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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 Jun 26 2019
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Synthesis of Acetylenic Derivatives of a Substituted 1, 3, 4-Thiadiazole as Antibacterial Agents
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Publication Date
Tue Apr 18 2023
Journal Name
Corporate Reputation Review
The Absorptive Capacity of Knowledge as an Approach for Building Strategic Reliability in the Sponge Organizations/Small Organizations in Kirkuk Governorate as a Model
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Publication Date
Tue Jul 01 2025
Journal Name
South African Journal Of Chemical Engineering
Expired azithromycin and cephalexin as corrosion inhibitors for aluminum in saline-acidic solution
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Publication Date
Fri Apr 01 2022
Journal Name
Baghdad Science Journal
Iron (II) Determination in Lipstick Samples using Spectrophotometric and Microfluidic Paper-based Analytical Device (µPADs) Platform via Complexation Reaction with Iron Chelator 1, 10-phenanthroline: A Comparative Study
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This study was undertaken to introduce a fast, accurate, selective, simple and environment-friendly colorimetric method to determine iron (II) concentration in different lipstick brands imported or manufactured locally in Baghdad, Iraq. The samples were collected from 500-Iraqi dinars stores to establish routine tests using the spectrophotometric method and compared with a new microfluidic paper-based analytical device (µPAD) platform as an alternative to cost-effective conventional instrumentation such as Atomic Absorption Spectroscopy (AAS). This method depends on the reaction between iron (II) with iron(II) selective chelator 1, 10-phenanthroline(phen) in the presence of reducing agent hydroxylamine (HOA) and sodium acetate (NaOAc) b

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Publication Date
Tue Apr 30 2024
Journal Name
Iraqi Journal Of Science
Topology-Based Modularity and Modularity Density for Detecting Protein Complexes: A Comparative Study
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     Binary relations or interactions among bio-entities, such as proteins, set up the essential part of any living biological system. Protein-protein interactions are usually structured in a graph data structure called "protein-protein interaction networks" (PPINs). Analysis of PPINs into complexes tries to lay out the significant knowledge needed to answer many unresolved questions, including how cells are organized and how proteins work. However, complex detection problems fall under the category of non-deterministic polynomial-time hard (NP-Hard) problems due to their computational complexity. To accommodate such combinatorial explosions, evolutionary algorithms (EAs) are proven effective alternatives to heuristics in solvin

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Publication Date
Wed Oct 05 2022
Journal Name
Research Journal Of Chemistry And Environment
Synthesis, Antioxidant ability and Docking study for new 4, 4'-((2-(Aryl)-1H-benzo [d] imidazole-1, 3 (2H)-diyl) bis (methylene)) diphenol
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New series of 4, 4'-((2-(Aryl)-1H-benzo [d] imidazole-1, 3 (2H)-diyl) bis (methylene)) Diphenol (3a-g) was successfully synthesized from cyclization of the reduction product of bis Schiff bases (2) with aryl aldehydes bearing phenolic hydroxyl in the presence of acetic acid. The structure of these compounds was identified from FT-IR, 1H NMR, 13C NMR and EIMs. The Antioxidant capability was screened by DPPH and FRAP assays. Both assays showed antioxidant capability more than BHT as well. Compounds 3b and 3c showed antioxidant capacity slightly less than ascorbic acid. The docking study for theses compound was carried out as III DNA polymerase inhibitor. The results of docking demonstrated that the increase in hinderances around phenolic hydr

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Publication Date
Wed Oct 26 2022
Journal Name
Research Journal Of Chemistry And Environment
Synthesis, Antioxidant ability and Docking study for new 4, 4'-((2-(Aryl)-1H-benzo [d] imidazole-1, 3 (2H)-diyl) bis (methylene)) diphenol
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New series of 4,4'-((2-(Aryl)-1H-benzo[d]imidazole1,3(2H)-diyl)bis(methylene))Diphenol(3a-g) was successfully synthesized from cyclization of the reduction product of bis Schiff bases (2) with aryl aldehydes bearing phenolic hydroxyl in the presence of acetic acid. The structure of these compounds was identified from FT-IR, 1H NMR, 13C NMR and EIMs. The Antioxidant capability was screened by DPPH and FRAP assays. Both assays showed antioxidant capability more than BHT as well. Compounds 3b and 3c showed antioxidant capacity slightly less than ascorbic acid. The docking study for theses compound was carried out as III DNA polymerase inhibitor. The results of docking demonstrated that the increase in hinderances around phenolic hy

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Publication Date
Sat Jun 19 2021
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
The Role of Ginkgo biloba Extract as Monotherapy in Improving the Outcomes of Patients with Metabolic Syndrome: A Pilot Comparative Study with Metformin
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The present study evaluates the effects of Ginkgo biloba extract as monotherapy on the glycemic status, insulin resistance (IR), body mass index (BMI), and visceral adiposity index (VAI), in addition to the inflammatory markers, oxidative status and leptin level in patients with metabolic syndrome in comparison with metformin.

The study is a randomized, double-blind pilot study conducted during the period May to September, 2020. Fifty patients were recruited in the study and they were allocated into two groups (25 per each group): Ginkgo biloba and Metformin groups, they received (120 mg Ginkgo biloba extract/ capsule) and (500 mg Metformin/ capsule) respectively; orally as a single dose for 90 days. Blood samples were taken at z

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Publication Date
Thu Dec 30 2021
Journal Name
Journal Of Legal Sciences
Violation of the rights of sound record producers (piracy) (A Comparative study)
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Piracy is one of the most important problems faced by sound record producers, because it is a problem that technology, evolves with the development of time and and although piracy is not a new problem, it has received great attention in recent years, because of the means by which (the Internet) and its size result from it, even In many of the ruler, describing it as (the crime of nd she participated in the great the electronic age) aharm it causes to all the groups involved in it producing the sound recording, because there are three categories that contribute to the production of the sound recording, which is (the author of the recorded work, the st who performs the work and the producer who artiperforms an operation Performance recording

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Publication Date
Sun Sep 30 2012
Journal Name
Al-hiqouq
Maintenance Contract - A Comparative Study with Islamic Jurisprudence
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Contemporary life is racing against time in its temptations and variables, and it has become shaped and changed in an amazing way in its various aspects and fields. This was facilitated by intellectual and scientific communication between civilizations, and the rapid progression in successive inventions and discoveries in the fields of science and arts of knowledge. This contributed to a great economic and commercial renaissance. Then, these economic developments entered the world into a very strong competition, which forced producers to calculate all production costs, to reach the highest profits by reducing the price of the produced commodity on the one hand, and achieving quality in appearance (especially) on the other hand. Since the ma

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