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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
Sat Jun 30 2018
Journal Name
College Of Islamic Sciences
What he finishes and what he does not leave Between Sibawayh and the cooler A descriptive study of their methodologies
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It was rumored in the grammatical circles that the (short) refrigerant is only a copy of (book) Sibweh, except some of the views that violated it, or some of the evidence that increased it; On the (brief) or not, the researcher has chosen the subject (what is going away and not leave) a field of study of the budget, has come on three demands, the first devoted to the study of the term, and the second to explain the methodology of scientists in the presentation of the topic, and the third was limited to the study of the evidence they invoked .
God grants success

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Publication Date
Wed May 10 2023
Journal Name
Journal Of Planner And Development
the Planning and Management of Services in Rural Areas, AL-Gharraf sub-district in Dhi Qar Governorate, a case study.
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         Bringing about urban, economic, and social changes in rural areas similar to those occurring in urban areas aims to reduce urban-rural disparities by providing services in those areas, decentralizing the management of these services, expanding citizen participation in local governance (decentralized administration), and achieving comprehensive development, developing and empowering localities, and keeping pace with new transformations and their impacts on the functions of the center and localities. In fact, the lack of clarity of the role of local government in planning and managing services has hindered development plans, and declined the level of services in rural areas, and has negative

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Publication Date
Tue Jun 11 2024
Journal Name
International Journal Of Civil Engineering
Strength Evaluation of CFRP-Strengthened RC Slab-Beams System by Load Test to Satisfy the Safety Requirements: A Case Study
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The primary goal of in-situ load testing is to evaluate the safety and performance of a structural system under particular loading conditions. Advancements in building techniques, analytical tools, and monitoring instruments are prompting the evaluation of the appropriate loading value, loading process, and examination criteria. The procedure for testing reinforced concrete (RC) structures on-site, as outlined in the ACI Building Code, involves conducting a 24-h load test and applying specific evaluation criteria. This article detailed a retrofitting project for an RC slab-beams system by utilizing carbon fiber-reinforced polymer (CFRP) sheets to strengthen the structure following a fire incident. The RC structure showed indicators of deter

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Publication Date
Sun Nov 07 2021
Journal Name
Review Of International Geographical Education Online
Assessment of Information Security Risk Management System based on ISO/IEC27005 in the Independent High Electoral Commission: A Case Study
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The current research aims to study the extent to which the Independent High Electoral Commission applies to information security risk management by the international standard (ISO / IEC27005) in terms of policies, administrative and technical procedures, and techniques used in managing information security risks, based on the opinions of experts in the sector who occupy positions (General Manager The directorate, department heads and their agents, project managers, heads of divisions, and those authorized to access systems and software). The importance of the research comes by giving a clear picture of the field of information security risk management in the organization in question because of its significant role in identifying risks and s

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Publication Date
Wed Dec 15 2021
Journal Name
Journal Of Baghdad College Of Dentistry
The Effect of Recipient Jaw and Implant Dimensions on Pre- and Post- Loading Dental Implant Stability: A Prospective Clinical Study
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Background: Implant stability is a mandatory factor for dental implant (DI) osseointegration and long-term success. The aim of this study was to evaluate the effect of implant length, diameter, and recipient jaw on the pre- and post-functional loading stability. Materials and methods: This study included 17 healthy patients with an age range of 24-61 years. Twenty-two DI were inserted into healed extraction sockets to replace missing tooth/ teeth in premolar and molar regions in upper and lower jaws. Implant stability was measured for each implant and was recorded as implant stability quotient (ISQ) immediately (ISQ0), and at 8 (ISQ8) and 12 (ISQ12) weeks postoperatively, as well as post-functional loading (ISQPFL). The pattern of implant

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Publication Date
Fri Jan 01 2021
Journal Name
Journal Of Social, Humanities And Administrative Sciences
QUESTIONING GENDER ROLES IN THE AWAKENING: A BEAUVOIRIAN STUDY (UYANIŞ ROMANINDA CİNSİYET SORUNU: BEAUVOİR'IN DÜŞÜNCEİNE DAYALI BİR ÇALIŞMA)
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Publication Date
Tue Feb 01 2022
Journal Name
Current Pharmaceutical Analysis
Analytical Methods for the Identification of Pigments in Tattoo Inks and Some of Their Physiological Side Effects: A Review
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In this review, numerous analytical methods to distinguish pigments in tattoo, paint, and ink items are discussed. The selection of a method was dependent upon the purpose, e.g., quantification or identification of pigments. The introductory part of this review focuses on describing the importance of setting up a pigment-associated safety profile. The formation of different degradation chemical substances as well as impurity trends can be indicated through the chemical investigation of pigments in tattoo products. It is noteworthy that pigment recognition in tattoo inks can work as a preliminary method to identify the pigments in a patient's tattoo before being removed by laser therapy. Contrary to the stud

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Publication Date
Fri Apr 09 2021
Journal Name
Education And Information Technologies
Evaluating the use of informational technologies by students of healthcare colleges for academic purposes over a five-year period
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Publication Date
Sun Jan 01 2023
Journal Name
International Journal Of Research In Social Sciences And Humanities
The Effect of Default Risk on Cash Flow Profitability Indicators: Analytical Research for a Sample of Iraqi Private Banks
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Focusing on the negative role of default risk on banks, as it is one of the most important risks facing banks, which are difficult to determine accurately, and its reflection on the indicators of profitability of cash flows. The increasing competition between banks led to an increase in the credit facilities granted by banks, and was accompanied by an increase in exposure to the risks of default, which led to an impact on the level of performance of banks in terms of achieving the required return according to the levels of high competition. Therefore, the problem of this study focused on the extent to which the risk indicators of default affect the profitability indicators of the cash flows of the banks research sample in the profit

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Publication Date
Tue Feb 01 2022
Journal Name
Current Pharmaceutical Analysis
Analytical Methods for the Identification of Pigments in Tattoo Inks and Some of Their Physiological Side Effects: A Review
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In this review, numerous analytical methods to distinguish pigments in tattoo, paint, and ink items are discussed. The selection of a method was dependent upon the purpose, e.g., quantification or identification of pigments. The introductory part of this review focuses on describing the importance of setting up a pigment-associated safety profile. The formation of different degradation chemical substances as well as impurity trends can be indicated through the chemical investigation of pigments in tattoo products. It is noteworthy that pigment recognition in tattoo inks can work as a preliminary method to identify the pigments in a patient's tattoo before being removed by laser therapy. Contrary to the stud

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Scopus (2)
Crossref (3)
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