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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
Sun Mar 02 2008
Journal Name
Baghdad Science Journal
Effect of Some Fungal Pathogen and Some Storage Treatments on Tomato and Cucumber Fruits Under Cold Storage (8? C)
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In study carried out in the cold storage in college of Agric./Univ. of Baghdad at 8 ? C. shows that Alternaria , Pencillium , Rhizoctonia , Mucor , are the fungi that causes tomato fruits decay. This is the first record of Rhizoctonia and Mucor as a Tomato fruits rot under 8º c in Iraq. There is no fungal infection on cucumber fruits under 8 ? C. . Waxing tomato fruits reduced the severity of the fungi infection and gave shelflife (19 days) under 8 ? C. There is an infection with Mucor was found in tomato fruits kept in perforated polyethylene bages with 16 bores prevent the infection and the lowest severity and frequency of infection was found in waxed tomato fruits. Part of M.Sc thesis of the Second author.

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Publication Date
Wed Sep 01 2021
Journal Name
Meta Gene
Genetic polymorphism of IL-17A (rs2275913) in Iraqi women with recurrent abortion and its relationship with susceptibility to toxoplasmosis
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Publication Date
Sun Jan 01 2012
Journal Name
The First Scientific Conference The Collage Of Education For Pure Sciences 2012
Synthesis, Spectroscopic and Biological Studies of some metal ions complexes with 2-hydroxy-N-pyridin-2-yl methyl-acetamide
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The ligand 2-Hydroxy-N-pyridin-2-ylmethyl-acetamide(L) has been prepared from reaction of 2-(aminomethyl)pyridin with chloroacetic acid (1:1).It has been characterized by elemental analysis (C,H,N) ,'H, 13 C-NMR, IR and electronic spectra. The complexes of divalent (Co,Ni,Cu,Zn,Cd and Hg) ions and trivalent(Cr) ion have been synthesized and characterized by IR, electronic spectra, molar conductivity, atomic absorption and molar ratio (Ni 2+) complex. The analytical studies for the complexes show; octahedral for (Cr 3+),square planar for (Cu 2+) and (Co,Ni Zn, Cd and Hg) tetrahedral geometries. The study of biological activity of the ligand (L) and its complexes (Co,Ni,Cu,Cd,Hg) in two deferent concentration (1and5) mg/ml showed various acti

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Publication Date
Sat Dec 01 2018
Journal Name
Ibn Al-haitham Jour. For Pure & Appl. Sci.
Estimation of Pentraxin-3(PTX3) in Rheumatoid Arthritis Males’ patients (with and without) Type II Diabetes Mellitus in Iraq
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Rheumatoid arthritis is a chronic inflammatory autoimmune disease its etiology is unknown. The classical autoimmune diseases, have adaptive immune genetic associations with autoantibodies and major histocompatibility complex (MHC) class II such as rheumatoid arthritis (RA), diabetes mellitus type two (DM II). Serum of99 males suffering from RA without DMII as group (G1), 45 males suffering from RA with DM II as group (G2) and 40 healthy males as group (G3) were enrolled in this study to estimation of alkaline phosphates (ALP), C-reactive protein (CRP) and Pentraxin-3(PTX). Results showed a highly significant increase in PTX3 levels in G1 and G2 compared to G3 and a significant decrease in G1comparing to G2. Results also revealed a significa

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Publication Date
Sun Jun 05 2016
Journal Name
Baghdad Science Journal
Determination of Water-Soluble Vitamins in Iraqi Honey Bee and Compare with Others Types by High –Performance Liquid Chromatography
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High-performance liquid chromatographic methods are used for the determination of water-soluble vitamins with UV-Vis. Detector. A reversed-phase high-performance liquid chromatographic has been developed for determination of water-soluble vitamins. Identification of compounds was achieved by comparing their retention times and UV spectra with those of standards solution. Separation was performed on a C18 column, using an isocratic 30% (v/v) acetonitril in dionozed water as mobile phase at pH 3.5 and flow rate 1.0m/min. The method provides low detection and quantification limits, good linearity in a large concentration interval and good precision. The detection limits ranged from 0.01 to 0.025µg/ml. The accuracy of the method was

