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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
Mon Jun 30 2025
Journal Name
Madenat Al-elem University College
The Ripple Effect of Plastic Pollution: Environmental and Public Health Perspectives: A review
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Abstract: Plastic pollution is a major issue of the current century. This waste is found in seas, freshwater, lakes, rivers, coastal areas, and soil. In this article, this article discusses the various sources of plastic pollution, including the manufacturing process of plastics and the addition of materials to improve their properties, as well as the use of single-use plastics that are not recyclable, in addition to burning and illegal waste disposal in the open. The impact on public health is through human exposure to toxins from plastics in the environment directly through inhaling dust and fumes, consuming contaminated food and drink, and skin contact. Indirectly, when marine creatures consume microplastics, they will find their way

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Publication Date
Sat Nov 01 2025
Journal Name
Iop Conference Series: Earth And Environmental Science
Evaluation the Structural Behavior of Lightweight Concrete-Filled Steel Tube Columns: A Review
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Abstract<p>Lightweight concrete-filled tube (CFST) columns offer numerous benefits, such as reduced weight, enhanced resistance to buckling, improved structural performance, and the ability to endure cyclic loading. This study considered key research on the structural behavior of CFST columns, covering various topics, including lightweight concrete, methods of concrete placement within steel tubes, and CFST columns with and without shear connectors. The literature review reveals that while several researchers have explored the use of shear connectors as a load-transfer mechanism in CFST columns, there is no consensus on the design methodology for connector resistance. Shear connectors signifi</p> ... Show More
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Publication Date
Fri Aug 01 2025
Journal Name
Cabi Reviews
Precision agriculture strategies to reduce the impacts of soil degradation: A comprehensive review
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This review discusses precision agriculture techniques that help reduce the effects of soil degradation and improve soil health, based on an analysis of studies published in scientific databases such as Web of Science, Scopus, IEEE Xplore, Google Scholar, and ScienceDirect, with an emphasis on recent field research. The methodology included a qualitative analysis of case studies and application experiments in different areas to evaluate the impact of technologies such as controlled traffic farming (CTF), mechanized guidance (MG), precision fertilization (PF), precision irrigation (PI), conservation tillage (CT), and precision tillage (PT). Research results showed, CT to maintain soil structure and reduce organic matter loss increases soil f

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Publication Date
Sat Oct 20 2018
Journal Name
Journal Of Economics And Administrative Sciences
THE IMPACT OF MANAGEMENT CONTROL SYSTEMS (MCS) ON ORGANIZATIONS PERFORMANCE A LITERATURE REVIEW
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The impact of management control systems (MCS) on organizations performance empirical research has been the subject of numerous studies during the past decade in developed and emerging economies. In the contemporary competitive, complex and changing global business environment, firms are being challenged to adopt business models that enable them to address the strategic uncertainties and risks they face in their business environments. The main issue of this study is that management accounting researchers argue that one of the ways firms can continually rejuvenate themselves to survive and succeed in these complex and uncertain environments is to understand the role of management control systems in Formulating a b

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Publication Date
Wed Feb 01 2023
Journal Name
Ecotoxicology And Environmental Safety
The role of environmental trace element toxicants on autism: A medical biogeochemistry perspective
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Publication Date
Tue Jun 01 2021
Journal Name
Jpras Open
The utility of a novel vacuum-assisted foreign body extraction technique from wounds
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Retained soft tissue foreign bodies following injuries are frequently seen in the Emergency and Plastic Surgery practice. The patients with such presentations require a watchful and detailed clinical as- sessment to overcome the anticipant possibility of missing them. However, the diagnosis based on the clinical evaluation is usually challenging and needs to be supported by imaging modalities that are suboptimal and may fail in identifying some types of foreign bodies. Owing to that, serious complications such as chronic pain, infection, and delayed wound healing can be faced that necessitate a prompt intervention to halt those detrimental consequences. The classical method of removal is a surgical exploration which is not free of risks.

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Publication Date
Thu May 18 2023
Journal Name
College Of Islamic Sciences
a base The origin of permissive things And its impact on Islamic law
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So I present in the hands of the honorable reader what God Almighty has made easy for me in terms of what I dealt with in the rule (the principle of permissive things) and what branches from it and what is related to it.
This research was divided into an introduction, a preface, three demands, and a conclusion.
The preamble is to explain the meaning of the rule in language and terminology and the definition of the legal rule and what is related to it. The first requirement is to explain the rule that we have in our hands and the words related to its text - and is it a fundamentalist or jurisprudential rule? .
As for the second requirement - in the difference of scholars and their opinions in whether the origin of things is permi

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Publication Date
Thu Dec 01 2022
Journal Name
Environmental Nanotechnology, Monitoring & Management
Challenges in the implementation of bioremediation processes in petroleum-contaminated soils: A review
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Environmental pollution is regarded as a major problem, and traditional strategies such as chemical or physical remediation are not sufficient to overcome the problems of pollution. Petroleum-contaminated soil results in ecological problems, representing a danger to human health. Bioremediation has received remarkable attention, and it is a procedure that uses a biological agent to remove toxic waste from contaminated soil. This approach is easy to handle, inexpensive, and environmentally friendly; its results are highly satisfactory. Bioremediation is a biodegradation process in which the organic contaminants are completely mineralized to inorganic compounds, carbon dioxide, and water. This review discusses the bioremediation of petroleum-

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Publication Date
Sun Dec 10 2023
Journal Name
Journal Of Applied Engineering And Technological Science (jaets)
The Role of Artificial Intelligence in Diagnosing Heart Disease in Humans: A Review
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The electrical activity of the heart and the electrocardiogram (ECG) signal are fundamentally related. In the study that has been published, the ECG signal has been examined and used for a number of applications. The monitoring of heart rate and the analysis of heart rhythm patterns, the detection and diagnosis of cardiac diseases, the identification of emotional states, and the use of biometric identification methods are a few examples of applications in the field. Several various phases may be involved in the analysis of electrocardiogram (ECG) data, depending on the type of study being done. Preprocessing, feature extraction, feature selection, feature modification, and classification are frequently included in these stages. Ever

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Publication Date
Sun Dec 22 2019
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
The Belief about Medicines among a Sample of Iraqi Patients with Rheumatoid Arthritis
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Rheumatoid arthritis is a chronic, progressive, inflammatory autoimmune disease of unidentified etiology, associated with articular, extra-articular and systemic manifestation that require long-standing treatment. Taking patient’s beliefs about the prescribed medication in consideration had been shown to be an essential factor that affects adherence of the patient in whom having positive beliefs is an essential for better adherence. The purpose of the current study was to measure beliefs about medicines among a sample of Iraqi patients with Rheumatoid arthritis and to determine possible association between this belief and some patient-certain factors. This study is a cross-sectional study carried out on 250 already diagnosed rheumatoid

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