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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
Fri Jan 01 2021
Journal Name
Journal Of Economics And Administrative Sciences
Formulating a strategy for the Northern Oil Company(Case Study)
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                  The research aims to present a proposed strategy for the North Oil Company, and the proposed strategy took into account the surrounding environmental conditions and adopted in its formulation on the basis and scientific steps that are comprehensive and realistic, as it covered the main activities of the company (production and exploration activities, refining and refining activities, export and transport of oil, research and development activity, financial activity, information technology, human resources) and the (David) model has been adopted in the environmental analysis of the factors that have been diagnosed according to a

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Publication Date
Thu Jan 31 2019
Journal Name
International Journal Of Ambient Energy
Energy generation by membraneless microfluidic fuel cell using acidic wastewater as a fuel
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A simple and novel membraneless paper-based microfluidic fuel cell was presented in this study. The occurrence of laminar flow was employed to ensure no mixing of the fuel and oxidant fluids along the bath of reaction. The acidic wastewater was used as a fuel. It was an air-breathing cell, so air and tab water were used as oxidants. Both the fuel and tab water flowed continuously under gravity. Whatman filter paper was used for preparation of the fuel cell channel and two carbon fibre electrodes were used and firmed on the edges of the cell. The performance of the cell was examined over three consecutive days. The results indicated that the present cell has the potential to generate electric power, but an extensive study is required to harv

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Publication Date
Mon May 15 2017
Journal Name
Journal Of Theoretical And Applied Information Technology
Anomaly detection in text data that represented as a graph using dbscan algorithm
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Anomaly detection is still a difficult task. To address this problem, we propose to strengthen DBSCAN algorithm for the data by converting all data to the graph concept frame (CFG). As is well known that the work DBSCAN method used to compile the data set belong to the same species in a while it will be considered in the external behavior of the cluster as a noise or anomalies. It can detect anomalies by DBSCAN algorithm can detect abnormal points that are far from certain set threshold (extremism). However, the abnormalities are not those cases, abnormal and unusual or far from a specific group, There is a type of data that is do not happen repeatedly, but are considered abnormal for the group of known. The analysis showed DBSCAN using the

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Publication Date
Sun Mar 15 2020
Journal Name
Journal Of The College Of Education For Women
Data-Driven Approach for Teaching Arabic as a Foreign Language: Eygpt
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Corpus linguistics is a methodology in studying language through corpus-based research. It differs from a traditional approach in studying a language (prescriptive approach) in its insistence on the systematic study of authentic examples of language in use (descriptive approach).A “corpus” is a large body of machine-readable structurally collected naturally occurring linguistic data, either written texts or a transcription of recorded speech, which can be used as a starting-point of linguistic description or as a means of verifying hypotheses about a language.  In the past decade, interest has grown tremendously in the use of language corpora for language education. The ways in which corpora have been employed in language pedago

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Publication Date
Mon Jun 01 2020
Journal Name
Journal Of Engineering
GIS as A Tool for Expansive Soil Detection at Sulaymaniyah City
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Geotechnical engineering like any other engineering field has to develop and cope with new technologies. This article intends to investigate the spatial relationships between soil’s liquid limit (LL), plasticity index (PI) and Liquidity index (LI) for particular zones of Sulaymaniyah City. The main objective is to study the ability to produce digital soil maps for the study area and determine regions of high expansive soil. Inverse Distance Weighting (IDW) interpolation tool within the GIS (Geographic Information System) program was used to produce the maps. Data from 592 boreholes for LL and PI and 245 boreholes for LI were used for this study. Layers were allocated into three depth ranges (1 to 2, 2 to 4 and 4 to 6)

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Publication Date
Sun Jan 01 2023
Journal Name
Materials Chemistry And Physics
BC2N nanotube as a promising anode for rechargeable calcium ion batteries
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Because of cost-effective production and abundant resources of calcium, Ca-ion batteries (CIBs) are an appropriate option to alternate Li-ion batteries (LIBs). A new category of anode materials for CIBs has emerged since the successful synthesis of carbon nanotubes, which are B and N doped derivatives of it. For high-performance CIBs, BC2N nanotube (BC2NNT) has been studied as promising anode materials. In order to comprehend electrochemical attributes, cycling stability, and adsorption behavior of BC2NNT, first-principles computations have been executed. Based on nuclear magnetic resonance computations, two types of hexagonal rings (B2C2N2 (I) and BC4N (II)) were specified that are non-aromatic. Ca has adsorption on B2C2N2 and BC4N with ad

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Publication Date
Fri Dec 30 2011
Journal Name
Al-kindy College Medical Journal
Postprandial Hyperglycemia as a Significant Risk Factor for Coronary Heart Disease
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Background: The highest concentrations of
blood glucose during the day are usually found
postprandialy. Postprandial hyperglycemia (PPH)
is likely to promote or aggravate fasting
hyperglycemia. Evidence in recent years suggests
that PPH may play an important role in functional
& structural disturbances in different body organs
particularly the cardiovascular system.
Objective: To evaluate the effect of (PPH) as a
risk factor for coronary Heart disease in Type 2
diabetic patients.
Methods: Sixty-three type2 diabetic patients
were included in this study. All have controlled
fasting blood glucose, with HbA1c correlation.
They were all followed for five months period
(from May to October 2008)

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Publication Date
Wed Jan 01 2025
Journal Name
Journal Of The Indian Chemical Society
Inspection the impact of mixing and external resistance on the Microbial Desalination Cell for electricity generation and desalination efficiency by using Macroalgae as a bio-cathode
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Publication Date
Mon Nov 11 2019
Journal Name
Journal Of Global Pharma Technology
Using the Water Quality Index as a Powerful Tool to Assess the Water Quality for Drinking Purposes in Al-Salam, Western Region of Baghdad City, Iraq
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Background: Tap waters play an important role in fulfilling the people needs for drinking and domestic purposes. Contaminate the tap water with different pollutants has become an issue of great concern for 90% of people who are depended on the tap water as the main source of drinking. Pollutants can make their way easily into the delivering pipes which suffer from the leaking resulting in decreasing the quality of water. Objective: Therefore, assess the water quality for drinking purpose by calculating the water quality index is an important tool to ascertain whether the water is suitable for human consumption or not. Methods: In the present work, the water quality of the Al-Salam, western region of Baghdad city, Iraq was investigated for 7

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Publication Date
Wed Mar 13 2019
Journal Name
Al-khwarizmi Engineering Journal
Transient Behavior Analysis for Solar Energy Storage in PCM-CFM Material Using Equivalent Heat Capacity Method as Storage Model
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A paraffin wax and copper foam matrix were used as a thermal energy storage material in the double passes air solar chimney (SC) collector to get ventilation effect through daytime and after sunset. Air SC collector was installed in the south wall of an insulated test room and tested with different working angles (30o, 45o and 60o). Different SC types were used; single pass, double passes flat plate collector and double pass thermal energy storage box collector (TESB). A computational model based on the finite volume method for transient tw dimensional domains was carried out to describe the heat transfer and storage in the thermal energy storage material of collector. Also, equivalent specific heat metho

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