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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 Dec 01 2022
Journal Name
Al-khwarizmi Engineering Journal
Comparative Study between Activated Carbon and Charcoal for the Development of Latent Fingerprints on Nonporous Surfaces
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For criminal investigations, fingerprints remain the most reliable form of personal identification despite developments in other fields like DNA profiling. The objective of this work is to compare the performance of both commercial charcoal and activated carbon powder derived from the Alhagi plant to reveal latent fingerprints from different non-porous surfaces (cardboard, plain glass, aluminum foil sheet, China Dish, Plastic, and Switch). The effect of three variables on activated carbon production was investigated. These variables were the impregnation ratio (the weight ratio of KOH: dried raw material), the activation temperature, and the activation time. The effect factors were investigated using Central Composite Design

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Publication Date
Mon Feb 19 2018
Journal Name
Al-academy
The preoccupation of mental image in the designs of internal spaces (cinema) is a model
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The design studies, especially in their contemporary stages, have not been isolated from the subjects that underpin advanced ideas in the field of technical treatments that enrich and improve the social life of users through those technological innovations that have enhanced and changed life styles, Especially in the field of general institutional techniques, including cinemas, as the ideal places for people and visitors to this space, which can contribute to the promotion of cultural, social and technical aspects within this millennium. DONC as reflected on the positive communication and communication between the intellectual and cognitive develop individuals, including cultural and technical side of the individual. The first chapter co

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
On The Dynamical Behavior of a Prey-Predator Model With The Effect of Periodic Forcing
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The dynamical behavior of a two-dimensional continuous time dynamical system describing by a prey predator model is investigated. By means of constructing suitable Lyapunov functional, sufficient condition is derived for the global asymptotic stability of the positive equilibrium of the system. The Hopf bifurcation analysis is carried out. The numerical simulations are used to study the effect of periodic forcing in two different parameters. The results of simulations show that the model under the effects of periodic forcing in two different parameters, with or without phase difference, could exhibit chaotic dynamics for realistic and biologically feasible parametric values.

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Publication Date
Fri Jul 01 2016
Journal Name
Journal Of Engineering
Study the Properties of Sodium Silicate Composite as a Barrier Separating Between the Internal Oil Distillation Towers and Chemical Fumes of Crude Oil
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The study of surface hardness, wear resistance, adhesion strength, electrochemical corrosion resistance and thermal conductivity of coatings composed from sodium silicate was prepared using graphite micro-size particles and carbon nano particles as fillers respectively of concentration of (1-5%), for the purpose of covering and protecting the oil distillation towers. The results showed that the sodium silicate coating reinforced with carbon nano-powder has higher resistance to stitches, mechanical wear, adhesive and thermal conductivity than graphite/sodium silicate composite especially when the ratio 5% and 1%, the electrochemical corrosion test confirmed that the coating process of stainless steel 304 lead to increasin

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Publication Date
Mon Mar 08 2021
Journal Name
Baghdad Science Journal
state selection of ammonia molecular beam using tapered ring focuser
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I've made extensive studies on the distribution of the electric field stable heterogeneous within intensive that contain metal rings with slope diagonal positive to a site halfway to be in its maximum value, followed by decline negative and equally to the other end of the concentrated distributed by electric stable thanking sequentially and have focused empirical studies in the pastthe molecules that you focused Pantqaúha during passage

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Publication Date
Wed Feb 22 2023
Journal Name
Iraqi Journal Of Science
Molecular Identification of Aspergillus fumigatus Using ISSR and RAPD Markers
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The aim of this stud to isolate and identified of A. fumigatus from different sources and study the genetic diversity among these isolates by using RAPD and ISSR markers.Collected 20 samples from 7samples were isolated A. fumigatusisolates were characterized depending on its morphological, then extracted DNA from its.RAPD markersrandomly bandingwith sitesof genome more than ISSR markers where the primer OPN-07 achieved discriminative power (19.1) and 43 bands, while ISSR6 achieved discriminative power (17.1) with 32 bands.ISSR were more efficiency in specific binding then RAPD, ISSR primers has great a binding to production unique band, when 9 primers from 01 primers, ISSR9 was produce (5) unique bands, while RAPD markers was low ability

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Publication Date
Sun Jan 01 2017
Journal Name
The Iraqi Journal Of Agricultural Science 48 (5), 1197-1205‏
Sex identification of date palm by using dna molecular markers
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Publication Date
Thu Dec 01 2011
Journal Name
International Review Of Physics (e-journal) (irephy)
Red shift band enhancement of the nanostructure ZnO100-xAlx thin films as a function of Al concentration for optoelectronic applications
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Publication Date
Thu Sep 01 2022
Journal Name
Brazilian Journal Of Chemical Engineering
A computational study on the potential application of Ca12O12 cluster for sensing of fungicide molecule
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Density functional theory calculations are employed to investigate the impact of edifenphos molecule on the reactivity and electronic sensitivity of pure calcium oxide (CaO) nanocluster. The strong adsorption of edifenphos molecule on CaO nanocluster occurs by the sulfur head of the adsorbate, and the amount of the energy of this adsorption is around − 84.40 kcal/mol. The adsorption of edifenphos molecules results in a decrease in the values of Eg of CaO from 4.67 to 3.56 eV, as well as an increase in the electrical conductance. Moreover, the work function of CaO nanocluster is significantly affected, which changes the current of the field emission electron. Eventually, the recovery time is calculated around 99 ms at ambient temperature f

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Publication Date
Wed Jun 01 2022
Journal Name
Journal Of The College Of Languages (jcl)
A comparative study of the pivotal characters in the novel "Al-Shahz" and the script "Hamoon": بررسی تطبیقی شخصیت¬های محوری در رمان «الشحّاذ» و فیلم‌نامۀ «هامون»
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The novel is the revelation of the attitudes of every age. And the writers do not know the winner of their stroke to express these events، The research has been working on a descriptive-analytical approach based on the American Comparative School، Al-Shahez's novel explores the work of the nobly and the film by Hamoun by Dariush Mehrjui By relying on the main characters of these two narratives, they depict a picture of Egypt and Iran From the symbolic lines of these works. In fact, the authors of this research have tried to initiate the introduction and analysis of these two works In fact, the authors of this research have tried to initiate the introduction and analysis of these two works.

 The results of the research show that

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