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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 Jan 01 2018
Journal Name
Internet And Distributed Computing Systems
A Proposed Adaptive Rate Algorithm to Administrate the Video Buffer Occupancy for Smooth Video Streaming
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Publication Date
Thu Dec 01 2022
Journal Name
Iraqi Journal Of Statistical Sciences
Use The Coiflets and Daubechies Wavelet Transform To Reduce Data Noise For a Simple Experiment
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In this research, a simple experiment in the field of agriculture was studied, in terms of the effect of out-of-control noise as a result of several reasons, including the effect of environmental conditions on the observations of agricultural experiments, through the use of Discrete Wavelet transformation, specifically (The Coiflets transform of wavelength 1 to 2 and the Daubechies transform of wavelength 2 To 3) based on two levels of transform (J-4) and (J-5), and applying the hard threshold rules, soft and non-negative, and comparing the wavelet transformation methods using real data for an experiment with a size of 26 observations. The application was carried out through a program in the language of MATLAB. The researcher concluded that

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Publication Date
Tue Jan 01 2019
Journal Name
Technologies And Materials For Renewable Energy, Environment And Sustainability: Tmrees19gr
Theoretical calculations involving a standard neutron yield distribution for the T-T nuclear fusion reaction
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A standard theoretical neutron energy flux distribution is achieved for the triton-triton nuclear fusion reaction in the range of triton energy about ≤10 MeV. This distribution give raises an evidence to provide the global calculations including the characteristics fusion parameters governing the T-T fusion reaction.

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Publication Date
Mon Feb 01 2021
Journal Name
Materials Science Forum
The Feasibility of Using Micro Silica Sand Powder as Partial Replacement of Cement in Production of Roller Compacted Concrete
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Roller compacted concrete (RCC) is a special type of concrete with zero or even negative slump consistency. In this work, it had aimed to produce an RCC mix suitable for roads paving with minimum cost and better engineering properties so, different RCC mixes had prepared i.e. (M1, M2, M3, and M4) using specified percentages of micro natural silica sand powder (SSP) as partial replacement of (0%, 5%, 10%, and 20%) by weight of sulfate resistant Portland cement. Additionally, M-sand, crushed stone, filler, and water had been used. The results had obtained after 28 days of water curing. The control mix (M1) had satisfied the required f ‘c with accepted results for the other tests. M2 mix with SSP of 5% had

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Publication Date
Thu Mar 30 2023
Journal Name
Iraqi Journal Of Science
A Tri-Gene Ontology Migration Operator for Improving the Performance of Meta-heuristics in Complex Detection Problems
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      Detecting protein complexes in protein-protein interaction (PPI) networks is a challenging problem in computational biology. To uncover a PPI network into a complex structure, different meta-heuristic algorithms have been proposed in the literature. Unfortunately, many of such methods, including evolutionary algorithms (EAs), are based solely on the topological information of the network rather than on biological information. Despite the effectiveness of EAs over heuristic methods, more inherent biological properties of proteins are rarely investigated and exploited in these approaches. In this paper, we proposed an EA with a new mutation operator for complex detection problems. The proposed mutation operator is formulate

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Publication Date
Tue Apr 19 2022
Journal Name
Chemistryselect
A Continuous Flow Injection/Indirect Photometric Method for the Detection of Fosetyl Aluminum in Commercial Pesticide Formulations
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Abstract<p>Because of their Physico‐chemical characteristics and its composition, the development of new specific analytical methodologies to determine some highly polar pesticides are required. The reported methods demand long analysis time, expensive instruments and prior extraction of pesticide for detection. The current work presents a new flow injection analysis method combined with indirect photometric detection for the determination of Fosetyl‐Aluminum (Fosetyl‐Al) in commercial formulations, with rapid and highly accurate determination involving only construction of manifold system combined with photometric detector without need some of the pre‐treatments to the sample before the analysis such a</p> ... Show More
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Publication Date
Fri Feb 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
Organizational spirituality and its implications for organizational performance: A survey of the opinions of employees of the General Company for Food Industries in Abu Ghraib (Baghdad)
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The research discusses with organizational spirituality and its implications on the organizational performance in the General Company for Food Industries in Abu Ghraib (Baghdad). The aim of the research was to determine the contribution of organizational spirituality in the organizational performance of the surveyed company. In order to achieve the objectives of the research، two main hypotheses were adopted. Several sub-hypotheses centered on the relationship between organizational spirituality and organizational performance in terms of its dimensions (Meaning work، self-esteem، community affiliation،

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Publication Date
Fri May 07 2021
Journal Name
Journal Of Evaluation In Clinical Practice
Exploring the acceptance of <scp>COVID</scp>‐19 vaccine among healthcare workers and general population using health belief model
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Abstract<sec><title>Rationale, aims and objectives

Little is known about hesitancy to receive the COVID‐19 vaccines. The objectives of this study were (1) to assess the perceptions of healthcare workers (HCWs) and the general population regarding the COVID‐19 vaccines, (2) to evaluate factors influencing the acceptance of vaccination using the health belief model (HBM), and (3) to qualitatively explore the suggested intervention strategies to promote the vaccination.

Methods

This was a cross‐sectional study based on electronic survey data that was collected in Iraq during December first‐19th, 2020. The electronic surve

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Publication Date
Sun Oct 18 2020
Journal Name
Diagnostics
Diagnostic Accuracy of Oral Fluids Biomarker Profile to Determine the Current and Future Status of Periodontal and Peri-Implant Diseases
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Severe periodontitis is ranked as the sixth most prevalent disease affecting humankind, with an estimated 740 million people affected worldwide. The diagnosis of periodontal diseases mainly relies upon assessment of conventional clinical parameters. However, these parameters reflect past, rather than current, clinical status or future disease progression and, likely, outcome of periodontal treatment. Specific and sensitive biomarkers for periodontal diseases have been examined widely to address these issues and some biomarkers have been translated as point-of-care (PoC) tests. The aim of this review was to provide an update on PoC tests for use in the diagnosis and management of periodontal diseases. Among the PoC tests developed so

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Publication Date
Wed Sep 08 2021
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Obstacles facing the application of electronic banking An exploratory: study of the opinions of a sample of bank employees operating in the city of Nasiriyah
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Electronic banking plays a prominent role in providing the best banking services and upgrading the banking sector for the better, so this study aimed to shed light on the most prominent obstacles that prevent the application of electronic banking in banks operating in the city of Nasiriyah, and in order to achieve this goal the researcher used the descriptive analytical approach And through a questionnaire form that was distributed to a group of employees, numbering (60) employees in the upper, middle and operational departments in a number of branches of private banks operating in the city of Nasiriyah, namely (the Iraqi Trade Bank, the Gulf Commercial Bank, the Bank of Baghdad, the Union Bank of Iraq), which represented The stu

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