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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
Mon Aug 26 2019
Journal Name
Global Proceedings Repository American Research Foundation
Preparation, Spectra and Biological Properties of Transition Metals ((III) and (II) Mixed - Ligand Complexes with 5-Chlorosalicylic Acid and L-Valine
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Mixed ligand metal complexes of CrIII, FeIII,II, NiII and CuII have been synthesized using 5-chlorosalicylic acid (5-CSA) as a primary ligand and L-Valine (L-Val) as secondary ligand. The metal complexes have been characterized by elemental analysis, electrical conductance, magnetic susceptibility measurements and spectral studies. The electrical conductance studies of the complexes indicate their electrolytic nature. Magnetic susceptibility measurements revealed paramagnetic nature of the all complexes. Bonding of the metal ion through –OHand –COOgroups of bidentate to the 5-chlorosalicylic acid and through –NH2 and –COOgroups of bidentate to the L-valine by FT-IR studies . The agar diffusion method has been used to study the antib

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Publication Date
Wed Jan 01 2020
Journal Name
Iraqi National Journal Of Nursing Specialties
Effectiveness of Health Educational Program on Nurses’ Knowledge About Communication Skills with Children at Welfare Children Teaching Hospital in Baghdad City
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Background: Therapeutic communication is the basis of interactive relationships among nursing team and their children: that affords opportunities to establish rapport, understand the client’s experience, formulate individualized or client interventions and optimize health care resources.

Objectives: The main aim of the study is to determine the Effectiveness of Education Program on Nurses’ Knowledge about Communication Skills with Children.

Methodology: A quasi-experimental study was conducted in Children Welfare Teaching Hospitals from 7th, October 2018 to the 20th, May 2019. The program and instruments have been constructed by the researcher for the purpose of the study. A non- prob

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Publication Date
Mon Apr 01 2024
Journal Name
Medical Journal Of Babylon
Clinical Evaluation and Comparison between Effects of Rituximab and Prednisolone with Imuran to Neutrophils and Platelet Counts in Pemphigus Vulgaris Patients
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Background: Pemphigus vulgaris (PV) is an autoimmune vesiculobullous mucocutaneous disease with life-threatening consequences. Rituximab (RTX) has recently emerged as an effective treatment for PV. Objectives: This study aims to determine changes in neutrophil and platelet counts for PV patients treated with RTX or corticosteroids combined with Imuran (azathioprine). Materials and Methods: The present cross-sectional study was conducted in the Department of Dermatology at Baghdad Teaching Hospital, Baghdad, Iraq. Thirty PV patients received two types of treatment: 15 patients were administered RTX and 15 patients took corticosteroids with Imuran (azathioprine). Neutrophil and platelet counts were detected at the hospital laboratory. Results

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Publication Date
Fri Mar 01 2019
Journal Name
Iraqi Journal Of Physics
Structural and optical properties of Fe- doped ZnO thin films prepared by Sol–Gel spin coating process and their photocatalytic activities
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Pure and Fe-doped zinc oxide nanocrystalline films were prepared
via a sol–gel method using -
C for 2 h.
The thin films were prepared and characterized by X-ray diffraction
(XRD), atomic force microscopy (AFM), field emission scanning
electron microscopy (FE-SEM) and UV- visible spectroscopy. The
XRD results showed that ZnO has hexagonal wurtzite structure and
the Fe ions were well incorporated into the ZnO structure. As the Fe
level increased from 2 wt% to 8 wt%, the crystallite size reduced in
comparison with the pure ZnO. The transmittance spectra were then
recorded at wavelengths ranging from 300 nm to 1000 nm. The
optical band gap energy of spin-coated films also decreased as Fe
doping concentra

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Publication Date
Sun Mar 01 2020
Journal Name
Baghdad Science Journal
Evaluation of Sex Hormone Levels in Benign Prostatic Hyperplasia Patients Treated with 5 Alpha-Reductase Inhibitor (Finasteride) in Amara city/Iraq
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The present study aimed to determine the serum sex hormone levels among Benign Prostatic Hyperplasia (BPH) patients before and after 3 months of oral administration of 5-α reductase inhibitor(finasteride). Forty BPH patients and 40 healthy men from Amara city were involved in this study, their ages were between 40-59 year. They were all subjected  to direct estimation of hormones by MinVidas method including Testosterone (T), Estradiol (E2), Follicle Stimulating Hormone (FSH), Luteinizing Hormone (LH), Prolactin (PRL), and Dihydrotestosterone (DHT) before and after 3 months of treatment with 5α-reductase inhibitor (finasteride) (the healthy individuals didn’t take finasteride).The results showed that T level was significantly lo

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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
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
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
Fri Sep 15 2017
Journal Name
Journal Of Baghdad College Of Dentistry
Impact of bitter taste threshold on caries experience in relation to ABO blood types among dental students at Al Kufa University
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Background: Blood group system and the ability to taste phenylthiocarbamide (PTC) are the most studied traits in human genetics which have been extensively used in describing genetic variations among human populations around the world that may had an effect on dental caries. The aims of present study were to investigate the caries experience among students with different bitter taste threshold in relation to blood type. Materials and Methods: The sample of present study includes dental students female aged19-21 years. The diagnosis of dental caries was done according to the criteria of Manjia et al, 1989 recording decayed lesion by severity (D1-4) MFS. Furthermore, bitter taste sensitivity was measured according to PTC (phenylthiocarbamid

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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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