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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
Sat Jan 01 2022
Journal Name
Revista Iberoamericana De Psicologia Del Ejercicio Y El Deporte
THE EFFECT OF A PROPOSED TRAINING PROGRAM USING INTERMITTENT TRAINING TO DEVELOP SOME PHYSICAL AND BIO-KINEMATIC VARIABLES AND ACCURACY OF THE JUMP SPIKE SERVE SKILL IN VOLLEYBALL
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The purpose of this paper is to identifying the values of some physical and Bio- Kinematic variables during the performance of the jump spike serve skill, and identifying the effect of the proposed training program using intermittent training to develop some physical and Bio- Kinematic variables and accuracy of the jump spike serve skill among the research sample. The experimental method was used and the research was conducted on a deliberately chosen sample of the players of the Army Club, who were primarily advanced in volleyball, and the number of the sample was (10) players. The conclusions were reached that the proposed training program using intermittent training has a positive effect on some of the physical and Bio- Kinematic variabl

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Publication Date
Tue Jul 11 2017
Journal Name
The 39th Annual International Conference Of The Ieee Engineering In Medicine And Biology Society (embc'17)
Higuchi fractal dimension of the electroencephalogram as a biomarker for early detection of Alzheimer's disease
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It is widely accepted that early diagnosis of Alzheimer's disease (AD) makes it possible for patients to gain access to appropriate health care services and would facilitate the development of new therapies. AD starts many years before its clinical manifestations and a biomarker that provides a measure of changes in the brain in this period would be useful for early diagnosis of AD. Given the rapid increase in the number of older people suffering from AD, there is a need for an accurate, low-cost and easy to use biomarkers that could be used to detect AD in its early stages. Potentially, the electroencephalogram (EEG) can play a vital role in this but at present, no reliable EEG biomarker exists for early diagnosis of AD. The gradual s

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Publication Date
Thu May 21 2026
Journal Name
Journal Of Economics And Administrative Sciences
The effect of creating knowledge according to the model (Nonaka & Takeuchi, 1995) on organizational ambidexterity: A study on a sample of Iraqi private banks
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Purpose - This study relies on the descriptive and analytical approach through collecting and analyzing the necessary data, as this approach focuses on polling the opinions of the research sample and its directions, and aims to develop a model that studies the relationship between knowledge creation and organizational ambidexterity in Iraqi private banks and verifying its validity experimentally. Design / Methodology / Introduction - A survey was conducted through a questionnaire form to collect data from a sample of (113) managers in private commercial banks. In addition, this study used the AMOS program and the ready-to-use statistical program package (SPSS V.25) to test the proposed hypotheses of the theoretical model experimentally. Res

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Publication Date
Tue May 16 2023
Journal Name
Political Sciences Journal
Institutional Reality Construction: Principles of its Construction and Functions of Language in its Production; Diplomacy as a Model
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This study aims to answer a significant problem of social sciences and philosophy: How do we construct an institutional reality such as diplomacy with an objective recognizable existence? The study assumes that the ability to build institutional reality is based on our biological capacity, as it takes different forms in all the institutions we construct. The study takes the theory of the American philosopher John Searle as an approach to examining the assumption. The study sums up important findings; cultures, although they share the biological capacity on which they produce institutional realities, differ in the form of the value standards on which the institutional realities are based. The study recommends the need of Arab social resea

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Publication Date
Fri Jan 01 2021
Journal Name
Systematic Reviews In Pharmacy
A COMPARATIVE STUDY OF CHEMICAL COMPOUNDS AND ANTI-BACTERIAL EFFICACY OF DIFFERENT ALLIUM CEPA PLANT EXTRACTS
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Publication Date
Fri Dec 15 2017
Journal Name
Journal Of Baghdad College Of Dentistry
The Influence of Different Fabrication and Impression Techniques on the Marginal Adaptation of Lithium Disilicate Crowns (A comparative in vitro study)
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Background: The marginal adaptation has a key role in the success and longevity of the fixed dental restoration, which is affected by the impression and the fabrication techniques .The objective of this in vitro study was to evaluate and compare the marginal fitness of lithium disilicate crowns using two different digital impression techniques (direct and indirect techniques) and two different fabrication techniques (CAD/CAM and Press techniques). Materials and Methods: Thirty two sound upper first premolar teeth of comparable size extracted for orthodontic reason were selected in this study .Standardized preparation of all teeth samples were carried out with modified dental surveyor to receive all ceramic crown restoration with 1 mm deep

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Publication Date
Thu May 21 2026
Journal Name
Journal Of Legal Sciences
A comparative study between the federal investment law No. 13 of 2006 and the Investment Law Kurdistan No. 4 of 2006
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Publication Date
Mon Jan 01 2018
Journal Name
Ibn Al-haitham Journal For Pure And Applied Science
A Sensitive Electrochemical Sensor for Rapid Determination of Mebeverine Hydrochloride and Metronidazole Benzoate Selective Molecular Imprinted Polymer in the PVC Membrane
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Publication Date
Sat Feb 11 2023
Journal Name
Applied Sciences
A Preliminary Study and Implementing Algorithm Using Finite State Automaton for Remote Identification of Drones
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Electronic remote identification (ER-ID) is a new radio frequency (RF) technology that is initiated by the Federal Aviation Authorities (FAA). For security reasons, traffic control, and so on, ER-ID has been applied for drones by the FAA to enable them to transmit their unique identification and location so that unauthorized drones can be identified. The current limitation of the existing ER-ID algorithms is that the application is limited to the Wi-Fi and Bluetooth wireless controllers, which results in a maximum range of 10–20 m for Bluetooth and 50–100 m for Wi-Fi. In this study, a mathematical computing technique based on finite state automaton (FSA) is introduced to expand the range of the ER-ID RF system and reduce the ene

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Publication Date
Fri Mar 26 2021
Journal Name
Chemical Papers
DFT, anticancer, antioxidant and molecular docking investigations of some ternary Ni(II) complexes with 2‑[(E)‑[4‑(dimethylamino) phenyl]methyleneamino]phenol
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The biological activities of some ternary nickel complexes with a Schiff base obtained from 4-dimethylaminobenzaldehyde and 2-aminophenol have been reported. The Schiff base ( HL1) acts as a primary ligand whereas, anthranilic acid ( HL2), 2-nitroaniline ( HL3), alanine ( HL4) and histidine ( HL5) act as secondary ligand or co-ligand. The anticancer activity of these compounds was studied against human colon carcinoma (HCT-116), human hepatocellular liver carcinoma (HEPG-2) and human breast carcinoma (MCF-7) cell lines. As per the results, the compounds were active against the cell lines. The antioxidant activity of the same compounds was evaluated using DPPH (1,1-diphenyl-2-picryl-hydrazyl) radical scavenging and compared with ascorbic aci

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