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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 Aug 08 2024
Journal Name
New Materials, Compounds And Applications
MOLECULAR MODELLING AND THEORETICAL DESIGN OF NOVEL NIRMATRELVIR DERIVATIVES AS SARS-COV-2 ENTRY INHIBITORS
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The pandemic SARS-CoV-2 is highly transmittable with its proliferation among nations. This study aims to design and exploring the efficacy of novel nirmatrelvir derivatives as SARS entry inhibitors by adapting a molecular modeling approach combined with theoretical design. The study focuses on the preparation of these derivatives and understanding their effectiveness, with a special focus on their binding affinity to the S protein, which is pivotal for the virus’s access to the host cell. Considering molecular docking aspects in the scope of a study on nirmatrelvir derivatives and S protein, dynamics simulations with 25 nanoseconds of their binding are explored. The study shows that these derivatives might work as effective antivi

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Publication Date
Sat Apr 01 2023
Journal Name
Baghdad Science Journal
A Theoretical Study of the Docking of Medicines with some Proteins
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A set of ten drug compounds containing an amino group in the structure were determined theoretically. The parameters were entered into a model to forecast the optimal values of practical (log P) medicinal molecules. The drugs were evaluated theoretically using different types of calculations which are AM1, PM3, and Hartree Fock at the basis set (HF/STO-3G). The Physico-chemical data like (entropy, total energy, Gibbs Free Energy,…etc were computed and played an important role in the predictions of the practical lipophilicity values. Besides, Eigenvalues named HOMO and LUMO were determined. Linearity was shown when correlated between the experimental data with the evaluated physical properties. The statistical analysis was used to analy

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Publication Date
Fri Dec 01 2023
Journal Name
History Of Medicine
A comparative study of integrin- linked kinase 1 and anti-smith antibody as diagnostic biomarkers in Iraqi patients with systemic lupus erythematosus
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Systemic lupus erythematosus (SLE) is the prototypic multisystem autoimmune disorder with a broad spectrum of clinical presentations encompassing almost all organs and tissues. Aimes of study determination of integrin- linked kinase 1(ILK-1) and anti-smith antibody(ASAB) levels in serum of Iraqi patients with systemic lupus erythematosus, in addition, that ILK-1 may be as a diagnostic marker of SLE disease, and study the effect of systemic lupus erythematosus on renal function in these patients. This study included 100 females’ patients with systemic lupus erythematosus attending to the Rheumatology Unit in Baghdad Teaching Hospital, Medical City, (Baghdad), in addition to 30 healthy females as controller group were chosen without any chr

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Publication Date
Mon Aug 05 2019
Journal Name
Gen. Lett. Math
Building a three-dimensional maritime transport model to find the best solution by using the heuristic algorithm
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The aim of this research is to construct a three-dimensional maritime transport model to transport nonhomogeneous goods (k) and different transport modes (v) from their sources (i) to their destinations (j), while limiting the optimum quantities v ijk x to be transported at the lowest possible cost v ijk c and time v ijk t using the heuristic algorithm, Transport problems have been widely studied in computer science and process research and are one of the main problems of transport problems that are usually used to reduce the cost or times of transport of goods with a number of sources and a number of destinations and by means of transport to meet the conditions of supply and demand. Transport models are a key tool in logistics an

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Publication Date
Sat Apr 01 2023
Journal Name
Baghdad Science Journal
A Study of a-Si:H Absorption Edge Using Dunstan’s Model
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The optical absorption data of Hydrogenated Amorphous Silicon was analyzed using a Dunstan model of optical absorption in amorphous semiconductors. This model introduces disorder into the band-band absorption through a linear exponential distribution of local energy gaps, and it accounts for both the Urbach and Tauc regions of the optical absorption edge.Compared to other models of similar bases, such as the O’Leary and Guerra models, it is simpler to understand mathematically and has a physical meaning. The optical absorption data of Jackson et al and Maurer et al were successfully interpreted using Dunstan’s model. Useful physical parameters are extracted especially the band to the band energy gap , which is the energy gap in the a

