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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 Dec 25 2019
Journal Name
Journal Of Engineering
Link Failure Recovery for a Large-Scale Video Surveillance System using a Software-Defined Network
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The software-defined network (SDN) is a new technology that separates the control plane from data plane for the network devices. One of the most significant issues in the video surveillance system is the link failure. When the path failure occurs, the monitoring center cannot receive the video from the cameras. In this paper, two methods are proposed to solve this problem.  The first method uses the Dijkstra algorithm to re-find the path at the source node switch. The second method uses the Dijkstra algorithm to re-find the path at the ingress node switch (or failed link).

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Publication Date
Sun Dec 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
Assess the Reality of the Process of Applying the strategic Innovation In Business organizations : A prospective Study of comparative analysis in anumber of business organizations the Iraqi Industrial
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Abstract :

      The research aims to Estimate the Strength of Strategic Innovation application in terms of application strength , and on the overall level in number of Iraqi Industrial business organizations . After wards determine whether their is differerences among those organizations in application process for the dimensions , and for the overall process .

      The Research revealed number of conclusions including that the process of strategic innovation is applied in a good Level , and demonstrates the desier of the industrial companies Leaders to Launch beyond the familiar products , and to provide new products that

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Publication Date
Sun Mar 04 2018
Journal Name
Journal Of The College Of Education For Women
Novel of (Ya Mariam), for Sinan Antwane : A Pragmatic Study
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Pragmatics looked at literary discourse as an external subject that needed an actor and based on a communicative relationship, that is, it examines literary work by focusing on the author's intent, and attempting to monitor the pilgrim and logical dimension in the text. It focuses on the practical and communicative aspect of the language, which aims to convince the recipient and his or her emotional influence.And the novel (Yamrim) starting from the title (Sos) communication, and building dialogue and pilgrims based on two different logic completely, the logic of optimism and look at things with absolute objectivity, the logic of pessimism and closure and look at things with absolute passion. These two tendencies are embodied by the char

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Publication Date
Thu Oct 29 2020
Journal Name
Toxicological Research
Liver functions in combined models of the gentamicin induced nephrotoxicity and metabolic syndrome induced by high fat or fructose diets: a comparative study
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Publication Date
Sun Aug 17 2025
Journal Name
Journal Of Baghdad College Of Dentistry
A Comparative Study between Flapped and Flapless Surgical Techniques in Dental Implant Stability According to Resonance Frequency Analysis
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Background: Recent implant surgical approach aims to cause less trauma, invasiveness and pain as much as possible and to reduce patient and surgeon discomfort, time of surgery and time needed for functional implant loading. Flapless surgical techniques considered recently as one of the most popular techniques that may achieve these aims especially enhancing osseointegration and subsequently implant stability within less time than the traditional flapped surgical technique. So this study aimed to make a comparison between flapped and flapless surgical techniques in resulted implant stability according to resonance frequency analysis RFA and in duration of surgical operation. Materials and methods: A total of 26 patients with 41 implants (o

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Publication Date
Wed Nov 07 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
The Effect of Different Types of Separating Medium On Some Physical Properties of Processing Acrylic Denture-base with Two Investment Materials: A comparative Study
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Objective(s): In the present study, glycerin is used as a substitute for tin-foil and cold mold seal (Alginate mould seal)
in the process of curing heat and cold-cure acrylic resin denture base against stone and plaster.
Methodology: 60 specimens were prepared from heat-cure acrylic resin and cold-cure acrylic resin denture base. The
study includes 12 groups of specimens depending on the type of processing, investment material and type of
separating medium that are used in curing process. Each group of them contains 5 specimens for each test.
Some of physical properties of the processed acrylic denture base that (water sorption and solubility) have been
compared with those processed using tin-foil and tin-foil substitut

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Publication Date
Tue Sep 01 2015
Journal Name
Journal Of Engineering
Cost of Optimum Design of Trunk Mains Network Using Geographical Information System and Support Programs
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Sewer network is one of the important utilities in modern cities which discharge the sewage from all facilities. The increase of population numbers consequently leads to the increase in water consumption; hence waste water generation. Sewer networks work is very expensive and need to be designed accurately. Thus construction effective sewer network system with minimum cost is very necessary to handle waste water generation.

 In this study trunk mains networks design was applied which connect the pump stations together by underground pipes for too long distances. They usually have large diameters with varying depths which consequently need excavations and gathering from pump stations and transport the sewage

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Publication Date
Mon Jul 18 2022
Journal Name
International Journal Of Early Childhood Special Education
The effectiveness of a proposed teaching strategy according to The Common Knowledge Construction Model in Mathematical Proficiency for middle school student
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This research aims to know the effectiveness of teaching with a proposed strategy according to the common Knowledge construction modelin mathematical proficiency among students of the second middle class. The researchers adopted the method of the experimental approach, as the experimental design was used for two independent and equal groups with a post-test. The experiment was applied to a sample consisting of (83) students divided into two groups: an experimental comprising (42) students and a control group, the second comprising (41) students., from Badr Shaker Al-Sayyab Intermediate School for Boys, for the first semester of the academic year (2021-2022), the two groups were rewarded in four variables: (chronological age calculated in mo

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Publication Date
Wed Jun 07 2023
Journal Name
Journal Of Educational And Psychological Researches
Multiple Intelligence Test Item Selection-Based on Howard Gardner's MI Model Using a Generalized Partial Estimation Model: Ministry of Education \ Karkh First Directorate of Education
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The aim of the research is to examine the multiple intelligence test item selection based on Howard Gardner's MI model using the Generalized Partial Estimation Form, generalized intelligence. The researcher adopted the scale of multiple intelligences by Kardner, it consists of (102) items with eight sub-scales. The sample consisted of (550) students from Baghdad universities, Technology University, al-Mustansiriyah university, and Iraqi University for the academic year (2019/2020). It was verified assumptions theory response to a single (one-dimensional, local autonomy, the curve of individual characteristics, speed factor and application), and analysis of the data according to specimen partial appreciation of the generalized, and limits

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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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