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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 Jul 02 2017
Journal Name
Journal Of Educational And Psychological Researches
Prevalence of Posttraumatic Stress Symptomatology and Distribution of Attachment Patterns 1 and 5 Months after a Terrorist Attack
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As a consequence of a terrorist attack, people may experience posttraumatic stress disorder (PTSD) and lack of feeling secure in relationships. This longitudinal study aimed to examine the prevalence of PTSD symptoms over time, the relationship between adult attachment styles and PTSD, as well as their association with degree of exposure, and finally to consider the distribution and the trajectory of attachment styles. The sample consisted of 235 students (M=125, F=110) who were exposed to different levels of trauma intensity in response to a bombing attack. Participants were recruited and assessed approximately 1 month and 5 months after the attack using a battery of questionnaires. Findings revealed, as expected, that 79.5% of the part

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Publication Date
Mon Feb 14 2022
Journal Name
Journal Of Educational And Psychological Researches
The Educational dimensions of children's television programs in the light of the universal rights of child
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The research aims at determining the type of educational dimensions to be broadcasted in children's television programs, clarifying the technical forms used in children's TV programs, analyzing the educational dimensions provided by children's television programs, and studying the educational dimensions of children's television programs. The researcher used a sample of children's programs: all of us heroes, which is a daily program on the mbc3 channel as well as the program of Tel flowers on the Algerian channel. The researcher designed an analysis content form included categories of analysis. Spss program was used to process the collected data. The research reached several results; the concentration of educational dimensions in

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Publication Date
Sun Dec 20 2020
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Negotiating policies for the granting of investment loans: A CASE STUDY ON IRAQI MIDDLE EAST BANK FOR INVESTMENT& COMMERCIAL GULF BANK
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The negotiation phase is gaining great importance in investment loans due to the magnitude of the amounts awarded and the need to obtain adequate lending guarantees and the development of better conditions, and this requires that negotiating policy with fixed principles that balance between meeting the demands of customers and maintain market share and achieve profits and avoid defaults and losses the bank, and so I have touched Find the concept of investment loans and procedures for granting and the concept of the negotiation process for the granting of loans. The practical side to ensure the preparation of examination form consists of questions commensurate with the methodology developed by the researchers, were directed to the officia

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Publication Date
Tue Dec 20 2022
Journal Name
Biomedical And Pharmacology Journal
Phytochemical Comparison Study for Evaluating the Hypolipidemic Effect Between Two Iraqi Pepper Spp in the Rats Model.
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Hypercholesterolemia is a predominant risk factor for atherosclerosis and cardiovascular disease (CVD). The World Health Organization (WHO), ) recommended reducing the intake of cholesterol and saturated fats. On the other hand, limited evidence is available on the benefits of vegetables in the diet to reduce these risk factors, so this research was conducted to compare the hypolipidemic effect between the extracts of two different types of Iraqi peppers, the fruit of the genus Capsicum traditionally known as red pepper extract (RPE), and Piper nigrum as black pepper extract (BPE), respectively, in different parameters and histology of the liver of the experimental animals. The red pepper was extracted by ethyl acetate, while the black pepp

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Publication Date
Fri Nov 01 2024
Journal Name
Current Medicinal Chemistry
Synthesis, In Silico Prediction, and In Vitro Evaluation of Anti-tumor Activities of Novel 4'-Hydroxybiphenyl-4-carboxylic Acid Derivatives as EGFR Allosteric Site Inhibitors
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Introduction:

Allosteric inhibition of EGFR tyrosine kinase (TK) is currently among the most attractive approaches for designing and developing anti-cancer drugs to avoid chemoresistance exhibited by clinically approved ATP-competitive inhibitors. The current work aimed to synthesize new biphenyl-containing derivatives that were predicted to act as EGFR TK allosteric site inhibitors based on molecular docking studies.

Methods:

A new series of 4'-hydroxybiphenyl-4-carboxylic acid derivatives, including hydrazine-1-carbothioamide (S3-S6) and 1,2,4-triazole (S7-S10) derivatives, were synthesized and characterized using IR, 1HNMR, 13CNMR

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Publication Date
Sun Dec 06 2009
Journal Name
Baghdad Science Journal
Study of Molecular Interactions of Water- Soluble Polymer at Several Temperatures in Solution
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Molecular interactions between 2-isopropenylnaphthalene-methacrylic acid (IPNMA) block copolymer( as a model for water- soluble polymer) and methanol at several temperatures were studied using fluorescence techniques , Fluorescence spectrum for (IPNMA) exhibits two emission bands at around 342 nm and 387 nm corresponding to the monomer and the excimer bands , respectively .The fluorescence spectra of dilute solution of (IPNMA) in methanol were recorded in temperature range of 8- 45?C . Plot of the excimer to monomer intensity ratio Ie/Im versus temperature was obtained, which shows double lines with positive slopes crossing at 25?C , the increasing of slope value above this temperature is s

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Publication Date
Sun Dec 18 2022
Journal Name
Journal Of The College Of Basic Education
A (k,ℓ) Span in Three Dimensional Projective Space PG(3,p) Over Galois Field where p=4
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الغرض من هذا العمل هو دراسة الفضاء الإسقاطي ثلاثي الأبعاد PG (3، P) حيث p = 4 باستخدام المعادلات الجبرية وجدنا النقاط والخطوط والمستويات وفي هذا الفضاء نبني (k، ℓ) -span وهي مجموعة من خطوط k لا يتقاطع اثنان منها. نثبت أن الحد الأقصى للكمال (k، ℓ) -span في PG (3،4) هو (17، ℓ) -span ، وهو ما يساوي جميع نقاط المساحة التي تسمى السبريد.

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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)
Formulation and Evaluation of Nystatin Microparticles as a Sustained Release System
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Nystatin is the drug of choice for treatment of cutaneous fungal infections with main disadvantage that is the need for multiple applications to achieve complete eradication which may reduce patient compliance. Microparticles offer a solution for such issue as they are one of sustained release preparations that achieve slow release of drug over an extended period of time. The objectives of this study were to fabricate nystatin-loaded chitosan microparticles with the ultimate goal of prolonging drug release and to analyze the influence of polymer concentration on various properties of microparticles. Microparticles were prepared by chemical cross-linking method using glutaraldehyde as cross-linking agent. Five formulas, namely N1C1, N1C2,

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Publication Date
Fri Jan 01 2016
Journal Name
International Journal Of Applied Pharmaceutics
Preparation of ferrous sulfate microcapsules as a sustained release dosage forms
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Publication Date
Mon Jan 01 2018
Journal Name
Journal Of Cosmetics, Dermatological Sciences And Applications
Cutaneous Leishmaniasis as Imitator of Skin Diseases and a Diagnostic Challenge
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