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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 Jun 20 2019
Journal Name
Baghdad Science Journal
A Comparative Analysis of the Zernike Moments for Single Object Retrieval
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Zernike Moments has been popularly used in many shape-based image retrieval studies due to its powerful shape representation. However its strength and weaknesses have not been clearly highlighted in the previous studies. Thus, its powerful shape representation could not be fully utilized. In this paper, a method to fully capture the shape representation properties of Zernike Moments is implemented and tested on a single object for binary and grey level images. The proposed method works by determining the boundary of the shape object and then resizing the object shape to the boundary of the image. Three case studies were made. Case 1 is the Zernike Moments implementation on the original shape object image. In Case 2, the centroid of the s

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Publication Date
Mon Jan 02 2017
Journal Name
Al-academy
Style and the jump in industrial product design - a comparative study
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Find cares studying ways in the development of industrial products and designs: the way the progressive development (how typical) and root development (jump design), was the aim of the research: to determine the effectiveness of the pattern and the jump in the development of designs and industrial products. After a process of analysis of a sample of research and two models of contemporary household electrical appliances, it was reached a set of findings and conclusions including:1-leaping designs changed a lot of entrenched perceptions of the user on how the product works and its use and the size and shape of the product, revealing him about the possibilities of sophisticated relationships with the product, while keeping the typical desi

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Publication Date
Wed Oct 05 2022
Journal Name
Research Journal Of Chemistry And Environment
Synthesis, Antioxidant ability and Docking study for new 4, 4'-((2-(Aryl)-1H-benzo [d] imidazole-1, 3 (2H)-diyl) bis (methylene)) diphenol
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New series of 4, 4'-((2-(Aryl)-1H-benzo [d] imidazole-1, 3 (2H)-diyl) bis (methylene)) Diphenol (3a-g) was successfully synthesized from cyclization of the reduction product of bis Schiff bases (2) with aryl aldehydes bearing phenolic hydroxyl in the presence of acetic acid. The structure of these compounds was identified from FT-IR, 1H NMR, 13C NMR and EIMs. The Antioxidant capability was screened by DPPH and FRAP assays. Both assays showed antioxidant capability more than BHT as well. Compounds 3b and 3c showed antioxidant capacity slightly less than ascorbic acid. The docking study for theses compound was carried out as III DNA polymerase inhibitor. The results of docking demonstrated that the increase in hinderances around phenolic hydr

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Publication Date
Wed Oct 26 2022
Journal Name
Research Journal Of Chemistry And Environment
Synthesis, Antioxidant ability and Docking study for new 4, 4'-((2-(Aryl)-1H-benzo [d] imidazole-1, 3 (2H)-diyl) bis (methylene)) diphenol
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New series of 4,4'-((2-(Aryl)-1H-benzo[d]imidazole1,3(2H)-diyl)bis(methylene))Diphenol(3a-g) was successfully synthesized from cyclization of the reduction product of bis Schiff bases (2) with aryl aldehydes bearing phenolic hydroxyl in the presence of acetic acid. The structure of these compounds was identified from FT-IR, 1H NMR, 13C NMR and EIMs. The Antioxidant capability was screened by DPPH and FRAP assays. Both assays showed antioxidant capability more than BHT as well. Compounds 3b and 3c showed antioxidant capacity slightly less than ascorbic acid. The docking study for theses compound was carried out as III DNA polymerase inhibitor. The results of docking demonstrated that the increase in hinderances around phenolic hy

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Publication Date
Sun Jan 01 2012
Journal Name
مجلة واسط للعلوم والطب
Study of nuclear characters to some 164, 166, 168 68 Er isotopes by using the interacting boson model IBM-1
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The aim of this study is to show the concepts of nuclear shape and the geometrical picture to the even-even nuclei of 164,166,168E isotopes in the context of the Interacting boson Model IBM-1. The energy spectra were calculated and the effective charge values (eB) of the electromagnetic transition strength were obtained and used to calculate the B(E2) values of the electromagnetic transitions and the quadrupole moment Q of 2+ -states. The Hamiltonian parameters were calculated by taking in account the properties of these nuclei. Comparison were made with the available experimental data and included in tables. The geometrical picture of these nuclei were looked at by calculating the deformation which were represented by the potentia

