdad Science Journal
Electrical Dielectric Authorship of Polyvinyl-Acetate and Toluene Diisocyanate (PVA-TDI) with Manufactured Sulfonated Phenol-formaldehyde (SPF) Viscous Mass Material Composite
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The electrical insulation of the manufacture sulfonated phenol-formaldehyde viscous material (product) has been studied with Polyvinyl-acetate (PVA) and toluene diisocyanate (TDI) blend has been prepared by fixing percentage by weight 3:1 and mixed with different percentages by weight of the product sulfonated phenol formaldehyde viscous mass (SPF). The Fourier transform infrared (FTIR) spectroscopy is done on (SPF) resin powder and prepared film of PVA-TDI-SPF viscous mass. The quality factor (Q), dissipation factor (D), parallel resistance (Rp), series resistance (Rs), parallel capacitance (Cp), series capacitance (Cs) and phase shift (?) are measured. The calculated maximum dielectric constant (??) is 3.49x107 at sample (1) wt.1% SPF vis

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Publication Date
Fri Jan 01 2016
Journal Name
Iraqi Journal Of Science
Effect of growth media components and growth condition on indole - 3 - acetic acid (IAA) production by Pseudomonas putida isolated from soil
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Publication Date
Thu Jun 15 2017
Journal Name
Journal Of Baghdad College Of Dentistry
Mechanical evaluation of nano hydroxyapatite, chitosan and collagen composite coating compared with nano hydroxyapatite coating on commercially pure titanium dental implant
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Background: Dental implants act as infrastructure for fixed restoration to look like as a natural tooth. Osseointegration is a biological events and considered as a base for success of dental implant. The aim of this study is to evaluate the bond strength between bone and Ti implant coated with mixture of nano hydroxyapatite-chitosan-collagen compared with Ti implants coated with nano hydroxyapatite implanted in rabbit tibia, after different period of implantation time (two and six weeks) by torque removal test. Material and methods: 36 screws of commercially pure titanium; 8mm in length and 3mm diameter , 18 screws coated with mixture of nano hydroxyapatite-chitosan-collagen and18 screws coated with nano hydroxyapatite by dip coating. St

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Publication Date
Thu Aug 01 2024
Journal Name
Baghdad Science Journal
Synthesis, Structural, Morphological Characterization, and Cytotoxicity Assays of Metal Complexes Decorated SiO2 Nanoparticles Against Breast Cancer Cell Lines (MDA-MB-231)
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في هذا البحث تم تحضير المركبات المعدنية الجديدة لأيونات البلاتين (الرباعي) و الذهب (الثلاثي) مع ليكاند قاعدة مانخ جديد مشتق من السيبروفلوكساسين . تم استخدام المعقدات بعد ذلك كمصدر  لتحضير جزيئات                              عن طريق ترسيب المعقدات على مسام دقائق السيليكا النانوية.                                                                      Si/Au2O3 Si/PtO2  تم تشخيص الليكاند و معقداته

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Publication Date
Sun Sep 01 2019
Journal Name
Meta Gene
Association of HLA-G + 3142G > C gene polymorphism and toll-like receptor-9 serum level in systemic lupus erythematosus patients
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Background: Human leukocyte antigen-G (HLA-G)and Toll-like receptor-9 (TLR-9)play a role in the regulation of autoimmune diseases and inflammatory processes. Aim of the study: To detect the HLA-G + 3142G > C gene polymorphism that associated with the susceptibility to SLE patients and associated with Hepatitis B infection and TLR-9 serum level. Patients and methods: This study was done on 75 SLE patients and 75 healthy control groups. Genotyping of HLA-G + 3142G > C were detected by PCR and PCR-RFLP methods. In addition to the estimation of Hepatitis B surface (HBs)antigen status by immunochromatography technique and TLR-9 serum level by ELISA technique. Results: The HLA-G + 3142G > C gene polymorphism between the SLE patients and controls

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Publication Date
Sun Jun 05 2022
Journal Name
Egyptian Journal Of Chemistry
Synthesis, Characterization, and Biological Activity of New Metal Ions Complexes with Schiff Base Derived from 2-Acetylthiophene and Isatin-3-Hydrazone
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This study describes the preparation of a new bidentate Schiff base derived from the condensation of Isatin-3-hydrazone with 2-acetylthiophene and the preparation of new series of complexes with a good yield. The prepared ligand was characterized by IR, UV-Vis, C.H.N.S elemental analysis, 1H and 13C NMR, LC-Mass spectroscopy, and physical measurements. Its complexes were analyzed by C.H.N.S elemental analyses, UV-Vis., FTIR, NMR, LC-Mass Spectra, atomic absorption spectroscopy, magnetic susceptibility, and conductivity measurements The results from spectroscopy and measurement studies showed that the ligand coordinated to the metal ion as a bidentate ligand via oxygen and nitrogen, forming an octahedral geometry around it. In vitro antimicr

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Publication Date
Mon Mar 01 2021
Journal Name
World Heart Journal
Change in Left Ventricular Size and Ejection Fraction in Patients at Rest vs. Stress with Different Degrees of Ischemic Heart Failure
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Background and Aim. Coronary artery disease (CAD) is a major risk factor for the progression to heart failure (HF), which is associated with an increase in left ventricular volume (LVV). This study aims to measure ventricular function and myocardial perfusion imaging markers of the left side of the heart, which can be performed with injection of a 99mTc at stress and rest by using single-photonemission-computed-tomography (SPECT). Subject and methods. The study included 121 patients with CAD, comprising 53 females and 68 males with ages between 25 to 88 years and 265 healthy subjects comprising 84 males and 181 females. All patients and healthy subjects volunteered to participate in this study. They were classified according to

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Publication Date
Sun Feb 25 2024
Journal Name
Baghdad Science Journal
Prioritized Text Detergent: Comparing Two Judgment Scales of Analytic Hierarchy Process on Prioritizing Pre-Processing Techniques on Social Media Sentiment Analysis
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Most companies use social media data for business. Sentiment analysis automatically gathers analyses and summarizes this type of data. Managing unstructured social media data is difficult. Noisy data is a challenge to sentiment analysis. Since over 50% of the sentiment analysis process is data pre-processing, processing big social media data is challenging too. If pre-processing is carried out correctly, data accuracy may improve. Also, sentiment analysis workflow is highly dependent. Because no pre-processing technique works well in all situations or with all data sources, choosing the most important ones is crucial. Prioritization is an excellent technique for choosing the most important ones. As one of many Multi-Criteria Decision Mak

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