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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 Feb 20 2020
Journal Name
Iraqi Poultry Sciences Journal
A precision use of thermostat in livestock monitoring system in a poultry house
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Nowadays, many new technologies developed in a lot of countries. These technologies are promising in many areas such as environmental monitoring, precision agriculture as well as in animal production. The purpose of this study was to define a better understanding of how new and advanced technologies affect the agriculture and livestock sector alike. Although agriculture and animal husbandry are among the most important sectors, advanced equipment and information technology cannot be used adequately. This situation leads to low production efficiency. It is also known that there can be a significant difference in temperature between the position of the climate control sensor (room temperature) and the area occupied by the animal. This study e

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Publication Date
Sat Dec 11 2021
Journal Name
Engineering, Technology And Applied Science Research
Efficiency Assessment of a Signalized Roundabout and a Traffic Intersection in Baghdad City
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In Baghdad city, Iraq, the traffic volumes have rapidly grown during the last 15 years. Road networks need to reevaluate and decide if they are operating properly or not regarding the increase in the number of vehicles. Al-Jadriyah intersection (a four-leg signalized intersection) and Kamal Junblat Square (a multi-lane roundabout), which are two important intersections in Baghdad city with high traffic volumes, were selected to be reevaluated by the SIDRA package in this research. Traffic volume and vehicle movement data were abstracted from videotapes by the Smart Traffic Analyzer (STA) Software. The performance measures include delay and LOS. The analysis results by SIDRA Intersection 8.0.1 show that the performance of the roundab

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Publication Date
Wed Sep 14 2016
Journal Name
Journal Of Baghdad College Of Dentistry
Assessment of Salivary Secretory Immunoglobulin A (sIg A) Level during Fixed Orthodontic Treatment
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Background: The immune system of the oral cavity suffers alterations due to fixed orthodontic treatment which act as potent stimulus for oral secretory immunity. The aims of this study are to estimate the effect of fixed orthodontic appliance on the level of salivary sIgA at different time intervals, and to verify the gender difference. Materials and method: The patient's history, clinical examination, and fixed orthodontic appliances were placed for 30 Iraqi orthodontic adult patients had class II division 1 and/ or class I malocclusion (15 males and 15 females) aged 18-25 years old. The unstimulated whole saliva was collected from each sample immediately before wearing fixed appliance (control group T0 as base line), and after 2 weeks (T1

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Publication Date
Sat Jan 01 2022
Journal Name
Aip Conference Proceedings
Study of ground properties of oxygen isotopes using Cosh potential
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Publication Date
Thu Jan 25 2024
Journal Name
Biomedical Materials
Enhancing the therapeutic potential of curcumin: a novel nanoformulation for targeted anticancer therapy to colorectal cancer with reduced miR20a and miR21 expression
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Abstract<p>Curcumin (Cur) possesses remarkable pharmacological properties, including cardioprotective, neuroprotective, antimicrobial, and anticancer activities. However, the utilization of Cur in pharmaceuticals faces constraints owing to its inadequate water solubility and limited bioavailability. To overcome these hurdles, there has been notable focus on exploring innovative formulations, with nanobiotechnology emerging as a promising avenue to enhance the therapeutic effectiveness of these complex compounds. We report a novel safe, effective method for improving the incorporation of anticancer curcumin to induce apoptosis by reducing the expression levels of miR20a and miR21. The established</p> ... Show More
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Publication Date
Mon Feb 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Employment of critical success factors in achieving the strategy Entrepreneurship: A field research for my company Oil Products Distribution and Midland Refineries
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Abstract

        The critical success factors of the means of the most modern in determining the main directions for organizations to achieve competitive advantage. and can be a critical success factors in organizations that overlap in the functional areas of the organization. that successful organizations use these factors to get to the uniqueness and distinction. as the entrance of critical success factors with the capacity Evaluative phase correction because discovery increases the perception of managers of what is important to the organization and using them to get to the Strategic Entrepreneurship. as it begins in terms of permanence of success and

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
Study for evidence of bacteria contamination in the southern part of the Diyala River / Iraq
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Were studied some bacteria evidence of pollution as well as the total number of live bacteria in the waters of the Diyala river and selected five stations within the 17 km final Diyala River before its mouth in the Tigris River was the first before the new bridge of the Diyala River about 4 km and the second after the mouth of the water purification plant Rustumiya suit inverselywith temperatures

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Publication Date
Fri Mar 17 2017
Journal Name
Elixir Mech. Engg. 109 (2017) 47879-47881, Www. Elixirpublishers. Com …‏
Effect of Cutting Angle for a Locally Assembling Motorized Vibration Cutter on Some Operational Characteristics Used for Date Palm Fronds Cutting
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Publication Date
Mon Sep 15 2025
Journal Name
Alustath Journal For Human And Social Sciences
Searching for Meaning in a Chaotic World: An Analysis of Tina Howe’s Birth and After Birth
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Publication Date
Sat Jan 01 2022
Journal Name
Journal Of Engineering
Efficient Energy Management for a Proposed Integrated Internet of Things-Electric Smart Meter (2IOT-ESM) System
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In this work, an efficient energy management (EEM) approach is proposed to merge IoT technology to enhance electric smart meters by working together to satisfy the best result of the electricity customer's consumption. This proposed system is called an integrated Internet of things for electrical smart meter (2IOT-ESM) architecture. The electric smart meter (ESM) is the first and most important technique used to measure the active power, current, and energy consumption for the house’s loads. At the same time, the effectiveness of this work includes equipping ESM with an additional storage capacity that ensures that the measurements are not lost in the event of a failure or sudden outage in WiFi network. Then then these measurement

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