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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
Wed Jul 06 2022
Journal Name
Journal Of Al-qadisiyah For Computer Science And Mathematics
Image Compression using Polynomial Coding Techniques: A review
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Publication Date
Fri Jan 01 2016
Journal Name
Middle-east Journal Of Scientific Research
Question Classification Using Different Approach: A Whole Review
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Publication Date
Fri Jan 01 2016
Journal Name
Bio-inspired Computing – Theories And Applications
Image Segmentation Using Membrane Computing: A Literature Survey
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Publication Date
Sun Jul 09 2023
Journal Name
Journal Of Engineering
Improving IoT Applications Using a Proposed Routing Protocol
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The main objective of this work is to propose a new routing protocol for wireless sensor network employed to serve IoT systems. The routing protocol has to adapt with different requirements in order to enhance the performance of IoT applications. The link quality, node depth and energy are used as metrics to make routing decisions. Comparison with other protocols is essential to show the improvements achieved by this work, thus protocols designed to serve the same purpose such as AODV, REL and LABILE are chosen to compare the proposed routing protocol with. To add integrative and holistic, some of important features are added and tested such as actuating and mobility. These features are greatly required by some of IoT applications and im

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Publication Date
Sun Dec 01 2024
Journal Name
Al-khwarizmi Engineering Journal
Defect Detection Using Thermography Camera Techniques: A review
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Individuals across different industries, including but not limited to agriculture, drones, pharmaceuticals and manufacturing, are increasingly using thermal cameras to achieve various safety and security goals. This widespread adoption is made possible by advancements in thermal imaging sensor technology. The current literature provides an in-depth exploration of thermography camera applications for detecting faults in sectors such as fire protection, manufacturing, aerospace, automotive, non-destructive testing and structural material industries. The current discussion builds on previous studies, emphasising the effectiveness of thermography cameras in distinguishing undetectable defects by the human eye. Various methods for defect

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Publication Date
Sun Oct 07 2018
Journal Name
Al-kindy College Medical Journal
Risedronate as a therapeutic trial post-hysterectomy in premenopausal women to prevent osteoporosis
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Background: Osteoporosis is a skeletal defect manifested by a reduction of bone strength as a result of reduced bone mass to the extent that there is a higher risk of fracture even on minor trauma. Hysterectomy in a premenopausal woman is a well known cause of ovarian failure resulting in an increased risk of osteoporosis.

Objective : To clarify bisphosphonate's preventive effect on osteopenia and osteoporosis in premenopausal women after hysterectomy.

Type of the study: Cross –sectional study.

Method:  84 premenopausal females post hysterectomy aged between 40 – 50 years, were enrolled in this randomized controlled double blinded trail a

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Publication Date
Mon Jun 26 2023
Journal Name
Journal Of Contemporary Medical Sciences
Glyceryl Trinitrate, a Vasodilating Drug Acts as an Antibiofilm Agent in Serratia marcescens
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Objectives: Serratia marcescens is a gram-negative pathogen of many species. The ability of S. marcescens to form biofilms and its potent innate resistance to antimicrobials and cleaning solutions are both essential for its pathogenicity and survival. The present study was conducted to investigate the effect of glyceryl trinitrate (GTN) on the biofilm of S. marcescens, as an alternative for antibiotic therapy. Methods: Different specimens, including ear swabs, burns, mid-stream urine, wound swabs, and sputum, were collected from patients who were brought to Al-Ramadi Hospital, Iraq. All samples were cultured, and the colonies that were obtained were detected using the VITEK® 2 compact. The ability of biofilms to develop was e

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Publication Date
Sat Dec 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Compare Estimate Methods of Parameter to Scheffʼe Mixture Model By Using Generalized Inverse and The Stepwise Regression procedure for Treatment Multicollinearity Problem
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Mixture experiments are response variables based on the proportions of component for this mixture. In our research we will compare the scheffʼe model with the kronecker model for the mixture experiments, especially when the experimental area is restricted.

     Because of the experience of the mixture of high correlation problem and the problem of multicollinearity between the explanatory variables, which has an effect on the calculation of the Fisher information matrix of the regression model.

     to estimate the parameters of the mixture model, we used the (generalized inverse ) And the Stepwise Regression procedure

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Publication Date
Sat Sep 16 2023
Journal Name
مجلة الدراسات المستدامة
A Review Article: Use of fertilizers and their gradual release of mineral nutrients as a remedy to this problem have an adverse environmental impact.
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Throughout Agriculture has mostly relied on the use of natural fertilizers throughout human history, which are compounds that increase the nitrogen levels in the soil. Modern agriculture was made possible by the introduction of synthetic fertilizers at the end of the 19th centuryproduction of agriculture. Their application enhanced crop yields and sparked an agricultural revolution unlike anything the world had ever seen.In the near future, synthetic fertilizers are anticipated to continue to have a significant impa ct on human life, both positively and negatively. They are frequently utilized for producing all t ypes of crops and are essential to plant growth. The significance of synthetic fertilizers is their ability to provide the soil w

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Publication Date
Tue Oct 30 2018
Journal Name
Journal Of Engineering
Accuracy Assessment of Stonex X-300 Laser Scanner Cameras
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Assessment the actual accuracy of laboratory devices prior to first use is very important to know the capabilities of such devices and employ them in multiple domains. As the manual of the device provides information and values in laboratory conditions for the accuracy of these devices, thus the actual evaluation process is necessary.

In this paper, the accuracy of laser scanner (stonex X-300) cameras were evaluated, so that those cameras attached to the device and lead supporting role in it. This is particularly because the device manual did not contain sufficient information about those cameras.

To know the accuracy when using these cameras in close range photogrammetry, laser scanning (stonex X-300) de

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