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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
Wed Sep 21 2022
Journal Name
Journal Of Planner And Development
The role of municipal councils in achieving and localizing sustainable development in the local community (The municipality of Al-Shafa area in Ajloun governorate in Jordan as a model)
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Ajloun Governorate is considered the smallest governorate in Jordan in terms of area, and its population density rises to 472.2 people/ km2 and is distributed among five municipalities. The Al-Shafa municipality is one of these municipalities. Al-Shafa is rich in its natural and human resources, and the first municipal council was established in it in 2001.

This study seeks to achieve the following general objective: inventory the natural and human resources that Al-Shafa enjoys, and highlight the role of Al-Shafa municipality in achieving and settling sustainable development for the local community. Certain content, which are: the comprehensive approach to geographical reality, the descriptive

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Publication Date
Wed Apr 01 2015
Journal Name
Ibn Al-haitham Journal For Pure And Applied Science
Security For Three -Tired Web Application
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Web application protection lies on two levels: the first is the responsibility of the server management, and the second is the responsibility of the programmer of the site (this is the scope of the research). This research suggests developing a secure web application site based on three-tier architecture (client, server, and database). The security of this system described as follows: using multilevel access by authorization, which means allowing access to pages depending on authorized level; password encrypted using Message Digest Five (MD5) and salt. Secure Socket Layer (SSL) protocol authentication used. Writing PHP code according to set of rules to hide source code to ensure that it cannot be stolen, verification of input before it is s

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Publication Date
Sun Mar 19 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Security For Three-Tiered Web Application
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          Web application protection lies on two levels: the first is the responsibility of the server management, and the second is the responsibility of the programmer of the site (this is the scope of the research).  This research suggests developing a secure web application site based on three-tier architecture (client, server, and database). The security of this system described as follows: using multilevel access by authorization, which means allowing access to pages depending on authorized level; password encrypted using Message Digest Five (MD5) and salt. Secure Socket Layer (SSL) protocol authentication used. Writing PHP code according to set of rules to hide source code to ensur

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Publication Date
Sun Dec 15 2019
Journal Name
Journal Of Baghdad College Of Dentistry
Effect of platelet rich-fibrin on alveolar osteitis incidence following surgical removal of impacted mandibular third molars: A comparative study
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Background: Postoperative morbidity after extraction of the impacted mandibular third molar (IMTM) is inevitable. One of the most common postoperative complication is alveolar osteitis (AO) which is a painful non healed socket. Many researches were attempted to prevent the occurrence of AO by introducing and applying a new materials inside the extraction socket. Platelet rich fibrin (PRF) is a biological complex fibrin matrix where autologous platelets and leucocytes are present, used to enhance tissue healing process and reduce the early adverse effects of the inflammation. Aims: To evaluate the effect of PRF on the incidence of AO. Also to assess PRF effect on pain, swelling, and trismus following the surgical removal of IMTM and

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Publication Date
Fri Jun 27 2025
Journal Name
Journal Of Baghdad College Of Dentistry
A Comparative Study of Immunohistochemical Expression of Moesin, Cytokeratin 14 andMMP7 in Oral Squamous Cell Carcinoma and Oral Verrucous Carcinoma
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Background: Squamous cell carcinoma (SCC) is the most prevalent malignant neoplasm of the oral cavity that exhibits certain histological variations. Verrucous carcinoma (VC) is an uncommon exophytic low-grade well-differentiated variant of SCC. Cellular differentiation and morphology play important roles in cell functions and maintenance of structural integrity .As the cancer is a malignant process in which disorder of the cell growth and behavior occurs, such changes may differ in different tumor types and within different grades of the same tumor. Materials and Methods:Forty two formalin – fixed, paraffin – embedded tissue blocks were included in this study (30 blocks were diagnosed as OSCC and 12 blocks were diagnosed as OV

