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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
Thu Dec 30 2021
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
Design a system for an approved video copyright over cloud based on biometric iris and random walk generator using watermark technique
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Publication Date
Tue Jan 01 2019
Journal Name
Technologies And Materials For Renewable Energy, Environment And Sustainability: Tmrees19gr
Study of the effect of using nanomaterial in radiological shielding
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Publication Date
Wed Sep 10 2025
Journal Name
Revista Iberoamericana De Psicología Del Ejercicio Y El Deporte, Issn 1886-8576, Vol. 18, Nº. 4, 2023, Págs. 361-363
The Effect of a Training Curriculum in Developing the Speed Endurance and Strength Characterized By Speed for the Muscles of the Legs for Female Basketball Students
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Autorías: Mariam Liwa Abdel Fattah, Liqaa Abdullah Ali. Localización: Revista iberoamericana de psicología del ejercicio y el deporte. Nº. 4, 2023. Artículo de Revista en Dialnet.

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Publication Date
Wed Dec 30 2015
Journal Name
Al-kindy College Medical Journal
Microbiological and Molecular study On Candida species Isolated From Catheterized ur ine specimen In Ramadi general Teaching Hospital
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Background: A Catheter-associated with candidiasis infection is the most common nosocomial infection and the objective of this work is to isolate and identify Candida species from catheterized patients by ordinary culture and PCR.Objective:To study the isolation and identification of Candida species from catheterized patients by culture media and polymerase chain reaction(PCR).Methods: One hundred and thirty five Candida species isolates were obtained from urine culture of catheterized specimens from male and female patients , During the period between October 2011 to April 2012 , attending AL-Ramadi general teaching Hospital. A quantitative urine culture for isolation and identification of Candida species was. The isolation of Candida s

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Publication Date
Fri Dec 01 2023
Journal Name
Iop Conference Series: Earth And Environmental Science
Effect of Addition Different Levels of Kojic Acid and Sodium Alginate as a substitutes of conventional Antibiotic on the Characteristics of Cryopreserved Semen of Buffalo Bulls
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Abstract<p>This experiment examined the effects of adding sodium alginate and KOJIC acid as substitutes of Conventional antibiotics to soybean lecithin extender on the characteristics of cryopreserved and frozen buffalo bull semen, as well as evaluation of their additions as antibiotics that to help lowering the microbial load. Following the collection and dilution of in the soybean lecithin extender, the experimental treatments were separated into five groups, as follows: T1: (control-) without adding any antibiotics; T2: (control+) adding the conventional antibiotics Gentamicin 0.4 IU and Tylosin 0.08 IU per 100 ml; T3: adding Kojic acid at (0.06 g/L) T4: adding sodium alginate at (0.6 mg/mL)T</p> ... Show More
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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
The impact of volatile oils of three medicinal plants on the bacteria isolated from patients with tonsillitis
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Were collected three types of medicinal plants from their natural habitat after Astkhalasalziot volatile manner steam distillation and determine the quality and quantity of vehicles chemical for each of the oils obtained using a technique JC discouraged when you merge oily thyme and lemon grass against bacteria either when using oils in three did not have a different effect

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Publication Date
Wed Sep 10 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Cephalometric evaluation of a sample of Iraqi adults with normal occlusion using tetragon analysis
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Background: This study aimed to determine the cephalometric values of tetragon analysis on a sample of Iraqi adults with normal occlusion. Material and methods: Forty digital true lateral cephalometric radiographs belong to 20 males and 20 females having normal dental relation were analyzed using AutoCAD program 2009. Descriptive statistics and sample comparison with Fastlicht norms were obtained. Results: The results showed that maxillary and mandibular incisors were more proclined and the maxillary/mandibular planes angle was lower in Iraqi sample than Caucasian sample. Conclusion: It's recommended to use result from this study when using tetragon analysis for Iraqis to get more accurate result.

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Publication Date
Tue Oct 30 2018
Journal Name
Iraqi Journal Of Physics
Evaluation of radioactivity of cereals and legumes using a nuclear impact detector CN-85
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The research aims to evaluate the radioactivity in elected samples of cereals and legume which are wide human consumption in Iraq using Nuclear Track Detectors (NTDs) model CN-85.
The samples were prepared scientifically according to references in this field. After 150 days of exposure, the detector were collected and chemically treated according to scientific sources (etching chemical), nuclear effects have been calculated using the optical microscope.
Radon (222Rn) concentration and uranium (238U) were calculated in unit Bq/m3 and (ppm), the results indicate that the highest concentration of radon and uranium was in yellow corn where the concentration of radon was 137.17×102 Bq/m3 and uranium concentration 2.63 (ppm). The lowest

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Publication Date
Sat Jan 30 2021
Journal Name
مجلة الجامعة العراقية
Organizational Sources of Burnout and determinants of work Performance in light of the COVID-19 Pandemic: a field study of a Sample of Workers in Social Protection Agencies in Iraq)
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The problem of job burnout has become one of the main problems for researchers in social welfare organizations (social protection bodies) - one of the formations of the Ministry of Labor and Social Affairs. Its negative effects increased in light of the COVID-19 pandemic, and in light of the Corona pandemic, the pressures and burdens of workers varied, which resulted in high rates of anxiety, tension, and intellectual and physical exhaustion, and then negatively affected their efficiency in performing work at the individual and organizational level, especially after the increasing tasks of these Bodies in carrying out their role in achieving the general goals and objectives as beingThe general goals are that they are responsible for providi

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Publication Date
Sat Apr 01 2023
Journal Name
Siriraj Medical Journal
The Potential of Vitamin-D-Binding Protein as a Urinary Biomarker to Distinguish Steroid-Resistant from Steroid-Sensitive Idiopathic Nephrotic Syndrome in Iraqi Children
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Objective: To determine the ability of uVDBP to discern SRNS from steroid-sensitive nephrotic syndrome (SSNS) in Iraqi children. Materials and Methods: This cross-sectional study enrolled children with SRNS (n=31) and SSNS (n=32) from the pediatric nephrology clinic of Babylon Hospital for Maternity and Pediatrics over three months. Patients' characteristics in terms of demographics, clinical data, and urinary investigations were collected. Quantitative analysis of uVDBP levels was undertaken via a commercially available ELISA kit. Results: The median uVDBP values were significantly higher (p-value<0.001) in the SRNS group (median=10.26, IQR=5.91 μg/mL) than in the SSNS group (median=0.953, IQR=4.12 μg/mL). A negative correlati

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