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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
Sun Feb 24 2019
Journal Name
Iraqi Journal Of Physics
The optical properties of a- (GeS2)100-xGax thin films
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Thin films whose compositions can be expressed by (GeS2)100-xGax (x=0, 6,12,18) formula were obtained by thermal evaporation technique  of bulk material at a base pressure of ~10-5 torr. Optical transmission spectra of the films were taken in the range of 300-1100 nm then the optical band gap, tail width of localized states,  refractive index, extinction coefficient were calculated. The optical constants were found to increase at low concentration of Ga (0 to12%) while they decreases with further addition of Ga. The optical band gap was found to change in opposite manner to that of optical constants. The variation in the optical parameters are explained in terms of average bond energy

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Publication Date
Tue Jan 09 2024
Journal Name
مجلة واسط للعلوم الریاضیة
The development of judo from a historical perspective (1880-1980)
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Judo has witnessed tremendous developments since its inception until the present day. It has been distinguished by its adaptation to the various challenges it has faced throughout the ages. Judo is one of the sports that have been affected by social, technological and cultural changes. These changes reflect its transformation from the traditional Japanese martial art to a global sport practiced. All over the world, therefore, studying the historical development of judo is important, as it provides valuable insights into the development of martial arts over a century, by studying the origins, principles and techniques of judo for the period (1880 - 1980), and also enables us to gain an understanding A deeper understanding of how the art form

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Publication Date
Mon Aug 01 2011
Journal Name
Journal Of Engineering
EXPERIMENTAL OBSERVATIONS ON THE BEHAVIOR OF A PILED RAFT FOUNDATION
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The piled raft is a geotechnical composite construction consisting of three elements: piles, raft and soil.
In the design of piled rafts, the load shared between the piles and the raft, and the piles are used up to a
load level that can be of the same order of magnitude as the bearing capacity of a comparable single
pile or even greater. Therefore, the piled raft foundation allows reduction of settlements in a very
economic way as compared to traditional foundation concepts.
This paper presents experimental study to investigate the behavior of piled raft system in sandy
soil. A small scale “prototype” model was tested in a sand box with load applied to the system through
a compression machine. The settlement was

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Publication Date
Tue Jun 15 2021
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
The Pathological Mechanisms of Obesity-Related Glomerulopathy: A review article
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The rising prevalence of obesity-related glomerulopathy (ORG) occurs in accordance with the rising prevalence of obesity worldwide. Clinically ORG is manifested by slowly progressing microalbuminuria that may develop to clinically evident proteinuria. Pathological characteristics of ORG include glomerular hypertrophy in the presence or absence of focal segmental glomerulosclerosis (FSGS). ORG can develop into clinically overt chronic renal insufficiency or even end-stage kidney disease. This article reviews the most important mechanisms for the development of ORG; that are abnormal renal hemodynamics, stimulation of renin-angiotensin-aldosterone system (RAAS), impairment of insulin sensetivity, ectopic lipid deposition, adipose tissue cy

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Publication Date
Wed Sep 29 2021
Journal Name
Al-khwarizmi Engineering Journal
Simulation of a Self-Balancing Platform on the Mobile Car
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        In the last years, the self-balancing platform has become one of the most common candidates to use in many applications such as flight, biomedical fields, industry. This paper introduced the simulated model of a proposed self-balancing platform that described the self–balancing attitude in (X-axis, Y-axis, or both axis) under the influence of road disturbance. To simulate the self-balanced platform's performance during the tilt, an integration between Solidworks, Simscape, and Simulink toolboxes in MATLAB was used. The platform's dynamic model was drawn in SolidWorks and exported as a STEP file used in the Simscape Multibody environment. The system is controlled using the proportional-integral-derivative (PID) co

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Publication Date
Sat Aug 30 2025
Journal Name
Gsc Biological And Pharmaceutical Sciences
The role of environmental stress in fish health: A review
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Fish are regarded as a crucial indicator of alterations in the aquatic environment due to their position at the apex of the food chain. Monitoring these alterations is crucial for identifying modifications in the aquatic ecosystem. The principal elements influencing fish health are temperature, pH, dissolved oxygen, salinity, pesticide contamination, microplastics, and algal presence. These elements substantially influence fish health regarding development, reproduction, respiration, oxygen stress, and the internal enzymes associated with digesting and other metabolic functions. Alterations in global environmental conditions and anthropogenic pollutants result in modifications to fish populations, their lives, and their behavior and

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Publication Date
Tue May 15 2018
Journal Name
Veterinary World
The crucial roles of inflammatory mediators in inflammation: A review
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The inflammatory response is a crucial aspect of the tissues’ responses to deleterious inflammogens. This complex response involves leukocytes cells such as macrophages, neutrophils, and lymphocytes, also known as inflammatory cells. In response to the inflammatory process, these cells release specialized substances which include vasoactive amines and peptides, eicosanoids, proinflammatory cytokines, and acute-phase proteins, which mediate the inflammatory process by preventing further tissue damage and ultimately resulting in healing and restoration of tissue function. This review discusses the role of the inflammatory cells as well as their by-products in the mediation of inflammatory process. A brief insight into the role of natural an

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Publication Date
Wed Oct 25 2023
Journal Name
College Of Islamic Sciences
The effect of fainting on a person’s behavior in (worship)
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The Messengers and the Imam of the God-fearing, Muhammad is God, his family, and all of his companions. As for what comes after... Fainting is one of the involuntary symptoms and states that occur to a person when carrying out his life’s tasks suddenly due to his loss of sense and movement, so he loses consciousness for a period of time that is short or may be long, and the person is held accountable and responsible for every moment of his life. He is required to perform duties specified by Sharia law, such as prayer, fasting, and Hajj...and fainting prevents him from performing these actions. We must consider the opinions of jurists and know the legal implications resulting from it. It was said that a person has a capacity that enable

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Publication Date
Mon Mar 15 2021
Journal Name
Energies
Intensifying the Charging Response of a Phase-Change Material with Twisted Fin Arrays in a Shell-And-Tube Storage System
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A twisted-fin array as an innovative structure for intensifying the charging response of a phase-change material (PCM) within a shell-and-tube storage system is introduced in this work. A three-dimensional model describing the thermal management with charging phase change process in PCM was developed and numerically analyzed by the enthalpy-porosity method using commercial CFD software. Efficacy of the proposed structure of fins for performing better heat communication between the active heating surface and the adjacent layers of PCM was verified via comparing with conventional longitudinal fins within the same design limitations of fin material and volume usage. Optimization of the fin geometric parameters including the pitch, numb

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Publication Date
Sun Dec 01 2019
Journal Name
Baghdad Science Journal
Studying the Crystal Structure, Topography, and Anti-bacterial of a Novel Titania (TiO2 NPs) Prepared by a Sol-gel Manner
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In this research, titanium dioxide nanoparticles (TiO2 NPs) were prepared through the sol-gel process at an acidic medium (pH3).TiO2 nanoparticles were prepared from titanium trichloride (TiCl3) as a precursor with Ammonium hydroxide (NH4OH) with 1:3 ratio at 50 °C. The resulting gel was dried at 70 °C to obtain the Nanocrystalline powder. The powder from the drying process was treated thermally at temperatures 500 °C and 700 °C. The crystalline structure, surface morphology, and particle size were studied by using X-ray diffraction (XRD), Atomic Force Microscopy (AFM), and Scanning Electron Microscope (SEM). The results showed (anatase) phase of titanium dioxide with the average grain size

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