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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
Wed Dec 10 2014
Journal Name
Desalination And Water Treatment
Groundwater protection from lead contamination using granular dead anaerobic sludge biosorbent as permeable reactive barrier
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Publication Date
Sat Dec 15 2018
Journal Name
Research Journal Of Pharmaceutical, Biological And Chemical Sciences
Synthesis, Spectroscopic and Antimicrobial Studies of Mixed Ligand Metal (II) Complexes with three amino acids
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The research includes synthesis and identification of novel three amino acids ligands complexes of some heavy metal (II) ions by using the amino acids like glycine, L-alanine and L-valine. New metal mixed ligand complexes with amino acids are prepared the reaction by reacting the three amino acids with the metals(II) chloride by using 50% ethanolic solution and 50% distall water in the molar ratio [1:1:1:1] ( M:Gly:Ala:Val) except for Co(II) and Ni(II) complexes were found after diagnosis the coordination with both Lalanine and L-valine. The prepared complexes identified by using physical properties, flame atomic absorption and conductivity measurements, in addition, mass, FT.IR and UV.vis spectrum as well magnetic moment data. The general

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Publication Date
Wed Mar 01 2017
Journal Name
Neural Computing And Applications
The potential of nonparametric model in foundation bearing capacity prediction
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Publication Date
Wed Dec 30 2015
Journal Name
Mathematical Theory And Modeling
On the stability of an SIS epidemic model involving treatment
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The objective of this paper is to study the stability of SIS epidemic model involving treatment. Two types of such eco-epidemiological models are introduced and analyzed. Boundedness of the system is established. The local and global dynamical behaviors are performed. The conditions of persistence of the models are derived.

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Publication Date
Thu Dec 26 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The impact of computerized planning on audit performance (Proposed model)
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The development of technology used in computerized programs is considered on of the most important topics that is responsible for creating tools that can be used in the business environment, the audit profession is one of those professions that received this development. In order for this profession to be more effective, there must be a tool based on sound (correct) scientific basis that can be based upon to enhance the quality of auditing. The research also aims to propose a computerized program to plan the auditing process according to the methods appropriate to the working environment in the audit offices and companies in Iraq. The computerized program was applied to the research sample and the hypothesis of the research has been prov

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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Effect of The Mental image Building Dimensions for The Company to Aattract Attention of Iraqi Consumers for local Products: Exploratory Study
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The survey showed sample opinions of officials in the general company for vegetable oils industry, and the statement of the order of the effect of these dimensions depending on the degree of importance, the questionnaire was used as a key tool in collecting data and information of the sample consisted of 30 officials, arithmetic mean, standard deviation, percentages, Spearman correlation coefficient and the global statistical analysis as a statistical methods that based on statistical program (SPSS), The researcher came to several conclusions, most important that there is high agreement by the respondents of the importance of the dimensions of building a mental picture of the company and to attract the consumer's attention, Also research

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Publication Date
Thu Oct 31 2024
Journal Name
Mathematical Modelling Of Engineering Problems
Investigating the Effects of Canard Dihedral Angle on the Wing Span Loading in a Forward-Swept Wing Aircraft at Transonic Speeds at Steady State Conditions Using Computational Fluid Dynamics
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Forward-swept wings were researched and introduced to improve maneuverability, control, and fuel efficiency while reducing drag and they are often used alongside canards, to further enhance their characteristics. In this research, the effects of canard dihedral angles on the wing loading of a forward-swept wing in transonic flow conditions were studied, as the wing loading provides a measure of wing’s efficiency (lift/drag). A generic aircraft model from literatures was selected, simulated, and compared to, using CFD software ANSYS/Fluent where the flow equations were solved to calculate the aerodynamic characteristics. The research was carried at two different Mach numbers, 0.6 and 0.9, for five different canard dihedral angles which tra

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Publication Date
Sat Nov 30 2024
Journal Name
Iraqi Journal Of Science
Evaluation of Syndecan-1 Expression in Iraqi Patients with Papillary Thyroid Carcinoma
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Papillary thyroid carcinoma (PTC) represents the most prevalent kind of thyroid gland cancer, making up around 80% of all occurrences of thyroid cancer. Evidence shows that Syndecan-1 (SDC-1) expression is lost in a number of benign and malignant epithelial neoplasms, although its expression profile in thyroid gland neoplasms is yet unknown. Therefore, the aim of this study was to assess SDC-1 expression in papillary thyroid carcinoma patients, as well as the relationship between age and gender and SDC-1 expression. To undertake a detailed investigation of SDC-1 in normal and malignant tissues, tissue sections were used to examine SDC-1 expression in 70 tissue samples, 50 distinct PTC (6 males and 44 females) and 20 normal tissue ty

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Publication Date
Sat Jan 01 2022
Journal Name
Tropical Journal Of Natural Product Research
Detection of Herpes Simplex Virus Type 1 in Patients Affected by Conjunctivitis
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Herpes simplex virus (HSV) is a common human pathogen that causes severe infections in newborns and immunocompromised patients. Conjunctivitis or corneal epithelial keratitis is caused by HSV type 1 all over the world and at all times of the year. The present study was aimed at detecting HSV in patients suffering from conjunctivitis. One hundred and ten (110) clinical samples (90 patients and 20 controls, both males and females) of eye conjunctiva swabs were collected from patients of different ages. The samples were analyzed using qPCR and ELISA techniques. The qPCR results revealed that HSV was present in 47 (52.2%) of the 90 patients who were infected. Of these patients, 25 (48.0%) were males and 22 (57.8%) were females, indicati

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Scopus
Publication Date
Mon Jan 01 2018
Journal Name
Journal Of Global Pharma Technology
Detection of HBME-1 and galectin-3 by immunohistochemistry in follicular lesions
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The main problem established by a discovery of a thyroid nodule is to discriminate between a benign and malignant lesion. Differential diagnosis between follicular thyroid cancer (FTC) and benign follicular thyroid adenoma (FTA) is a great challenge for even an experienced pathologist and requires special effort. A developing number of some encouraging IHC markers for the differential diagnosis of thyroid lesions have emerged, including, Hector Battifora mesothelial (HBME-1) and galectin-3 (Gal-3). There was significant positive correlation between Galectin-3 and HBME-1 in follicular carcinoma and follicular variant of papillary carcinoma (r= 0.380, P= 0.041) and (r= 0.315, P=0.047) respectively. There was no significant correlation between

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