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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
Tue Oct 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
Over application courier company (DHL) to keep the quality of service to achieve customer satisfaction the adoption of precedence delivery time - A prospective study))
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Over application courier company (DHL) to keep the quality of service to achieve customer satisfaction the adoption of precedence delivery time - A prospective study))

Become attention to quality is a global phenomenon, and I took organizations and governments around the world attaches special attention, but we can say that quality has become the first function for many organizations, and has become a management philosophy

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Publication Date
Sun Dec 01 2019
Journal Name
Ieee Xplore
A Hybrid Modified Lightweight Algorithm Combined of Two Cryptography Algorithms PRESENT and Salsa20 Using Chaotic System
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Cryptography algorithms play a critical role in information technology against various attacks witnessed in the digital era. Many studies and algorithms are done to achieve security issues for information systems. The high complexity of computational operations characterizes the traditional cryptography algorithms. On the other hand, lightweight algorithms are the way to solve most of the security issues that encounter applying traditional cryptography in constrained devices. However, a symmetric cipher is widely applied for ensuring the security of data communication in constraint devices. In this study, we proposed a hybrid algorithm based on two cryptography algorithms PRESENT and Salsa20. Also, a 2D logistic map of a chaotic system is a

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Publication Date
Sat Jan 25 2020
Journal Name
Indian Journal Of Forensic Medicine & Toxicology
A Stereomicroscopic Analysis of Dentinal Micro Cracks after Root Canal Preparation Using Four Different Rotary Instruments.
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A variety of single-engine driven files and inematics have been introduced to improve the clinical performance of NiTi rotary files. The purpose of this in vitro study was to measure and compare the incidence of dentinal defects after root canal preparation with different single file systems.

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Publication Date
Sat Mar 30 2024
Journal Name
Al-qadisiyah Journal For Engineering Sciences
Investigation of an automobile air-conditioner with a liquid-suction heat exchanger using R134a and R1234yf
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Air-conditioning systems (ACs) are essential in hot and humid climates to ensure acceptable ambient air quality as well as thermal comfort for buildings users. It is essential to improve refrigeration system performance without increasing the effects of global warming potential (GWP) and ozone depletion potential (ODP). The main objective of this study is to evaluate the performance of an air conditioning system that operates with a liquid suction heat exchanger (LSHX) through implementing refrigerants with zero OPD and low GWP (i.e., R134a and R1234yf). Liquid suction heat exchanger (LSHX) was added to an automobile air conditioning system (AACS).When Liquid suction heat exchanger was added to the cycle, primary results indicated t

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Publication Date
Mon Aug 27 2018
Journal Name
Al-khwarizmi Engineering Journal
Efficiency Enhancement of a Dual-axis Solar PV Panel Tracker Using Water-Flow Double Glazing Technique
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The fall angle of sun rays on the surface of a photovoltaic PV panel and its temperature is negatively affecting the panel electrical energy produced and efficiency. The fall angle problem was commonly solved by using a dual-axis solar tracker that continually maintains the panel orthogonally positioning to the sun rays all day long. This leads to maximum absorption for solar radiation necessary to produce maximum amount of energy and maintain high level of electrical efficiency. To solve the PV panel temperature problem, a Water-Flow Double Glazing WFDG technique has been introduced as a new cooling tool to reduce the panel temperature. In this paper, an integration design of the water glazing system with a dual-axis tracker has been ac

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Publication Date
Mon Sep 30 2024
Journal Name
Iraqi Journal Of Science
Overlapping Structure Detection in Protein-Protein Interaction Networks Using a Modified Version of Particle Swarm Optimization
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In today's world, the science of bioinformatics is developing rapidly, especially with regard to the analysis and study of biological networks. Scientists have used various nature-inspired algorithms to find protein complexes in protein-protein interaction (PPI) networks. These networks help scientists guess the molecular function of unknown proteins and show how cells work regularly. It is very common in PPI networks for a protein to participate in multiple functions and belong to many complexes, and as a result, complexes may overlap in the PPI networks. However, developing an efficient and reliable method to address the problem of detecting overlapping protein complexes remains a challenge since it is considered a complex and har

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Publication Date
Sun Sep 05 2010
Journal Name
Baghdad Science Journal
Design and Testing a Neutrons and Gamma-Rays Multilayer Shield Using Different Groups of Cross – Sections
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A preventing shield for neutrons and gamma rays was designed using alternate layers of water and iron with pre-fixed dimensions in order to study the possibility of attenuating both neutrons and gamma-rays. ANISN CODE was prepared and adapted for the shield calculation using radiation doses calculation: Two groups of cross-section were used for each of neutrons and gamma-rays that rely on the one – dimensional transport equation using discrete ordinate's method, and through transforming cross-section values to values that are independent on the number of groups. The memory size required for the applied code was reduced and the results obtained were in agreement with those of standard acceptable document samples of cross –section, this a

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Publication Date
Wed Dec 01 2021
Journal Name
Bioresource Technology Reports
Biosynthesis of polyhydroxyalkanoate (PHA) by a newly isolated strain Bacillus tequilensis ARY86 using inexpensive carbon source
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Publication Date
Sat Jul 01 2023
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Form that is a Proposed of Procedures for Auditing the Technical Reserves of General Insurances Branches in the Insurance Activity : applied research
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The research aims to identify the theoretical framework of technical reserves in the insurance activity and the role of the auditor in verifying the integrity of the estimates of technical provisions (technical reserves) for the branches of general insurance in insurance companies based on the relevant international auditing standards, as a proposed audit program has been prepared in accordance with international auditing standards that enable the auditor to express a sound opinion on the fairness of the financial statements of these companies , The research has reached many conclusions, the most important of which is the existence of deficiencies in the audit procedures of insurance companies, as the audit program of those companies did

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Publication Date
Tue Jun 11 2002
Journal Name
Iraqi Journal Of Laser
The Use of a Pulsed Nd: YAG Laser Radiation for the Removal of Intracanal Debris and Smear Layer in Extracted Human Teeth
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The efficiency of Nd:YAG laser radiation in removing debris and smear layer from prepared root
canal walls was studied. Fifty-seven human extracted single rooted anterior teeth were divided into three
groups. A group that was not lased is considered as a control group. The remaining teeth were exposed to
different laser parameters regarding laser energy, repetition rate and exposure time. For the case of the set of
parameters of 7 mJ laser energy, the cleaning was maximum at 3 p.p.s. repetition rate for 3 seconds exposure
time for, the coronal, middle and apical thirds. Above and below this energy level, there was an overdose
(melting) or under dose (no effect). Nevertheless for 10mJ laser energy case, the cleaning effi

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