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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 Jul 01 2018
Journal Name
Journal Of Global Pharma Technology
Synthesis, Characterization and Investigation Liquid Crystalline, Properties of 1, 2, 3-triazole Derivatives via Cycloaddition Reaction
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The new of compounds synthesized by sequence reactions starting from a reaction of 3-phenylenediamine or 4-phenylenediamine with chloroacetyl chloride to produce the compounds [I]a,b, then the compounds[I]a,b reacted with sodium azide to yield compounds[II]a,b that reacted 1,3-dipolarcycloaddition reaction with acrylic acid to give compounds [III]a,b these compounds reacted with methanol led to ester compounds[IV]a,b then reacted with hydrazine to give acid hydrazide [V]a,b . Finally compounds [V]a,b reacted with aromatic aldehydes to product shiff bases derivatives. The compounds characterized by mp. , IR, 1HNMR in addition to mass spectroscopy for some of them the liquid crystals properties were studied by using polarized optical microsco

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Publication Date
Tue Sep 01 2015
Journal Name
Journal Of Engineering
Mixed Convection Heat Transfer in a Vertical Saturated Concentric Annulus Packed with a Metallic Porous Media
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Mixed convection heat transfer in a vertical concentric annulus packed with a metallic porous media and heated at a constant heat flux is experimentally investigated with water as the working fluid. A series of experiments have been carried out with a Rayleigh number range from Ra=122418.92 to 372579.31 and Reynolds number that based on the particles diameter of Red=14.62, 19.48 and 24.36. Under steady state condition, the measured data were collected and analyzed. Results show that the wall surface temperatures are affected by the imposed heat flux variation and Reynolds number variation. The variation of the local heat transfer coefficient and the mean Nusselt number are presented and analyzed. An empirical

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Publication Date
Tue Dec 31 2019
Journal Name
Journal Of Economics And Administrative Sciences
A Try to combine more than approaches and competitive strategies to achieve a sustainable competitive advantage.
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The objective of this research paper is two-fold. The first is a precise reading of the theoretical underpinnings of each of the strategic approaches: "Market approach" for (M. Porter), and the alternative resource-based approach (R B V), advocates for the idea that the two approaches are complementary. Secondly, we will discuss the possibility of combining the two competitive strategies: cost leadership and differentiation. Finally, we propose a consensual approach that we call "dual domination". 

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Publication Date
Tue Jul 01 2025
Journal Name
Journal Of Studies In Humanities And Educational Sciences
The Effect of the Needham Constructivist Model on the Achievement of Third Year Biology Department Students in the Subject of Teaching Methods
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The current research aims to know the effect of Needham's constructivist model on the achievement of third-year students in the Life Sciences Department in the teaching methods subject. To achieve the research objectives, the experimental method was followed for the experimental and control groups with dimensional measurement of the achievement variable of the teaching methods subject. The research sample included (62) students in the third year of the Life Sciences Department, distributed into two equal groups in the variables (self-assessment of learning methods - chronological age in years - intelligence level - previous information). To measure the level of students' achievement, an achievement test was constructed consisting of (40) te

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Publication Date
Sat Feb 01 2025
Journal Name
Pharmaceutical Nanotechnology
Preparation, <i>In-vitro, Ex-vivo</i>, and Pharmacokinetic Study of Lasmiditan as Intranasal Nanoemulsion-based <i>In Situ</i> Gel
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Background:

Lasmiditan (LAS) is a recently developed antimigraine drug and was approved in October, 2019 for the treatment of acute migraines; however, it suffers from low oral bioavailability, which is around 40%.

Objective:

This study aimed to improve the LAS bioavailability via formulation as nanoemulsionbased in situ gel (NEIG) given intranasally and then compare the traditional aqueous-LASsuspension (AQS) with the two successful intranasal prepared formulations (NEIG 2 and NEIG 5) in order to determine its relative bioavailability (F-relative) via using rabbits.

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Publication Date
Thu Jun 08 2023
Journal Name
University Of Thi-qar Journal Of Agricultural Research
A review: Machine relationship with the tractor and its effect on the productivity and compaction of agricultural soil
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The influence of process speed (PS) and tillage depth (TD) , on growth of corn (Zea mays L) yield, for Maha cultivar, were tested at two ranges of PS of 2.483 and 4.011 km.hr-1, and three ranges of TD of 15,20 and 25cm. The experiments were conducted in a factorial experiment under complete randomized design with three replications. The results showed that the PS of 2.483 km.hr-1 was significantly better than the PS of 4.011km.hr-1 in all studied conditions. The , slippage ratio (SR) and the machine efficiency (ME), the physical soil characteristics represented by the soil density and porosity (SBD and TSP), and the plant characteristics represented the roots dry weight, PVI and the crop productivity (CP), except adjective of the fu

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Publication Date
Sun Jul 01 2018
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
KEY TO THE SPECIES OF THE ORTHETRUM NEWMAN, 1833 (ODONATA, LIBELLULIDAE) WITH A NEW RECORD SPECIES IN IRAQ
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This paper provides an identification key to the species of Orthetrum Newman, 1833 (Odonata, Libellulidae), including six species that were collected from different localities in Iraq.

 

    The species of O. anceps (Schneider, 1845) is registered as a new record in Iraq; the most important characters which are used in diagnostic key are included

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Publication Date
Wed Mar 09 2022
Journal Name
Technium Social Sciences Journal
The layered structure of the clause in English and Arabic ditransitive verbs: A Role and Reference Grammar Perspective
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This paper presents the syntactic dimension of ditransitive verbs in terms of the universal theory of Role and Reference Grammar (RRG). This theory is syntactic in nature, but it also covers the semantic as well as the pragmatic aspects of any linguistic phenomenon. It assumes a universal framework through which syntactic constructions can be analyzed. However, the morphological structure that each language enjoys renders the universal treatment more complicated and can question the universal nature of such a theory. In this paper, an attempt is made to check if the universal tenet of the theory is maintained over two typologically different languages: English and Arabic in respect of the way that double-object constructions (DOCs)

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Publication Date
Sat Aug 30 2025
Journal Name
Iraqi Journal Of Science
A Face Mask Detection Method in the Era of the COVID-19 Pandemic Based on GLCM and YOLO
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In recent decades, the identification of faces with and without masks from visual data, such as video and still images, has become a captivating research subject. This is primarily due to the global spread of the Corona pandemic, which has altered the appearance of the world and necessitated the use of masks as a vital measure for epidemic prevention. Intellectual development based on artificial intelligence and computers plays a decisive role in the issue of epidemic safety, as the topic of facial recognition and identifying individuals who wear masks or not was most prominent in the introduction and in-depth education. This research proposes the creation of an advanced system capable of accurately identifying faces, both with and

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Publication Date
Mon Dec 24 2018
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
ROCK SLOPE FAILURE BLOCKS AND THEIR RELATION TO TECTONIC ACTIVITY: A CASE STUDY IN 3B HIGHWAY, XUATHOA AREA, BACKAN PROVINCE, VIETNAM
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    This paper presents the results of the slope failure analyses from fracture distributions and their relation to tectonic activity; the analytical results have indicated that the phenomena of plane failure, wedge failure and toppling failure can occur at almost of the survey sites within the study area.

 

    The statistical data show that the fracture orientation mainly develop in the E-W, N-S and NW-SE due to the influence of tectonic activity. The occurrence of them together with the rock slope surface orientation has formed plane failure on the slope surface of the 3B highway in the E-W direction and the types of wedge failure and toppling failure on the slope surface of the highw

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