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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 Nov 24 2023
Journal Name
International Journal Of Statistics In Medical Research
A Novel Algorithm for Predicting Antimicrobial Resistance in Unequal Groups of Bacterial Isolates
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Choosing antimicrobials is a common dilemma when the expected rate of bacterial resistance is high. The observed resistance values in unequal groups of isolates tested for different antimicrobials can be misleading. This can affect the decision to recommend one antibiotic over the other. We analyzed recalled data with the statistical consideration of unequal sample groups. Data was collected concerning children suspected to have typhoid fever at Al Alwyia Pediatric Teaching Hospital in Baghdad, Iraq. The study period extended from September 2021 to September 2022. A novel algorithm was developed to compare the drug sensitivity among unequal numbers of Salmonella typhi (S. Typhi) isolates tested with different antibacterials.

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Publication Date
Wed Dec 29 2021
Journal Name
Al-khwarizmi Engineering Journal
Analysis and Evaluation of a Quasi-Passive Lower Limb Exoskeleton for Gait Rehabilitation
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Lower extremity exoskeletons can assist with performing particular functions such as gait assistance, and physical therapy support for subjects who have lost the ability to walk. This paper presents the analysis and evaluation of lightweight and adjustable two degrees of freedom, quasi-passive lower limb device to improve gait rehabilitation. The exoskeleton consists of a high torque DC motor mounted on a metal plate above the hip joint, and a link that transmits assistance torque from the motor to the thigh. The knee joint is passively actuated by spring installed parallel with the joint. The action of the passive component (spring) is combined with mechanical output of the motor to provide a good control on the designed exoskeleton whi

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Publication Date
Fri Feb 26 2021
Journal Name
Life-cycle Civil Engineering: Innovation, Theory And Practice
Shear performance of a novel demountable connector for reusable steel-concrete composite structures
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A novel demountable shear connector is proposed to link a concrete slab to steel sections in a way that resulting steel-concrete composite floor is demountable, i.e. it can be easily dismantled at the end of its service life. The proposed connectors consist of two parts: the first part is a hollow steel tube with internal threads at its lower end. The second part is a compatible partially threaded bolted stud. After linking the stud to the steel section, the hollow steel tube can be fastened over the threaded stud, which create a complete demountable shear connector. The connector is suitable for use in both composite bridges and buildings, and using cast in-situ slabs, precast solid slabs, or hollow-core precast slabs. A series of push-off

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Publication Date
Sun Mar 01 2020
Journal Name
Baghdad Science Journal
Dynamic Response of a Nonlinear Fabry-Perot Etalon for Various Medium Response Times
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     In this work, the switching nonlinear dynamics of a Fabry-Perot etalon are studied. The method used to complete the solution of the differential equations for the nonlinear medium. The Debye relaxation equations solved numerically to predict the behavior of the cavity for modulated input power. The response of the cavity filled with materials of different response time is depicted. For a material with a response time equal to = 50 ns, the cavity switches after about (100 ns). Notice that there is always a finite time delay before the cavity switches. The switch up time is much longer than the cavity build-up time of the corresponding linear cavity which was found to be of the order of a few round-trip ti

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Publication Date
Fri May 18 2018
Journal Name
International Journal Of Simulation: Systems, Science & Technology
A Review of Advances in Pressurizer Response Research for Pressurized Water Reactor Systems
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Publication Date
Sat Apr 15 2023
Journal Name
Journal Of Robotics
A New Proposed Hybrid Learning Approach with Features for Extraction of Image Classification
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Image classification is the process of finding common features in images from various classes and applying them to categorize and label them. The main problem of the image classification process is the abundance of images, the high complexity of the data, and the shortage of labeled data, presenting the key obstacles in image classification. The cornerstone of image classification is evaluating the convolutional features retrieved from deep learning models and training them with machine learning classifiers. This study proposes a new approach of “hybrid learning” by combining deep learning with machine learning for image classification based on convolutional feature extraction using the VGG-16 deep learning model and seven class

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Publication Date
Mon Feb 25 2019
Journal Name
Iraqi Journal Of Physics
Simulation of indoor solar illumination system for a library hall in Baghdad city
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A concept of indoor solar illumination is described and simulated. The solar illumination system is composed of a tracking primary reflector, a selective secondary reflector, a visible light guide and a scattering solid glass tube fixture. Each part of the solar illumination system is optically suited and compatible with other parts to realize high efficiency. The simulation is conducted for Baghdad city for a library hall. Two major days over a year are chosen to investigate the illumination system for acceptable visible light level for reading hall. The two days are: summer solstice day and winter solstice day at 8:00 AM and 12:00 PM for each. Research results showed that the design of the solar system is achieved on the base of minimu

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Publication Date
Fri Jan 01 2016
Journal Name
Ieee Access
Towards an Applicability of Current Network Forensics for Cloud Networks: A SWOT Analysis
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In recent years, the migration of the computational workload to computational clouds has attracted intruders to target and exploit cloud networks internally and externally. The investigation of such hazardous network attacks in the cloud network requires comprehensive network forensics methods (NFM) to identify the source of the attack. However, cloud computing lacks NFM to identify the network attacks that affect various cloud resources by disseminating through cloud networks. In this paper, the study is motivated by the need to find the applicability of current (C-NFMs) for cloud networks of the cloud computing. The applicability is evaluated based on strengths, weaknesses, opportunities, and threats (SWOT) to outlook the cloud network. T

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Publication Date
Mon Jan 01 2018
Journal Name
Image And Video Technology: 8th Pacific-rim Symposium
A New Scheme for QoE Management of Live Video Streaming in Cloud Environment
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Publication Date
Mon Jul 10 2023
Journal Name
Journal Of Engineering
Theoretical Evaluation of Solar Assisted Desiccant Cooling System for a Small Meeting-Hall
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The performance of a solar assisted desiccant cooling system for a meeting-hall located in the College of Engineering/University of Baghdad was evaluated theoretically. The system was composed of four components; a solar air heater, a desiccant dehumidifier, a heat exchanger and an evaporative cooler. A computer simulation was developed by using MATLAB to assess the effect of various design and operating conditions on the performance of the system and its components. The actual weather data on recommended days were used to assess the load variation and the system performance during those days. The radiant time series method (RTS) was used to evaluate the hourly variation of the cooling load. Four operation modes were employed for perform

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