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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
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
Wed Sep 01 2021
Journal Name
Baghdad Science Journal
A Posteriori L_∞ (L_2 )+L_2 (H^1 )–Error Bounds in Discontinuous Galerkin Methods For Semidiscrete Semilinear Parabolic Interface Problems
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The aim of this paper is to derive a posteriori error estimates for semilinear parabolic interface problems. More specifically, optimal order a posteriori error analysis in the - norm for semidiscrete semilinear parabolic interface problems is derived by using elliptic reconstruction technique introduced by Makridakis and Nochetto in (2003). A key idea for this technique is the use of error estimators derived for elliptic interface problems to obtain parabolic estimators that are of optimal order in space and time.

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Publication Date
Sat Jul 26 2025
Journal Name
Arab World English Journal
YouTube as a Learning Tool Among EFL Learners: A Systematic Review
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This review paper examines the crucial impact of YouTube on learning English as a Foreign Language. Recently, learners’ interaction and development of their skills have been improved due to the integration of digital platforms into language education. YouTube is regarded as one of the most prevalent platforms due to its accessibility, multimodal content, and capacity to simulate real-life communication. This study tackles thirty selected research articles from various cultural and institutional backgrounds to identify the pedagogical benefits and challenges associated with using YouTube in teaching English. Conventional methods of teaching English as a foreign language encounter difficulties in improving students’ engagement and

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Publication Date
Sun Jan 01 2023
Journal Name
Journal Of Population Therapeutics And Clinical Pharmacology
Evaluation of the Expression of RCC and KIM-1 Biomarkers in Nephrotoxicity of Rabbits Treated with Ochratoxins A
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Publication Date
Fri Sep 29 2023
Journal Name
International Journal Of Nanoscience
Preparation of N-A Cysteine-capped CdTe/CdS/ZnS core/shell/shell QDs as a Selective Probe for Detecting Damaged DNA
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In this study, NAC-capped CdTe/CdS/ZnS core/double shell QDs were synthesized in an aqueous medium to investigate their utility in distinguishing normal DNA from mutated DNA extracted from biological samples. Following the interaction between the synthesized QDs with DNA extracted from leukemia cases (represents damaged DNA) and that of healthy donors (represents undamaged DNA), differential fluorescent emission maxima and intensities were observed. It was found that damaged DNA from leukemic cells DNA-QDs conjugates at 585 nm while intact DNA (from healthy subjects) DNA–QDs conjugates at 574 nm. The obtained results from the optical analyses indicate that the prepared QDs could be utilized as probe for detecting disrupted DNA th

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Publication Date
Wed Dec 01 2021
Journal Name
Journal Of Physics: Conference Series
Study of the matter density distributions of halo nuclei 6He and 16C using the binary cluster model
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The harmonic oscillator (HO) and Gaussian (GS) wave functions within the binary cluster model (BCM) have been employ to investigate the ground state neutron, proton and matter densities as well as the elastic form factors of two- neutron 6He and 16C halo nuclei. The long tail is a property that is clearly revealed in the density of the neutrons since it is found in halo orbits. The existence of a long tail in the neutron density distributions of 6He and 16C indicating that these nuclei have a neutron halo structure. Moreover, the matter rms radii and the reaction cross section (𝜎𝑅 ) of these nuclei have been calculated using the Glauber model.

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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
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 Jul 09 2023
Journal Name
Journal Of Engineering
Comparative Study for Risk Criteria of Al-Qudus Plant between the Present and Planning of MOE
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The main function of a power system is to supply the customer load demands as economically as possible. Risk criterion is the probability of not meeting the load. This paper presents a methodology to assess probabilistic risk criteria of Al-Qudus plant before and after expansion; as this plant consists of ten generating units presently and the Ministry Of Electricity (MOE) is intending to compact four units to it in order to improve the performance of Iraqi power system especially at Baghdad region. The assessment is calculated by a program using Matlab programming language; version 7.6. Results show that the planned risk is (0.003095) that is (35 times) less than that in the present plant risk; (0.1091); which represents respectable imp

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Publication Date
Sun Sep 15 2019
Journal Name
Al-academy
Role of the Internet in Spreading Rumors Social networking sites "Facebook" model For the duration of 1-7-2017 until 30-11-2017: يوسف محمد حسين
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This study is about the role of the Internet in spreading rumors, especially through social networking sites "Facebook" model as the effectiveness of social networks lies in the speed of transmission of events; these two characteristics are important to the public, making the Internet a strong contender for television and its relationship with the public. That's why we find that the Internet today has become a fertile environment for the growth and spread of rumors. The more limited the platforms and places of publication, the greater the responsibility in the search for the original source in   spreading this or that rumor, as the Internet is considered an easy means in the production, spreading  and re-spreading  of

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