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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
Ieee Access
Keratoconus Severity Detection From Elevation, Topography and Pachymetry Raw Data Using a Machine Learning Approach
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Publication Date
Thu Dec 12 2013
Journal Name
Iraqi Journal Of Science
Determination of Optimum Mechanical Drilling Parameters for an Iraqi Field with Regression Model
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Publication Date
Mon Nov 24 2025
Journal Name
Misan Journal Of Academic Studies
Some of Parametric and Non Parametric Estimations for Circular Regression Model via Simulation
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Circular data (circular sightings) are periodic data and are measured on the unit's circle by radian or grades. They are fundamentally different from those linear data compatible with the mathematical representation of the usual linear regression model due to their cyclical nature. Circular data originate in a wide variety of fields of scientific, medical, economic and social life. One of the most important statistical methods that represents this data, and there are several methods of estimating angular regression, including teachers and non-educationalists, so the letter included the use of three models of angular regression, two of which are teaching models and one of which is a model of educators. ) (DM) (MLE) and circular shrinkage mod

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Publication Date
Fri Jan 01 2016
Journal Name
Journal Of Engineering
Application of SWAT Model for Sediment Loads from Valleys Transmitted to Haditha Reservoir
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This study included the extraction properties of spatial and morphological basins studied using the Soil and Water Assessment Tool (SWAT) model linked to (GIS) to find the amount of sediment and rates of flow that flows into the Haditha reservoir . The aim of this study is determine the amount of sediment coming from the valleys and flowing into the Haditha Dam reservoir for 25 years ago for the period (1985-2010) and its impact on design lifetime of the Haditha Dam reservoir and to determine the best ways to reduce the sediment transport. The result indicated that total amount of sediment coming from all valleys about (2.56 * 106 ton). The maximum annual total sediment load was about (488.22 * 103 ton) in year 1988

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Publication Date
Mon May 11 2020
Journal Name
Baghdad Science Journal
Proposing Robust LAD-Atan Penalty of Regression Model Estimation for High Dimensional Data
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         The issue of penalized regression model has received considerable critical attention to variable selection. It plays an essential role in dealing with high dimensional data. Arctangent denoted by the Atan penalty has been used in both estimation and variable selection as an efficient method recently. However, the Atan penalty is very sensitive to outliers in response to variables or heavy-tailed error distribution. While the least absolute deviation is a good method to get robustness in regression estimation. The specific objective of this research is to propose a robust Atan estimator from combining these two ideas at once. Simulation experiments and real data applications show that the p

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Publication Date
Wed Jun 27 2018
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Building Geological Model for Tertiary Reservoir of Exploration Ismail Oil Field, North Iraq
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Geologic modeling is the art of constructing a structural and stratigraphic model of a reservoir from analyses and interpretations of seismic data, log data, core data, etc. ‎[1].

   A static reservoir model typically involves four main stages, these stages are Structural modeling, Stratigraphic modeling, Lithological modeling and Petrophysical modeling ‎[2].

   Ismail field is exploration structure, located in the north Iraq, about 55 km north-west of Kirkuk city, to the north-west of the Bai Hassan field, the distance between the Bai Hassan field and Ismael field is about one kilometer ‎[3].

   Tertiary period reservoir sequences (Main Limestone), which comprise many economica

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Publication Date
Mon May 11 2020
Journal Name
Baghdad Science Journal
Proposing Robust LAD-Atan Penalty of Regression Model Estimation for High Dimensional Data
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         The issue of penalized regression model has received considerable critical attention to variable selection. It plays an essential role in dealing with high dimensional data. Arctangent denoted by the Atan penalty has been used in both estimation and variable selection as an efficient method recently. However, the Atan penalty is very sensitive to outliers in response to variables or heavy-tailed error distribution. While the least absolute deviation is a good method to get robustness in regression estimation. The specific objective of this research is to propose a robust Atan estimator from combining these two ideas at once. Simulation experiments and real data applications show that the proposed LAD-Atan estimator

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Publication Date
Sun Sep 01 2013
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The contractual budget: the ideal technique in planning and implementing capital budgeting projects: a strategy of preparing the contractual budget for Baghdad local government
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Public budget is the government's tool in achieving the objectives of economic and social development is the accounting curriculum to estimate state revenues and expenditures for years to come, as well as to have legal status as it is after the adoption of an official statement of government units to spend funds on items planned at the same time is a statement collect resources to finance these appropriations, if the primary objective of the budget initially limited to the achievement of financial and legislative control have evolved this function in the area of public administration turned attention from mere imposition of control over the money, which provides information to assist the Department to utilize available resources and prog

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Publication Date
Mon Feb 01 2021
Journal Name
Journal Of Physics: Conference Series
Bayesian Computational Methods of the Logistic Regression Model
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Abstract<p>In this paper, we will discuss the performance of Bayesian computational approaches for estimating the parameters of a Logistic Regression model. Markov Chain Monte Carlo (MCMC) algorithms was the base estimation procedure. We present two algorithms: Random Walk Metropolis (RWM) and Hamiltonian Monte Carlo (HMC). We also applied these approaches to a real data set.</p>
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Publication Date
Tue Dec 01 2020
Journal Name
Nature Environment And Pollution Technology
The Kinetic Model for Decolourization of Commercial Direct Blue 2 Azo Dye Aqueous Solution by the Fenton Process and the Effect of Inorganic Salts
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