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Publication Date
Wed Nov 16 2022
Journal Name
Res Militaris
Public Relations Employment of Foreign Oil Corporate Social Responsibility Programs Operating in Iraq Analytical Study of Programs from 1/1/2013 to 31/12/2021
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This research addresses the employment of public relations for foreign oil corporate social responsibility programs operating in Iraq. It is a study of the programmes of six petroleum companies operating in Basra Governorate, which were selected for research as the highest production of Iraqi oil, as well as its enjoyment of strategic oil stores in Iraq.It contains the largest oil fields operatedby major international companies. This study aims at a number of objectives, notably the following:1)Recognize the most prominent corporate social responsibility projects and initiatives the companies have introduced to the local public.2)Investigate the extent to which the Iraqi publ

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Publication Date
Mon Sep 08 2025
Journal Name
Journal Of Baghdad College Of Dentistry
The antibacterial evaluation of dandelion extracts as root canal irrigating solutions (A comparative study)
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Background: Irrigation has a central role in endodontic treatment. Several irrigating solutions have the antimicrobial activity and actively kill bacteria and yeasts when introduced in direct contact with the microorganisms. The purpose of this study was to evaluate the antimicrobial effectiveness of Dandelion (Taraxacum officinale) root and leaf extracts as possible irrigant solutions, used during endodontic treatments, and both were compared to Sodium hypochlorite, Propolis and Ethyl alcohol. Materials and Method: Forty seven human extracted single rooted teeth were selected. The teeth were decoronated using a diamond disk to have a length of 15 mm ±1 mm and they were instrumented using the hybrid technique. All roots were sterilized

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Publication Date
Tue Apr 28 2020
Journal Name
Journal Of Law And Humanities Sciences
Fair compensation for expropriation for the public benefit (A comparative study)
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The right to property is one of the most fundamental rights enjoyed by individuals, and most national constitutions and laws, as well as international conventions, have to be respected and protected only in accordance with the economic and social development of the country (the so-called public benefit) and in return for just compensation. What is fair compensation?

Publication Date
Wed Dec 23 2020
Journal Name
2020 International Conference On Advanced Science And Engineering (icoase)
A Comparative Study Using LZW with Wavelet or DCT for Compressing Color Images
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As a result of the significance of image compression in reducing the volume of data, the requirement for this compression permanently necessary; therefore, will be transferred more quickly using the communication channels and kept in less space in memory. In this study, an efficient compression system is suggested; it depends on using transform coding (Discrete Cosine Transform or bi-orthogonal (tap-9/7) wavelet transform) and LZW compression technique. The suggested scheme was applied to color and gray models then the transform coding is applied to decompose each color and gray sub-band individually. The quantization process is performed followed by LZW coding to compress the images. The suggested system was applied on a set of seven stand

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Publication Date
Thu Feb 01 2024
Journal Name
Russian Journal Of Bioorganic Chemistry
Synthesis, Identification, Antioxidant, Molecular Docking, and In Silico ADME Study for Some New Derivatives Containing Thiourea Moiety
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Objective: Synthesized a series of new thiourea (TU) derivatives, tested their antioxidant activity, and investigated their expected biological activity by theoretical study (computational methods). Methods: The derivatives were made using a one-pot reaction with two steps. Initially, succinyl chloride was mixed with KSCN to make succinyl isothiocyanate. Then, primary and secondary amines were used to make TU derivatives. The theoretical studies were done by Swiss ADME and molecular docking via Genetic Optimization of Linkage Docking (GOLD). Then evaluate antioxidant activity using the DPPH scavenging method. Results: FT-IR, 1H NMR, and 13C NMR spectroscopy show the verification of all the prepared derivatives. Compounds (II), (VIII),

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