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Publication Date
Tue Aug 16 2022
Journal Name
World Journal Of Biology Pharmacy& Health Science
Long-term results of balloon pulmonary valvuloplasty in pediatric age group in surgical specialty teaching hospital/cardiac center/Hawler
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Congenital valvular pulmonary stenosis accounts for 5-10% of all congenital heart disease. Balloon pulmonary valvuloplasty is a safe and effective method in reduction of moderate to severe valvular pulmonary stenosis. This retrospective study done in Hawler surgical specialty cardiac center on pediatric patients who had pulmonary valve stenosis (with echocardiographic peak gradient 2:50mmHg) and treated by balloon pulmonary valvuloplasty. A total of 178 cases were involved, 93(52.25%) patient was male and 85 (47.75%) patients was female. 160 patient (89.89%) were treated with single balloon method 18 patient (10.11%) were managed by double balloon method technique. Follow up period of these patients range from 1 year to 10 years (mean of 5.

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Publication Date
Sat Apr 29 2023
Journal Name
Research Journal Of Pharmacy And Technology
Effect of Omega 7 on Some Parameters Related to WBCs and RBCs in Methotrexate-induce Blood Toxicity in Mice
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Background: Although methotrexate (MTX) is a frequently used chemotherapy drug, its effectiveness is sometimes hampered by the drug's toxic consequences. Omega 7 is a monounsaturated fatty acid, with different anti-inflammatory, anti-diabetic anti-obesity applications, and its possible protective effects against MTX-induced blood toxicity were investigated in this study. Objective: Evaluation of possible protective effects of omega7 against MTX-induced blood toxicity. Methods: 30 mice were divided into five groups, the First group take liquid paraffin orallyfor 7 days for served as negative control and the second group take methotrexate (20mg/kg) intraperitoneallyto serve as a positive control,the third group takes omega 7 (100mg/kg

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Publication Date
Sun Mar 04 2012
Journal Name
Baghdad Science Journal
Biochemical and Kinetic Studies on Alkaline Phosphatase and other Biochemical Features in Sera of Patients with type 2 Diabetes
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Background :Alkaline phosphatase (ALP) was a widely used marker for skeletal and hepatobiliary disorders, but its activity was also increased in atherosclerosis and peripheral vascular disease. Several study has showed that ALP activity was increased in the sera of diabetic patients. The current study was conducted to evaluate ALP activity in type 2 diabetic patients and optimum conditions for enzyme activity in their sera.Methods: This study was carried out at in AL-Yarmok hospital(diabetic center) between February /2009 and April /2009. Fifty two patients with type 2 diabetes have been enrolled. Besides BMI, WHR, serum fasting blood glucose, ALP, HbA1C,uric acid and lipid profile levels have been performed .The relationship bet

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Publication Date
Thu Dec 01 2022
Journal Name
Archives Of Razi Institute
Assessment of Interleukin-13(rs20541) Genomic Polymorphism in Patients with Acute Respiratory Distress Syndrome in Relation to COVID19 Infection
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Elevated Interleukin-13 (IL-13) may play an important role in the pathophysiology of COVID-19, yet, the attenuated response did not notice across all severe cases. Susceptibility to asthma in specific populations is associated with several SNPs of multifunctional cytokines, such as IL-13, IL-31 and IL-33. This prospective case-control study is designed to investigate the extent of genetic susceptibility in subsets of Iraqi patients with COVID-19 by targeting the variants of interleukin IL-13rs20541 polymorphism in relation to disease susceptibility and severity of clinical presentation. One hundred samples were obtained from the throat, nasopharyngeal and nasal swabs enrolled in this study. Eighty samples of the throat, nasopharyngeal and

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
Effect of Capsicum grossum L. and Allium cepal L. Juice on some bacterial species isolated from contamiinated vegetable salad
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Twenty four bacterial isolates were identified from (10) places for wandering sellers in south Baghdad city (Bayaa garage). They were Staphylococcus aureus (9 isolates), Bacillus subtilis (6 isolates), Salmonella spp. (4 isolates) and Psudomonas aeruginosa (5 isolates). Agar well diffusion method was used to definition sensitivity of the fresh and dried juice of Capsicum grossum L. and Allium cepal L. at different concentrations. The fresh juice had no inhibitory activity against the bacterial isolates in contrast to the fresh juice , dried juice which show marked activity against all bacterial isolates at (30) mg/ml.

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