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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 Apr 06 2020
Journal Name
Bmc Oral Health
The reliability of surgeons to avoid traumatic insertion of dental implants into high-risk regions: a panoramic radiograph study
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Abstract<sec> <title>Background

The posterior regions of the jaws usually represent a significant risk for implant surgery. A non-valid assessment of the available bone height may lead to either perforation of the maxillary sinus floor or encroachment of the inferior alveolar nerve and consequently to implant failure. This study aimed to evaluate the reliability of surgeon’s decision in appraising the appropriate implant length, in respect to vital anatomical structures, using panoramic radiographs.

Methods

Only implants that are inserted in relation to the maxillary sinus (MS) or the mandibular canal (MC) were enrolled

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Publication Date
Tue Mar 03 2020
Journal Name
International Journal Of Psychosocial Rehabilitation
A Study of Some Biochemical Variables and Functional Indicators and Their Relationship to the Achievement of 200m Young Runners
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ES Hussein

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Publication Date
Wed Jun 01 2022
Journal Name
Political Sciences Journal
Terrorism and its impact on the right of Human in development - A study case of ISIS (Daesh) in Iraq
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       Iraq is one of the most important countries in the world that has received its share of terrorist acts by the terrorist organization the Islamic State of Iraq and al-Sham (ISIS), which has caused instability, especially during the period of ISIS's control of seven Iraqi provinces (2014-2017). This stage has caused a decline in the levels of human and economic development and its inconsistency with the capabilities and needs of the Iraqi population. Therefore, this study aims to investigate the hypothesis that there is a close relationship between the decline in development in Iraq and the brutal practices of ISIS that it committed during his period of control over many Iraqi cities and regions. This study used several method

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Publication Date
Sat Mar 01 2014
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The use of technology review and evaluate programs PERT to improve the cost method on the basis of activity: بحث تطبيقي في الشركة العامة للصناعات النسيجية /واسط
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Suffer most of the industrial sector companies from high Kperfi magnitude of the costs of industrial indirect, lack of equitable distribution of these costs on the objectives of cost, increased competition, and the lack of proper planning in line and changes faced by the industrial sector (general) and sample (private), as well as the difficulty in re- directing efforts to improve profitability and in-depth analysis of activities, and to identify untapped resource activities, then link these activities to the final products  The research aims to apply the technology review and evaluate programs with the method (ABC) through the application stages of planning, scheduling and control and a comparison to get to the products of dev

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Publication Date
Fri Jan 01 2021
Journal Name
Bionatura
STUDY THE TIGRIS RIVER IN SOUTH OF BAGHDAD CITY AND MAY USE IT AS IRRIGATION WATER
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Publication Date
Tue Aug 30 2016
Journal Name
Mechanical Engineering
The Effect of Different Furrow Depths and Speeds of Machinary Units Using A Locally Assembled Combine Implement on Planting Maize
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Publication Date
Thu Aug 04 2022
Journal Name
Journal Of Nanomaterials
Thermal Management of the Melting Process in a Latent Heat Triplex Tube Storage System Using Different Configurations of Frustum Tubes
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In this study, the energy charging mechanism is mathematically modeled to determine the impact of design modifications on the thermofluidic behavior of a phase change material (PCM) filled in a triplex tube containment geometry. The surface area of the middle tube, where the PCM is placed, is supported by single or multi-internal frustum tubes in vertical triplex tubes to increase the performance of the heating and cooling of the system. In addition to the ordinary straight triplex tubes, three more scenarios are considered: (1) changing the middle tube to the frustum tube, (2) changing the inner tube to the frustum tube, and (3) changing both the internal and central tubes to the frustum tubes. The impact of adopting the tube desig

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Publication Date
Sun Oct 09 2022
Journal Name
Journal Of Research In Medical And Dental Science
Efficacy of Locally Applied K-Carrageenan on the Healing of Thermal Burn in Rat-Experimental Model: Histological Study
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ABSTRACT Wound is damage or disruption to the normal anatomical structure and function. Carrageenan is sulphated polysaccharide found in Gigartina, Chondrus and Eucheuma species in the red algal family. Having anticancer, anti-inflammatory and renewal of tissues. Our study aimed to detect the role of kappa carrageenan in the burned skin wound repair. Skin burn were performed in the right and left cheek of 20 male rats (aged 7-8 weeks weighing 300-350 g). Burned skin rats were categorized into two equal groups. Burned areas of right side were treated with a local application of 1 ml of kappa carrageenan solution once daily (treatment group) and the left side receive no treatment (control group). After 5, and 10 days, 5 rats from each

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Publication Date
Sun Dec 31 2023
Journal Name
Sumer Journal For Pure Science
COVID-19Disease Diagnosis using Artificial Intelligence based on Gene Expression: A Review
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Publication Date
Fri Jan 01 2021
Journal Name
Computers, Materials &amp; Continua
A New Hybrid Feature Selection Method Using T-test and Fitness Function
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