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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
Thu Aug 28 2025
Journal Name
Journal Of Baghdad College Of Dentistry
The effect of autologous bone marrow-derived stem cells with estimation of molecular events on tooth socket healing in diabetic rabbits (Histological and histomorphometric study)
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Background: Diabetes is a metabolic disorder characterized by chronic hyperglycemia due to an inability to produce insulin. Uncontrolled or poorly controlled diabetes is clinically associated with increased susceptibility to delay healing. Many recent researches have shown that stem cell therapy can be the best choice for treatment of this disease. The aims of this research were investigating regeneration of pancreatic beta cells of diabetic induced rabbits after stem cell transplantation. Materials and Methods: 64 rabbits weighting an average of (2.5 - 3 kg) were used in this experimental study, and divided into 4 groups as follows; group A ( contains 16 healthy rabbits regarded as control group ) , Group B ( contains 16 diabetic rabbits

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Publication Date
Sun Mar 04 2012
Journal Name
Baghdad Science Journal
A proposed Mathematical Expression for Computer Design of Electrostatic Mirror
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A computational investigation has been carried out on the design and properties of the electrostatic mirror. In this research, we suggest a mathematical expression to represent the axial potential of an electrostatic mirror. The electron beam path under zero magnification condition had been investigated as mirror trajectory with the aid of fourth – order – Runge – Kutta method. The spherical and chromatic aberration coefficients of mirror has computed and normalized in terms of the focal length. The choice of the mirror depends on the operational requirements, i.e. each optical element in optical system has suffer from the chromatic aberration, for this case, it is use to operate the mirror in optical system at various values

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Publication Date
Tue May 01 2018
Journal Name
Journal Of Engineering
Design of an Optimal Integral Backstepping Controller for a Quadcopter
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In this paper, an Integral Backstepping Controller (IBC) is designed and optimized for full control, of rotational and translational dynamics, of an unmanned Quadcopter (QC). Before designing the controller, a mathematical model for the QC is developed in a form appropriate for the IBC design. Due to the underactuated property of the QC, it is possible to control the QC Cartesian positions (X, Y, and Z) and the yaw angle through ordering the desired values for them. As for the pitch and roll angles, they are generated by the position controllers. Backstepping Controller (BC) is a practical nonlinear control scheme based on Lyapunov design approach, which can, therefore, guarantee the convergence of the position tracking

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Publication Date
Sun Jul 31 2022
Journal Name
Iraqi Geological Journal
A Review of Historical Studies for Water Saturation Determination Techniques
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Water saturation is the most significant characteristic for reservoir characterization in order to assess oil reserves; this paper reviewed the concepts and applications of both classic and new approaches to determine water saturation. so, this work guides the reader to realize and distinguish between various strategies to obtain an appropriate water saturation value from electrical logging in both resistivity and dielectric has been studied, and the most well-known models in clean and shaly formation have been demonstrated. The Nuclear Magnetic Resonance in conventional and nonconventional reservoirs has been reviewed and understood as the major feature of this approach to estimate Water Saturation based on T2 distribution. Artific

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Publication Date
Tue Nov 01 2022
Journal Name
Japanese Dental Science Review
Pathogenesis of periodontitis – A potential role for epithelial-mesenchymal transition
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Publication Date
Sat Sep 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
A comparison Of Some Semiparametric Estimators For consumption function Regression
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    This article aims to explore the importance of estimating the a semiparametric regression function ,where we suggest a new estimator beside the other combined estimators and then we make a comparison among them by using simulation technique . Through the simulation results we find  that the suggest estimator is the best with the first and second models ,wherealse for the third model we find Burman and Chaudhuri (B&C) is best.

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Publication Date
Thu Aug 28 2025
Journal Name
Journal Of Engineering
Construction of a General-Purpose Infrastructure for Rfid – Based Applications
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Publication Date
Sun Sep 07 2014
Journal Name
Baghdad Science Journal
A New Operational Matrix of Derivative for Orthonormal Bernstein Polynomial's
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Publication Date
Fri Mar 01 2019
Journal Name
Al-khwarizmi Engineering Journal
Design and Implementation of a Telemetry System for Environmental Applications
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The Environmental Data Acquisition Telemetry System is a versatile, flexible and economical means to accumulate data from multiple sensors at remote locations over an extended period of time; the data is normally transferred to the final destination and saved for further analysis.

This paper introduces the design and implementation of a simplified, economical and practical telemetry system to collect and transfer the environmental parameters (humidity, temperature, pressure etc.) from a remote location (Rural Area) to the processing and displaying unit.

To get a flexible and practical system, three data transfer methods (three systems) were proposed (including the design and implementation) for rural area services, the fi

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Publication Date
Mon Jun 05 2023
Journal Name
Journal Of Engineering
Construction of a General-Purpose Infrastructure for Rfid – Based Applications
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The aim of advancements in technologies is to increase scientific development and get the overall human satisfaction and comfortability. One of the active research area in recent years that addresses the above mentioned issues, is the integration of radio frequency identification (RFID) technology into network-based systems. Even though, RFID is considered as a promising technology, it has some bleeding points. This paper identifies seven intertwined deficiencies, namely: remote setting, scalability, power saving, remote and concurrent tracking, reusability, automation, and continuity in work. This paper proposes the construction of a general purpose infrastructure for RFID-based applications (IRFID) to tackle these deficiencies. Finally

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