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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
Sat Aug 01 2020
Journal Name
Journal Of Engineering Science And Technology (jestec)
Influence of A River Water Quality on The Efficiency of Water Treatment Using Artificial Neural Network
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Tigris River is the lifeline that supplies a great part of Iraq with water from north to south. Throughout its entire length, the river is battered by various types of pollutants such as wastewater effluents from municipal, industrial, agricultural activities, and others. Hence, the water quality assessment of the Tigris River is crucial in ensuring that appropriate and adequate measures are taken to save the river from as much pollution as possible. In this study, six water treatment plants (WTPs) situated on the two-banks of the Tigris within Baghdad City were Al Karkh; Sharq Dijla; Al Wathba; Al Karama; Al Doura, and Al Wahda from northern Baghdad to its south, that selected to determine the removal efficiency of turbidity and

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Publication Date
Sun Dec 07 2008
Journal Name
Baghdad Science Journal
Improvement of the monochrome image hologram by using a random phase and increasing number of Samples
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This paper present a study about effect of the random phase and expansion of the scale sampling factors to improve the monochrome image hologram and compared it with previous produced others. Matlab software is used to synthesize and reconstruction hologram.

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Publication Date
Wed Apr 15 2020
Journal Name
Journal Of Engineering Science And Technology
INFLUENCE OF A RIVER WATER QUALITY ON THE EFFICIENCY OF WATER TREATMENT USING ARTIFICIAL NEURAL NETWORK
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Publication Date
Thu Apr 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Rainwater Drainage Service Improvement Using a Number Of Quality Tools at the Directorate of Karbala Sewage
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The basic objective of the research is to study the quality of the water flow service in the Directorate of Karbala sewage and how to improve it after identifying the deviations of the processes and the final product and then providing the possible solutions in addressing the causes of the deviations and the associated quality gaps. A number of quality tools were used and applied to all data Stations with areas and activities related to the drainage of rainwater, as the research community determines the stations of lifting rainwater in the Directorate of the streams of Karbala holy, and the station was chosen Western station to apply the non-random sampling method intended after meeting a number of. It is one of the largest and m

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Publication Date
Sat Aug 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
A conceptual Framework For the Relationship between Human and Social Capital
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Purpose: The research seeks to develop the implications of intellectual human capital, and social capital in business organizations, and will be accomplished on three levels, the first level (the level of description) to identify, diagnose and display content philosophical Strategic Human Resource Management at the thought of modern administrative represented by human capital and Ras social capital. The second level (level of analysis) and the analysis of the extent of the impact of alignment between human capital, and social capital in the organizational strength of the organizations. The third level (Level predict) the formulation of a plan to strengthen the organizational strength in business organizations and to develop speci

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Publication Date
Sun Apr 11 2021
Journal Name
Environment, Development And Sustainability
Developing a system for assessing the sustainability in school building projects
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Publication Date
Tue Mar 01 2022
Journal Name
International Journal Of Nonlinear Analysis And Applications
The suggested threshold to reduce data noise for a factorial experiment
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In this research, a factorial experiment (4*4) was studied, applied in a completely random block design, with a size of observations, where the design of experiments is used to study the effect of transactions on experimental units and thus obtain data representing experiment observations that The difference in the application of these transactions under different environmental and experimental conditions It causes noise that affects the observation value and thus an increase in the mean square error of the experiment, and to reduce this noise, multiple wavelet reduction was used as a filter for the observations by suggesting an improved threshold that takes into account the different transformation levels based on the logarithm of the b

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Publication Date
Sat Sep 04 2021
Journal Name
Neuroquantology
Nanotechnology and the Most Important Characterization Techniques for Nanomaterial's: A Review
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Due to the importance of nanotechnology because of its features and applications in various fields, it has become the focus of attention of the world and researchers. In this study, the concept of nanotechnology and nanomaterials was identified, the most important methods of preparing them, as well as the preparation techniques and the most important devices used in their characterization.

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Publication Date
Thu Feb 15 2024
Journal Name
Journal Of Theoretical And Applied Information Technology
CHOOSING THE RIGHT CHAOTIC MAP FOR IMAGE ENCRYPTION: A DETAILED EXAMINATION
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This article investigates how an appropriate chaotic map (Logistic, Tent, Henon, Sine...) should be selected taking into consideration its advantages and disadvantages in regard to a picture encipherment. Does the selection of an appropriate map depend on the image properties? The proposed system shows relevant properties of the image influence in the evaluation process of the selected chaotic map. The first chapter discusses the main principles of chaos theory, its applicability to image encryption including various sorts of chaotic maps and their math. Also this research explores the factors that determine security and efficiency of such a map. Hence the approach presents practical standpoint to the extent that certain chaos maps will bec

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Publication Date
Mon Jan 01 2018
Journal Name
Al–bahith Al–a'alami
Using Social Media sites by the Iraqi women and the Achieved The Use of Iraqi Women of Social Networking Sites and the Satisfactions Generated from Them.: A Survey Study of the City of Baghdad
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The problem of this research lies in the fact that there is a lack of accurate scientific perceptions about the size of the use of Iraqi women’s social networking sites and the motives behind this use and the expectations generated by them.
The goals of the research are as follows:
1- Determine the extent of Iraqi women’s use of social networking sites (Facebook, YouTube, twitter, and Instagram).
2- Investigative the motives behind the use of social networking sites by Iraqi women.
3- Detecting the repercussions of Iraqi women’s use of social networking sites (Facebook, you tube, twitter, and Instagram).
The research is classified as a descriptive one. The researchers use the survey methodology. The research commu

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