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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 Dec 01 2023
Journal Name
Case Studies In Chemical And Environmental Engineering
Removal of copper from a simulated wastewater by electromembrane extraction technique using a novel electrolytic cell provided with a flat polypropylene membrane infused with 1-octanol and DEHP as a carrier
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Publication Date
Wed Mar 01 2023
Journal Name
International Journal Of Research In Social Sciences And Humanities
The Role of Value Chain Analysis as well as Programs and Performance Budget in Reducing Waste of Public Money(Applied Study)
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Programs and performance budget represents a sophisticated method of public budget numbers, which includes all allocations to be determined for each job or activity within a government entity, which is analyzed according to their needs and costs, and this method can be applied using one of the cost accounting techniques, which is the technique of analyzing the value chain that reduces costs by avoiding activities that do not add value and enhance activities that add value to the economic entity, the current research aims to develop the budget system in government entity by using the budget of programs and performance as a tool for planning and monitoring events and activities, thereby reducing the waste of public money by reducing unnecessa

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Publication Date
Tue Jul 31 2018
Journal Name
Revue Académique De La Recherche Juridique
Jurisdiction in the Professional Football Player Contract – A Comparative Study
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Is no longer a football player looks to sport as a means of entertainment and physical development. But become see as part of The economic and is getting in return for the effort of، Through a contract with a club to organize the activity which is called a contract of professional, This contract is similar to the rest of the contracts in terms of problems and dispute that arise during the implementation or after it ends because of the nature of sports to such disputes and privacy being subject to special rules (regulations, national and international professional) required that subject to judicial bodies private mission confined settle sports disputes these entities and is affiliated unions legal committees and the court of arbitration for

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Publication Date
Mon Jun 30 2003
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Study of the Drying of Ethanol using Zeolite Molecular Sieves
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Publication Date
Sat Mar 01 2014
Journal Name
Journal Of The College Of Languages (jcl)
The Impact of Holy Qur’an on Pushkin’s Poetry A Comparative Study
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Praise be to Allah , the Lord of Heavens , Who revealed His Scripture in plain Arabic, and prayers and peace be upon the Master of all creatures and the chosen one , Muhammad (PBUH).Pushkin was known as a poet in Russia, the sun of its poetry that set, the father of the Russian literature and the founder of its literary language. When he published his poems, trying to express his inner poetic feelings and creative visions, he presented them with creativity and special touch. The reason behind the selection of Pushkin as the subject of this study is that he was affected by Islam and Arabs. For the purpose of this study, the dissertation has been divided into introduction and three chapters; each chapter includes two topics. In the introdu

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Publication Date
Mon Oct 01 2018
Journal Name
Iraqi Journal Of Physics
A three-stage blumlein-circuit to generate transversely excited atmospheric nitrogen laser by using three spark gaps
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In this research constructed N2 laser system by use developed method of electric discharge. In this method used four step of electric discharge by using four capacitors, three spark gaps, high tension power supply varying in range from 12kV to 24 kV and three resistors, this method called three stage blumlein circuit. The breakdown time delay of these parallel spark gaps cement strong ultraviolet preionization in the laser channel, thus the result of these amendments the laser output is many doubled and is more increasing than that obtained using the one and two stage blumlein circuits. This system has been designed and operated to give pulse laser with wavelength at 337.1 nm. This laser system can operate without mirrors and optical res

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Publication Date
Sat May 27 2017
Journal Name
Journal Of Pharmaceutical Sciences And Research
Synthesis, Preliminary Antimicrobial Evaluation and Molecular Docking of new Schiff bases of Ceftizoxime
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Schiff bases of Ceftizoxime sodium were synthesized in an attempt to improve the antimicrobial spectrum of Ceftizoxime. Aminothiazole ring of Ceftizoxime is linked directly through an imino group to different aromatic aldehydes reacted by nucleophilic addition using trimethylamine (TEA), as a catalyst and refluxed in methanol. The antimicrobial activity was evaluated for such Schiff bases using disc diffusion method. Molecular docking was conducted on certain penicillin-binding proteins (PBPs) and carboxypeptidases using 1- click docking software. Schiff bases of Ceftizoxime were prepared with reasonable yields and their chemical structures were confirmed by spectral analysis (FTIR, 1H-NMR) and elemental microanalysis (CHNS). The antibacter

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Publication Date
Fri Jan 01 2016
Journal Name
Advances In Computing
A New Abnormality Detection Approach for T1-Weighted Magnetic Resonance Imaging Brain Slices Using Three Planes
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Generally, radiologists analyse the Magnetic Resonance Imaging (MRI) by visual inspection to detect and identify the presence of tumour or abnormal tissue in brain MR images. The huge number of such MR images makes this visual interpretation process, not only laborious and expensive but often erroneous. Furthermore, the human eye and brain sensitivity to elucidate such images gets reduced with the increase of number of cases, especially when only some slices contain information of the affected area. Therefore, an automated system for the analysis and classification of MR images is mandatory. In this paper, we propose a new method for abnormality detection from T1-Weighted MRI of human head scans using three planes, including axial plane, co

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Publication Date
Thu May 14 2026
Journal Name
Alrafidain Of Law
The Effects of the research and technology development contract -A comparative study-
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Researching the effects of the research and technological development contract, determining its extent and demarcating the boundaries of the obligations imposed in it, is the cornerstone of economic growth and development, because defining these obligations removes the ambiguity and conflict between interests, by stating the rights owed to each party and even trying to reconcile them, or impose protection by specifying guarantees that are compatible with the essence of the R&D contract, For the purpose of studying the subject thoroughly, we will divide this research into two sections. The first is devoted to identifying the parties to the research and technological development contract. As for the other topic, we will explain the obligation

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Publication Date
Thu Dec 27 2018
Journal Name
Revue Académique De La Recherche Juridique
The Scope of the Judge’s Authority in Completing a Contract and the Limitations Thereon – A Comparative Study
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The contractual imbalance is perceived today by the majority of the doctrine as being one of the pitfalls to the execution of the contracts. As a result, most legislations grant judges the power to intervene to restore it. Granting the judge the power to complete the contract raises the question of the extent to which the judge can obtain such power. Is it an absolute authority that is not limited? If so, is it a broad discretion in which the judge operates in his conscience, or is it a power of limited scope by specific legal texts and conventions? This is what we will try to answer in this research.

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