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Publication Date
Sun Jan 01 2012
Journal Name
European Journal Of Experimental Biology
A comparative study on cytotoxicity and apoptotic activity of pyocyanin produced by wild type and mutant strains of Pseudomonas aeruginosa
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Nutrient agar medium with various concentrations of cefotaxime was used for isolation spontaneous mutants from wild type strain of P.aeruginosa PHA-1. Eighty-two mutants were successfully isolated with the viable count 52×107 , these mutants were confirmed as spontaneous not physiological adaption mutants by reculture on the same medium. Then, wild type PHA-1 and mutants were examined for production pyocyanin; a blue greenish pigment was clearly noticed on King A medium. Remarkably the mutant strain named S300-8 was distinguished in productivity in comparison with wild type strain PHA-1; the amount of pigment was 56.0667mg/l and 74.53mg/l respectively. In addition, pyocyanin produced by mutant strain S300-8 revealed a potent efficacy again

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Publication Date
Tue Jan 01 2019
Journal Name
Biochem. Cell. Arch
A comparative study of amino acids in stomach regions of Felis catus (Domestic cat) and Sciurus carolinesis (Eastern gray squirrel)
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Amino acids were analyzed in stomach regions of males & females of Felis catus (Domestic Cat) & Sciurus carolinesis (Eastern Gray Squirrel ), where it was stated that there are (18) amino acids as following : Aspartic acid (Asp), Glutamic acid (Gla), Serine (Ser), Arginine (Arg), Aspargine ( Asn), Cysteine (Cys), Alanine (Ala), Proline (Pro), Glyscine (Gly), Threonine (Thr), Tyrosine (Tyr), Valine (Val), Methionine (Met), Histidine ( His), Isoleucine (ile), Leucine (leu), Phenylalanine (Phe ) and Lysine (lys). Results have shown there are significant differences in concentration of amino acids between different region of stomach between males & females of Felis catus in part and between males & females of Sciurus carolinesis (Eastern Gray S

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Publication Date
Tue Dec 15 2020
Journal Name
Technologies And Materials For Renewable Energy, Environment And Sustainability: Tmrees20
A comparative study of Williamson-Hall method and size-strain method through X-ray diffraction pattern of cadmium oxide nanoparticle
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In this research, the Williamson-Hall method and of size-strain plot method was employed to analyze X- ray lines for evaluating the crystallite size and lattice strain and of cadmium oxide nanoparticles. the crystallite size value is (15.2 nm) and (93.1 nm) and lattice strain (4.2 x10−4 ) and (21x10−4) respectively. Also, other methods have been employed to evaluate the crystallite size. The current methods are (Sherrer and modified Sherrer methods ) and their results are (14.8 nm) and (13.9nm) respectively. Each method of analysis has a different result because the alteration in the crystallite size and lattice strain calculated according to the Williamson-Hall and size-strain plot methods shows that the non-uniform strain in nan

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Publication Date
Sun Dec 15 2019
Journal Name
Journal Of Baghdad College Of Dentistry
Effect of platelet rich-fibrin on alveolar osteitis incidence following surgical removal of impacted mandibular third molars: A comparative study
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Background: Postoperative morbidity after extraction of the impacted mandibular third molar (IMTM) is inevitable. One of the most common postoperative complication is alveolar osteitis (AO) which is a painful non healed socket. Many researches were attempted to prevent the occurrence of AO by introducing and applying a new materials inside the extraction socket. Platelet rich fibrin (PRF) is a biological complex fibrin matrix where autologous platelets and leucocytes are present, used to enhance tissue healing process and reduce the early adverse effects of the inflammation. Aims: To evaluate the effect of PRF on the incidence of AO. Also to assess PRF effect on pain, swelling, and trismus following the surgical removal of IMTM and compa

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Crossref (5)
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Publication Date
Tue Feb 18 2025
Journal Name
International Journal Of Scientific Research In Science, Engineering And Technology
A Comprehensive Review on Cryptography Algorithms: Methods and Comparative Analysis
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The evolution of cryptography has been crucial to preservation subtle information in the digital age. From early cipher algorithms implemented in earliest societies to recent cryptography methods, cryptography has developed alongside developments in computing field. The growing in cyber threats and the increase of comprehensive digital communications have highlighted the significance of selecting effective and robust cryptographic techniques. This article reviews various cryptography algorithms, containing symmetric key and asymmetric key cryptography, via evaluating them according to security asset, complexity, and execution speed. The main outcomes demonstrate the growing trust on elliptic curve cryptography outstanding its capabi

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