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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
Thu Jan 01 2015
Journal Name
Journal Of The College Of Basic Education
Synthesis and Characterization of some biologically active transition metal complexes for a ligand derived from dimedone with mixed ligands.
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The aim of the work is synthesis and characterization of bidentate ligand [3-(3-acetylphenylamino)-5,5-dimethylcyclohex-3-enone][HL], from the reaction of dimedone with 3-amino acetophenone to produce the ligand [HL], the reaction was carried out in dry benzene as a solvent under reflux. The prepared ligand [HL] was characterized by FT-IR, UV-Vis spectroscopy, 1H, 13C-NMR spectra, Mass spectra, (C.H.N) and melting point. The mixed ligand complexes were prepared from ligand [HL] was used as a primary ligand while 8-hydroxy quinoline [HQ] was used as a secondary ligand with metal ion M(Π).Where M(Π) = (Mn ,Co ,Ni ,Cu ,Zn ,Cd and Pd) at reflux ,using ethanol as a solvent, KOH as a base. Complexes of the composition [M(L)(Q)] with (1

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Publication Date
Wed Jan 01 2025
Journal Name
Special Topics & Reviews In Porous Media: An International Journal
EXPERIMENTAL AND NUMERICAL INVESTIGATION OF A DOUBLE PASS SOLAR AIR HEATER PROVIDED WITH POROUS ABSORBER PLATE FOR DRYING APPLICATIONS
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This investigation integrates experimental and numerical approaches to study a novel solar air heater aimed at achieving an efficient design for a solar collector suitable for drying applications under the meteorological conditions of Iraq. The importance of this investigation stems from the lack of optimal exploitation of solar energy reaching the solar collector, primarily attributable to elevated thermal losses despite numerous designs employed in such solar systems. Consequently, enhancing the thermal performance of solar collectors, particularly those employed in crop drying applications, stands as a crucial focal point for researchers within this domain. Two identical double-pass solar air heaters were designed and constructed for

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Publication Date
Fri Mar 21 2014
Journal Name
International Journal Of Antennas And Propagation
Development of a Compact Wide-Slot Antenna for Early Stage Breast Cancer Detection Featuring Circular Array Full-View Geometry
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A novel planar type antenna printed on a high permittivity Rogers’ substrate is proposed for early stage microwave breast cancer detection. The design is based on a p-shaped wide-slot structure with microstrip feeding circuit to eliminate losses of transmission. The design parameters are optimized resulting in a good reflection coefficient at −10 dB from 4.5 to 10.9 GHz. Imaging result using inhomogeneous breast phantom indicates that the proposed antenna is capable of detecting a 5 mm size cancerous tumor embedded inside the fibroglandular region with dielectric contrast between the target and the surrounding materials ranging from 1.7 : 1 to 3.6 : 1.

Publication Date
Tue Jun 01 2021
Journal Name
Swarm And Evolutionary Computation
A review of heuristics and metaheuristics for community detection in complex networks: Current usage, emerging development and future directions
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Sensibly highlighting the hidden structures of many real-world networks has attracted growing interest and triggered a vast array of techniques on what is called nowadays community detection (CD) problem. Non-deterministic metaheuristics are proved to competitively transcending the limits of the counterpart deterministic heuristics in solving community detection problem. Despite the increasing interest, most of the existing metaheuristic based community detection (MCD) algorithms reflect one traditional language. Generally, they tend to explicitly project some features of real communities into different definitions of single or multi-objective optimization functions. The design of other operators, however, remains canonical lacking any inte

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Publication Date
Tue Jun 01 2021
Journal Name
Swarm And Evolutionary Computation
A review of heuristics and metaheuristics for community detection in complex networks: Current usage, emerging development and future directions
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Publication Date
Sun Oct 13 2019
Journal Name
Spe Kuwait Oil & Gas Show And Conference
Optimization of Fracture Parameters for Hydraulic Fractured Horizontal Well in a Heterogeneous Tight Reservoir: An Equivalent Homogeneous Modelling Approach
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Abstract<p>Building numerical reservoir simulation model with a view to model actual case requires enormous amount of data and information. Such modeling and simulation processes normally require lengthy time and different sets of field data and experimental tests that are usually very expensive. In addition, the availability, quality and accessibility of all necessary data are very limited, especially for the green field. The degree of complexities of such modelling increases significantly especially in the case of heterogeneous nature typically inherited in unconventional reservoirs. In this perspective, this study focuses on exploring the possibility of simplifying the numerical simulation pr</p> ... Show More
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Publication Date
Tue Jun 01 2021
Journal Name
Swarm And Evolutionary Computation
A review of heuristics and metaheuristics for community detection in complex networks: Current usage, emerging development and future directions
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Publication Date
Tue Sep 01 2020
Journal Name
Al-nahrain Journal Of Science
Spectrophotometric Determination of Co(II) in Vitamin B12 Using2-(biphenyl-4-yl)-3-((2-(2,4-dinitrophenyl) hydrazono)methyl) imidazo [1,2-a]pyridine as Ligand by Flow Injection–Merging Zone Analysis
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Publication Date
Fri May 19 2023
Journal Name
Revista Iberoamericana De PsicologÍa Del Ejercicio Y El Deporte
The Effect of a Training Curriculum According To the Physiological Index and the Transitional Speed of the 100m Hurdles Runner
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Recently, that there has been a decline in the levels of female players for this event in recent years compared to developments in the world, as this activity depends to achieve the highest level of performance on the physical capabilities and physiological indicators of the player who It is reflected in the achievement, which results in the loss of time for Iraqi female runners compared to the world champions in the (100) meter hurdles competition, which reflects on the level of achievement. The two researchers used the experimental approach in addressing the research problem, and the experimental design used the method of the two equal groups, the two experiments with the pre and post-tests. Female runner and second experimental group (4)

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Publication Date
Fri Jan 01 2016
Journal Name
Procedia Economics And Finance
The Mediating Role of Knowledge Sharing on Relationship between IT Capability and IT Support as Predictors of Innovation Performance: An Empirical Study on Mobile Companies in Iraq
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