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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
Tue Feb 26 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Role Lean Accounting in Support Corporate Governance to Achieve a Competitive Advantage: An Application Study in Diala State Company for Electrical industrial
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        The modern business environment has witnesses tremendous developments as a result of the globalization of markets and economic openness and technological as well as the acquisition of the issue of corporate governance of great importance regarding it as one of the global innovations trends of control provisions on the management of companies as result of these developments ,increasing on competition between economic unit ,thus a decrease in market share because they do not take into account the response to the requirements of customers ,which kept her to search a modern management accounting methods to help them keep up with the changes and the availability of information for the various adminis

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Publication Date
Mon Jan 01 2018
Journal Name
Journal Of Physics: Conference Series
Study electron transport coefficients for Ar, O2 and their mixtures by using EEDF program
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Publication Date
Sat Oct 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Harnessing Innovative Solutions for Achieving Continuous Quality Improvement Requirements in Water Treatment Plants: A Case Study of Continuous Quality Improvement in Baghdad Water Authority.
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Abstract

This Research aims for harnessing critical and innovative thinking approaches besides innovative problem solving tools in pursuing continual quality improvement initiatives for the benefit of achieving operations results effectively in water treatment plants in Baghdad Water Authority. Case study has been used in fulfilling this research in the sadr city water treatment plant, which was chosen as a study sample as it facilitates describing and analyzing its current operational situation, collecting and analyzing its own data, in order to get its own desired improvement opportunity be done. Many statistical means and visual thinking promoting methods has been used to fulfill research task.

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Publication Date
Mon Jan 01 2024
Journal Name
Journal Of Industrial And Engineering Chemistry
Petroleum refinery wastewater treatment using a novel combined electro-Fenton and photocatalytic process
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Publication Date
Wed Feb 06 2013
Journal Name
Eng. & Tech. Journal
A proposal to detect computer worms (malicious codes) using data mining classification algorithms
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Malicious software (malware) performs a malicious function that compromising a computer system’s security. Many methods have been developed to improve the security of the computer system resources, among them the use of firewall, encryption, and Intrusion Detection System (IDS). IDS can detect newly unrecognized attack attempt and raising an early alarm to inform the system about this suspicious intrusion attempt. This paper proposed a hybrid IDS for detection intrusion, especially malware, with considering network packet and host features. The hybrid IDS designed using Data Mining (DM) classification methods that for its ability to detect new, previously unseen intrusions accurately and automatically. It uses both anomaly and misuse dete

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Publication Date
Wed Jun 30 2021
Journal Name
Journal Of Economics And Administrative Sciences
A Comparison between robust methods in canonical correlation by using empirical influence function
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       Canonical correlation analysis is one of the common methods for analyzing data and know the relationship between two sets of variables under study, as it depends on the process of analyzing the variance matrix or the correlation matrix. Researchers resort to the use of many methods to estimate canonical correlation (CC); some are biased for outliers, and others are resistant to those values; in addition, there are standards that check the efficiency of estimation methods.

In our research, we dealt with robust estimation methods that depend on the correlation matrix in the analysis process to obtain a robust canonical correlation coefficient, which is the method of Biwe

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Publication Date
Fri Jan 20 2023
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
A Review Article: Green Synthesis by using Different Plants to preparation Oxide Nanoparticles
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Green nanotechnology is a thrilling and rising place of technology and generation that bracesthe ideas of inexperienced chemistry with ability advantages for sustainability, protection, andthe general protection from the race human. The inexperienced chemistry method introduces aproper technique for the production, processing, and alertness of much less dangerous chemicalsubstances to lessen threats to human fitness and the environment. The technique calls for inintensity expertise of the uncooked materials, particularly in phrases in their creation intonanomaterials and the resultant bioactivities that pose very few dangerous outcomes for peopleand the environment. In the twenty-first century, nanotechnology has become a systematic

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Publication Date
Thu Jan 11 2018
Journal Name
Al-khwarizmi Engineering Journal
Control on a 2-D Wing Flutter Using an Adaptive Nonlinear Neural Controller
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An adaptive nonlinear neural controller to reduce the nonlinear flutter in 2-D wing is proposed in the paper. The nonlinearities in the system come from the quasi steady aerodynamic model and torsional spring in pitch direction. Time domain simulations are used to examine the dynamic aero elastic instabilities of the system (e.g. the onset of flutter and limit cycle oscillation, LCO). The structure of the controller consists of two models :the modified Elman neural network (MENN) and the feed forward multi-layer Perceptron (MLP). The MENN model is trained with off-line and on-line stages to guarantee that the outputs of the model accurately represent the plunge and pitch motion of the wing and this neural model acts as the identifier. Th

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Publication Date
Fri Oct 02 2020
Journal Name
Biochem. Cell. Arch.
MORPHOLOGICAL DESCRIPTION AND COMPARATIVE HISTOLOGICAL STUDY OF THE LIVER IN TWO IRAQI MAMMALS : WEASEL (HERPESTES JAVANICUS) AND EASTERN GRAY SQUIRREL (SCIURUS CAROLINENSIS
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The results of the current study showed that the liver of H. javanicus appeared as large lobulated organ divided into six distinct lobes, that filled the cranial region and little extended to the middle region of abdominal cavity. On the other hand, liver of S. carolinensis laid against the diaphragm, occupied the cranial region of the abdominal cavity and consisted of five lobes. The liver is surrounded with a thin capsule of dense regular collagenous connective tissue and few numbers of smooth muscles fibers can be seen in the capsule that covered the squirrel liver. The liver parenchyma divided into a large number of interconnected hepatic lobules marked only by the abundant amount of connective tissue bordered the triads, and within the

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Publication Date
Sun Nov 01 2015
Journal Name
Journal
Topical 40% Loranthus europaeus Ointment Versus Topical 25% Podophyllin Solution in the Treatment of Acute Cutaneous Leishmaniasis (Single Blinded, Therapeutic, Comparative study)
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KE Sharquie, AA Noaimi, BAM Saleh, 2015

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