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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 Mar 31 2025
Journal Name
Iraqi Statisticians Journal
Hypothesis Testing for Non-Normal Multiple Compact Regression Model
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Generalized multivariate transmuted Bessel distribution belongs to the family of probability distributions with a symmetric heavy tail. It is considered a mixed continuous probability distribution. It is the result of mixing the multivariate Gaussian mixture distribution with the generalized inverse normal distribution. On this basis, the paper will study a multiple compact regression model when the random error follows a generalized multivariate transmuted Bessel distribution. Assuming that the shape parameters are known, the parameters of the multiple compact regression model will be estimated using the maximum likelihood method and Bayesian approach depending on non-informative prior information. In addition, the Bayes factor was used

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Publication Date
Sat May 01 2021
Journal Name
Journal Of Physics: Conference Series
Runge-kutta Numerical Method for Solving Nonlinear Influenza Model
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Abstract<p>The main object of this study is to solve a system of nonlinear ordinary differential equations (ODE) of the first order governing the epidemic model using numerical methods. The application under study is a mathematical epidemic model which is the influenza model at Australia in 1919. Runge-kutta methods of order 4 and of order 45 for solving this initial value problem(IVP) problem have been used. Finally, the results obtained have been discussed tabularly and graphically.</p>
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Publication Date
Mon Apr 25 2022
Journal Name
Knowledge And Information Systems
Unsupervised model for aspect categorization and implicit aspect extraction
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People’s ability to quickly convey their thoughts, or opinions, on various services or items has improved as Web 2.0 has evolved. This is to look at the public perceptions expressed in the reviews. Aspect-based sentiment analysis (ABSA) deemed to receive a set of texts (e.g., product reviews or online reviews) and identify the opinion-target (aspect) within each review. Contemporary aspect-based sentiment analysis systems, like the aspect categorization, rely predominantly on lexicon-based, or manually labelled seeds that is being incorporated into the topic models. And using either handcrafted rules or pre-labelled clues for performing implicit aspect detection. These constraints are restricted to a particular domain or language which is

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Publication Date
Thu Jan 16 2020
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Suggested Model for activating the roleof the regulators for the auditing professionin achieving quality audit: دراسة تطبيقية في الشركة العامة للصناعات النسيجية- واسط
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The modern business environment Witness tremendous.These developments result from globalization of markets and economic and technological openness. Those developments resulting a heightened competition between economic units and higher the costs of their products and lower their functional characteristics. They do not take into account the response to the requirements of customers. This matter commit it to search for scientific methods to help it to cope with the happening changes and improve its competitive position, The current study acquired its importance by providing significance through by applicable integrated framework to reduce the costs of products. This reduction should be without compromising their quality by using the integr

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Publication Date
Wed Jun 01 2011
Journal Name
Journal Of Economics And Administrative Sciences
Diagnosis of the reality of marketing knowledge management"A survey of the views of a sample of telecom operatorsIn the city of Sulaymaniyah "
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This research aimed to diagnose the perception based on Telecommunications of Iraq to the importance of activating knowledge management marketing in possession, as well as Indication of impediments to activate the management of marketing knowledge in the researched companies, also aimed to show the extent of the existence of significant differences in perception based on Telecommunications Iraqi importance of activating the management marketing knowledge in possession. To achieve the objectives of this research, the questionnaire was developed and distributed to a sample of telecommunications companies in the city of Sulaimaniya, was selected on the criterion according to the company's life in terms of seniority in the telecommunication

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Publication Date
Mon May 19 2025
Journal Name
Retos
The effect of the cube model on visual-spatial intelligence and learning the skill of spiking in volleyball for female students
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Objective: To identify the effect of the cube model on visual-spatial intelligence and learning the skill of spikinging in volleyball for female students, The researchers used the experimental method by designing two equivalent groups with pre- and post-measurements. Research methodology: The main research sample of (30) female students was selected from the research community represented by second-stage students in the College of Physical Education and Sports Sciences - University of Baghdad for the academic year (2024-2025). The sample was divided equally into two control and experimental groups. The researchers conducted the sample homogenization process and the equivalence process between the two groups in the variables of visua

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Publication Date
Fri May 16 2025
Journal Name
Asean Journal Of Science And Engineering
Enhancing Predictive Maintenance in Energy Systems Using a Hybrid Kolmogorov-Arnold Network (KAN) with Short-Time Fourier Transform (STFT) Framework for Rotating Machinery
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This study proposes a hybrid predictive maintenance framework that integrates the Kolmogorov-Arnold Network (KAN) with Short-Time Fourier Transform (STFT) for intelligent fault diagnosis in industrial rotating machinery. The method is designed to address challenges posed by non-linear and non-stationary vibration signals under varying operational conditions. Experimental validation using the FALEX multispecimen test bench demonstrated a high classification accuracy of 97.5%, outperforming traditional models such as SVM, Random Forest, and XGBoost. The approach maintained robust performance across dynamic load scenarios and noisy environments, with precision and recall exceeding 95%. Key contributions include a hardware-accelerated K

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Publication Date
Wed Mar 15 2023
Journal Name
Journal Of Baghdad College Of Dentistry
Effect of a novel coating material on the microleakage of glass hybrid restoration in primary teeth – An in vitro study
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Background: Glass ionomer restorations are widely employed in the field of pediatric dentistry. There is a constant demand for a durable restoration that remains functional until exfoliation. This study aimed to measure and compare the effect of a novel coating material (EQUIA Forte Coat) on the microleakage of glass hybrid restoration (EQUIA Forte HT) in primary teeth. Material and method: Thirty cavitated (class-II) primary molars were allocated randomly into two groups based on the coat application; uncoated (control) and coated group (experimental). Cavities were prepared by the use of a ceramic bur (CeraBur) and restored with EQUIA Forte HT with or without applying a protective coat (EQUIA Forte Coat). Samples went through the therm

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Publication Date
Fri Jan 01 2021
Journal Name
Ecology, Environment And Conservation
A qualitative study of Periphytic algae attached to thesurface of river boats in the Tigris River in AlAadhamiya, Baghdad, Iraq
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A seasonal study of periphytic algae attached to the surface of river boats was conducted in Tigris river in Al Aadhamiya site for the period from October 2016 to May 2017. A total of 107 taxa of periphytic algae were identified belonging to the four classes of algae. The periphytic algae community dominated by Bacillariophyceae was (60.7%) followed by Chlorophyceae (20.5%) and Cyanophyceae (17.7%) Chrysophyceae was constituted (0.9%) of the total number. During the whole period of study filamentous taxa such as Oscillatoria amphibian, Phormidium spp., Spirulinagigantean, Cladophoreglomerata and Melosira roeseana remained the dominant colonizer which may be reflect the ability of this species to grow multiplies under different environmental

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Publication Date
Wed Mar 15 2023
Journal Name
Journal Of Baghdad College Of Dentistry
Effect of a novel coating material on the microleakage of glass hybrid restoration in primary teeth – An in vitro study
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Background: Glass ionomer restorations are widely employed in the field of pediatric dentistry. There is a constant demand for a durable restoration that remains functional until exfoliation. This study aimed to measure and compare the effect of a novel coating material (EQUIA Forte Coat) on the microleakage of glass hybrid restoration (EQUIA Forte HT) in primary teeth. Material and method: Thirty cavitated (class-II) primary molars were allocated randomly into two groups based on the coat application; uncoated (control) and coated group (experimental). Cavities were prepared by the use of a ceramic bur (CeraBur) and restored with EQUIA Forte HT with or without applying a protective coat (EQUIA Forte Coat). Samples went through the

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