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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 Jan 30 2020
Journal Name
Telecommunication Systems
Nature-inspired optimization algorithms for community detection in complex networks: a review and future trends
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Publication Date
Wed Jan 01 2025
Journal Name
Biomaterials Science
Single-atom silver-borophene hybrid hydrogels for electrically stimulated wound healing: a multifunctional antibacterial platform
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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
STUDY OF TEMPERATURE EFFECT ON THE HARDNESS FOR EPOXY RESIN AND UNSATURATED POLYESTER
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This search aim to measure Hardness for Epoxy resin and for unsaturated Polyester resin as base materials for composite Hybrid and the materials used is Hybrid fiber Carbon-Kevlar. The Hand Lay-up method was used to manufacture plates of Epoxy resin (EP) and unsaturated Polyester EP,UPE backed by Hybrid fiber (Carbon-Kevlar) and with small volume fraction 5,10 and 15 for every there are Layer of fibers (1,2 and 3). The hardness test was count for material EP, UPE resin and there composites and that we notice that the Hardness (HB) decreased with increase of temperatures.

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Publication Date
Sat May 08 2021
Journal Name
Social Science And Humanities Journal
The impact of accounting for material flow costs in reducing costs: Exploratory study
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Rapid and continuous developments and changes in the modern business environment in all areas of economic, environmental, social, technology and communications push economic units to search for modern methods and methodologies to produce products at low cost as well as produce products that meet the wishes of customers in terms of quality and environment to maintain their market position, and accounting for the costs of the flow of materials is one of the most prominent environmental management accounting techniques capable of providing information to help produce

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Publication Date
Tue Jan 01 2019
Journal Name
Aip Conference Proceedings
Fabricating and study effect of the concentrations electrolyte for an alkaline electrolysis cell
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Publication Date
Fri Jun 07 2024
Journal Name
Medicine
Impact of TYMS gene polymorphism on the outcome of methotrexate treatment in a sample of Iraqi rheumatoid arthritis patients – identification of novel single nucleotide polymorphism: Cross-sectional study
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The current work aims to evaluate the association between genetic mutations in thymidylate synthetase (TYMS gene in exon1 and partial regions of promotor and intron 1 [877 bp, 657,220–658,096 bp]) and the therapeutic outcomes for rheumatoid arthritis (RA) Iraqi patients. An observational cross-sectional study involving 95 RA patients with established RA patients based on their methotrexate treatment responsiveness. Genetic sequencing of the TYMS gene was performed for all patients according to the instruction manuals of the sequencing company (Macrogen Inc. Geumchen, South Korea). Four polymorphisms were identified by sequencing 95 randomly selected patients in the noncoding region of TYMS

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Publication Date
Thu Jun 01 2017
Journal Name
Journal Of The College Of Languages (jcl)
Plain Language Movement and Legal Translation : An Analytical Study of Two Translations of a Contract of Lease from Arabic into English
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The present paper addresses one of the most challenging topics in translation; namely legal translation in the framework of two different approaches; the classical (formal) and the more recent (functional). The latter approach is the outcome of the process of simplifying legal language known technically as Plain Language Movement. The advent of this movement dates back to the 1950s, in response to the widely-held complain about the awkwardness of the legal register. Within this framework, the salient features of legal language, at the various linguistic and textual levels, underwent reconsideration in favor of more publicly digested expressions. The paper then subjects two translations of a lease contract to analysis in the ligh

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Publication Date
Wed Feb 20 2019
Journal Name
Political Sciences Journal
A political perusal of Initiations in Declaring Middle East a District vacant of mass Destruction weapons
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A political perusal of Initiations in Declaring Middle East a District vacant of mass Destruction weapons

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Publication Date
Tue Oct 01 2024
Journal Name
International Journal Of Body, Mind & Culture (2345-5802)
Comparative analysis of the conventional primary healthcare services and family health program in Cairo, Egypt
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Background: Primary healthcare in Egypt has undergone significant reforms since the 1990s, including the pioneering Family Health Program (FHP). However, limited evaluation exists regarding the FHP's impact on enhancing the delivery of primary healthcare services. The primary objective of this study was to analyze and understand the efficiency and effectiveness of the FHP in altering the delivery of primary healthcare in Egypt. We aimed to outline the fundamental characteristics of the primary healthcare system, compare them between the conventional and the newly reformed FHP centers, and gauge the awareness level of these variances among key decision-makers, focusing specifically on Cairo, Egypt. Methods: This cross-sectional study employe

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Publication Date
Mon Mar 01 2021
Journal Name
Journal Of Physics: Conference Series
The Bifurcation Analysis and Persistence of the Food Chain Ecological Model with Toxicant
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Abstract<p>In this work, the occurrence conditions of both local Bifurcation and persistence were studied, Saddle-node bifurcation appears near fourth point, near the first point, the second point and the third point a transcritical bifurcation occurred but no pitchfork bifurcation happened near any of the four equilibrium points. In addition to study conditions for Hopf-bifurcation near positive stable point that is the fourth point. Besides discuss persistence occurrence as globally property of the food chain of three species include prey, first predator and top predator with impact of toxin in all species and harvesting effect on the predator’s only. Numerical results for the set of hypothe</p> ... Show More
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