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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 Jan 01 2024
Journal Name
International Journal Of Clinical And Diagnostic Pathology
Evaluation of transferrin saturation and serum ferritin in assessing body iron status in patients with end stage renal disease
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The study aimed to evaluate the benefits of transferrin saturation percentage (TSAT) and serum ferritin in assessing body iron status, which can influence erythropoietin treatment in patients with ESRD. Forty end-stage renal disease patients on regular hemodialysis participated in this study. Clinical data were obtained. Serum iron, total iron binding capacity, transferrin saturation, ferritin, albumin, creatinine, and C-reactive protein were investigated. Thirty healthy people were enrolled as a control group. ESRD patients had a mean age of 45.1±13.9 years, with 60% being males. They exhibited significantly lower hematocrit (25.3±6.5%), and higher platelet (285.7±148.1x10^9/L) and WBC (9.4±3.1x10^9/L) counts compared to healthy contro

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Publication Date
Thu Mar 15 2018
Journal Name
Journal Of Baghdad College Of Dentistry
In vitro Performance of Polymethyl–methacrylate with Ultra High Density Poly Ethylene Fiber and Nano Zirconium Oxide Particles Composite
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Background: Poly (methyl methacrylate) has been widely utilized for fabrication of dentures for many years as it has good advantages but not achieved all demands of the mechanical properties such as low transverse strength, low impact strength, low surface hardness, high water solubility and high water sorption. Material and method: To provide bonding between ZrO2 nanoparticles and PMMA matrix, the ZrO2 Nano-fillers were surface-treated with a saline coupling agent. Plasma surface treatment of polyethylene (PE) fiber was done to change surface fiber by using DC- glow discharge system. For characterization of interring any functional groups, the (FTIR) spectrum were done .then the mechanical properties studied to choose the appropriate perc

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Publication Date
Tue Oct 01 2024
Journal Name
Journal Of The Faculty Of Medicine Baghdad
Evaluation of Interleukin-31 Serum Levels in Patients with Chronic Kidney Disease on Hemodialysis with and without Uremic Pruritus
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الخلاصة: الحكة اليوريمية لدى مرضى غسيل الكلى يؤثر على أكثر من 40٪ من المرضى. وربما ترتبط الحكة المستمرة بمستويات عالية من الإنترلوكين 31. الاهداف: النظر إلى مستويات مصل إنترلوكين 31 لدى مرضى غسيل الكلى المصابين بمرض الكلى في المرحلة النهائية، سواء مع أو بدون حكة يوريمية. النتائج: لم يكن مستوى المصل [الوسيط (] لـ IL-31 في المرضى الذين يعانون من الحكة اليوريميةأو بدون حكة في عينة مصل ما قبل غسيل الكلى مختلفًا بشكل م

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Publication Date
Fri Dec 14 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Effectiveness of Women's Self-care Instructions concerning Wound, Perineal & Urinary System Care post cesarean section in Baghdad teaching hospital
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Aim: to determine the effectiveness of women's self-care instructions on their post cesarean section care in Baghdad
teaching hospital.
Methodology: The present study used quasi-experimental study design in maternity words in Baghdad teaching
hospital. The sample was collected and follow up for the period (15) January 2014 until 15 May 2014 Nonprobability
(purposive sample) of (100) women post cesarean section divided in to two groups (50) women post
cesarean section considered as a study group, and another (50) women post cesarean section considered as the
control one, A questionnaire designed as a tool to collect data fit the purpose of the study a questionnaire include
demographic variables, Reproductive variables

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Publication Date
Wed Jul 01 2015
Journal Name
Drug Design, Development And Therapy
Effect of Clausena excavata Burm. f. (Rutaceae) leaf extract on wound healing and antioxidant activity in rats
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Publication Date
Thu Jul 31 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Salivary assessment of Interleukin-6, C-reactive protein and albumin in ulcerative colitis patients in relation to oral findings
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Background: Ulcerative colitis disease is a chronic inflammatory condition that affects the gastrointestinal tract. In regulation of this inflammatory process, Interleukin-6, C-reactive proteins and albumin have a major role. Overproduction of IL-6 by immunocompetent cells contributes to activate the liver to produce CRP, transudation of plasma albumin and development of the inflammatory condition. Elevated levels of IL-6 in saliva could be expected, because the saliva-producing cells are part of the digestive system. The purpose of this study was to assess salivary IL-6, CRP and albumin in ulcerative colitis patients in relation to oral findings. Materials and methods: Forty eight saliva specimens collected from three groups of subjects (s

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Publication Date
Mon Feb 25 2019
Journal Name
Iraqi Journal Of Physics
Simulation of thermal lensing in an end-pumped Nd:YAG laser rod with Gaussian and super-Gaussian pump beam profile
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A numerical simulation is made on the thermal lensing effect in an laser diode end-pumped Nd:YAG laser rod. Based on finite element method (FEM), the laser rod temperature distribution is calculated and the focal length is deduced for a Gaussian and super-Gaussian pump beam profiles.

At the pump power of 20W, the highest temperature located at the center of end-pumped face was 345K, and the thermal lens focal length was 81.4mm along the x-z axis. 

The results indicate that the thermal lensing effect sensitively depend on the pump power, waist radius of the pump beam and the pump distribution in a laser rod geometry.

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Publication Date
Sat Jul 01 2017
Journal Name
Energy Procedia
Preparation and Physical Properties of Doped CdBa 2-x Sr x Ca 2 Cu 3 O 8+δ Compound
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Publication Date
Mon Jun 15 2020
Journal Name
Journal Of Baghdad College Of Dentistry
Effect of diabetes mellitus on periodontal health status, salivary flow rate and salivary pH in patients with chronic periodontitis
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Background: Diabetes and periodontitis are considered as chronic diseases with a bidirectional relationship between them. This study aimed to determine and compare the severity of periodontal health status and salivary parameters in diabetic and non-diabetic patients with chronic periodontitis. Materials and Methods: Seventy participants were enrolled in this study. The subjects were divided into three groups: Group I: 25 patients had type 2 diabetes mellitus with chronic periodontitis, Group 2: 25 patients had chronic periodontitis and with no history of any systemic diseases, Group 3: 20 subjects had healthy periodontium and were systemically healthy. Unstimulated whole saliva was collected for measurement of salivary flow rate and pH.

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Publication Date
Thu Jul 15 2021
Journal Name
University Of Samarra
Preparation, Diagnosis and Biological ‎Efficacy of new Ligands Derived from ‎Succinyl Chloride and Their Metal ‎Complexes and non metallic
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The purpose of my thesis is to synthesis two new bidentate ligands ‎which were used to prepare series of metal complexes by reacting the ‎ligands with (M+2 = Mn, Co, Ni, Cu, Cd and Hg) ‎ ‎ Succinyl chloride was used as starting material to synthesis two ‎bidentate ligands (L1) and (L2) by reaction it with 4-chloroaniline ‎‎(L1) and ‎ ‎ (4-aminoacetophenone) (L2) in dichloromethane as a solvent, that ‎are:‎ ‎(L1) = N1,N4-bis (4-chloro phenyl ) succinamide ‎(L2) =N1,N4-bis(4-acetylphenyl)succinamide ‎ The new ligands were characterize by using spectroscopic study ‎‎(Fourier-transform infrared spectroscopy (FT-IR), electronic spectra ( ‎UV-Vis) ,nuclear magnetic resonance(1H,13C-NMR), Mass spectra ‎

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