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Publication Date
Sat Feb 09 2019
Journal Name
Journal Of The College Of Education For Women
A comparative Study to calculate the Runs Property in the encryption systems
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Cryptographic applications demand much more of a pseudo-random-sequence
generator than do most other applications. Cryptographic randomness does not mean just
statistical randomness, although that is part of it. For a sequence to be cryptographically
secure pseudo-random, it must be unpredictable.
The random sequences should satisfy the basic randomness postulates; one of them is
the run postulate (sequences of the same bit). These sequences should have about the same
number of ones and zeros, about half the runs should be of length one, one quarter of length
two, one eighth of length three, and so on.The distribution of run lengths for zeros and ones
should be the same. These properties can be measured determinis

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Publication Date
Tue Mar 28 2023
Journal Name
International Journal Of Dentistry
The Effect of Different Obturation Techniques in Primary Teeth on the Apical Microleakage using Endoflas: A Comparative In Vitro Study
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Objectives. This study was carried out to quantitatively evaluate and compare the sealing ability of Endoflas by using differentobturation techniques. Materials and Methods. After 42 extracted primary maxillary incisors and canines were decoronated, theircanals were instrumented with K files of size ranging from #15 to #50. In accordance with the obturation technique, the sampleswere divided into three experimental groups, namely, group I: endodontic pressure syringe, group II: modified disposable syringe,and group III: reamer technique, and two control groups. Dye extraction method was used for leakage evaluation. Data wereanalyzed using one-way ANOVA and Dunnett’s T3 post hoc tests. The level of significance was set at p<0:05. Results.

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Publication Date
Thu May 18 2023
Journal Name
Journal Of Engineering
A Comparative Study of Single-Constraint Routing in Wireless Mesh Networks Using Different Dynamic Programming Algorithms
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Finding the shortest route in wireless mesh networks is an important aspect. Many techniques are used to solve this problem like dynamic programming, evolutionary algorithms, weighted-sum techniques, and others. In this paper, we use dynamic programming techniques to find the shortest path in wireless mesh networks due to their generality, reduction of complexity and facilitation of numerical computation, simplicity in incorporating constraints, and their onformity to the stochastic nature of some problems. The routing problem is a multi-objective optimization problem with some constraints such as path capacity and end-to-end delay. Single-constraint routing problems and solutions using Dijkstra, Bellman-Ford, and Floyd-Warshall algorith

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Publication Date
Sat Jun 01 2019
Journal Name
Al-nahrain Journal Of Science
THREE DIMENSIONAL EXPLICIT MODEL FOR COMETARY TAIL IONSINTERACTIONSWITH SOLAR WIND
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The different interactions between cometary tail and solar wind ions are studied in the present paper based on three-dimensional Lax explicit method. The model used in this research is based on the continuity equations describing the cometary tail-solar wind interactions. Three dimensional system was considered in this paper. Simulation of the physical system was achieved using computer code written using Matlab 7.0. The parameters studied here assumed Halley comet type and include the particle density , the particles velocity v, the magnetic field strength B, dynamic pressure p and internal energy E. The results of the present research showed that the interaction near the cometary nucleus is mainly affected by the new ions added to the

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Publication Date
Thu Feb 07 2019
Journal Name
Iraqi Journal Of Laser
Gingival Enlargement Management using Diode Laser 940 nm and Conventional Scalpel Technique (A Comparative Study)
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Diode lasers are becoming popular in periodontal surgery due to their highly absorption by pigments such as melanin and hemoglobin their weak absorption by water and hydroxyapatite makes them safe to be used around dental hard tissues. Objective: The aim of the present study was to evaluate the efficiency of diode laser in performing gingivectomy in comparison to conventional scalpel technique in patients with chronic inflammatory enlargement. Materials and methods: Thirty patients were selected for this study. All of them required surgical treatment of gingival enlargements and were randomly divided into two groups: Control group (treated by scalpel and include sixteen patients) and study group (treated with diode laser 940nm and includ

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