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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 Sep 30 2020
Journal Name
College Of Islamic Sciences
The Breadth in the meaning of the "from Surah Maryam as a model.
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Prepositions have a key function, which is to associate parts of a sentence, called letters In addition, it adds the meanings of the verbs to the names, ie reached by them, and called by the coffin characters Qualities..

          I chose to search for the meaning of the preposition "from" in Surat Maryam to know its meanings in terms of originality and expansion, so the title of the research (the meanings of preposition "from" in terms of originality and expansion in Surat Maryam model(

 

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Publication Date
Fri Jun 28 2024
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
Synthesis, Characterization, Molecular Docking, ADMET Study, and Antimicrobial Evaluation of New Mannich Bases of Isatin–Thiazole Imine Bases
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Background: The isatin molecule is present in many natural substances, including plants and animals, and is used to prepare compounds with various biological activities. Objectives: To synthesize a new series of isatin derivatives with the expectation that they will have antimicrobial activity. Methods: Thiazole Schiff bases were synthesized from various Mannich bases of isatin to evaluate their antimicrobial properties. Initially, Mannich bases (2a–e) were synthesized by reacting isatin with formaldehyde and different secondary amines. Subsequently, they were treated with 2-aminothiazole to yield the final compounds (3a–e). Spectroscopic characterization was done via FT-IR and 1H-NMR. The antimicrobial screening was conducted o

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Publication Date
Sun Mar 01 2020
Journal Name
Baghdad Science Journal
A Comparative Study on the Double Prior for Reliability Kumaraswamy Distribution with Numerical Solution
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This work, deals with Kumaraswamy distribution. Kumaraswamy (1976, 1978) showed well known probability distribution functions such as the normal, beta and log-normal but in (1980) Kumaraswamy developed a more general probability density function for double bounded random processes, which is known as Kumaraswamy’s distribution. Classical maximum likelihood and Bayes methods estimator are used to estimate the unknown shape parameter (b). Reliability function are obtained using symmetric loss functions by using three types of informative priors two single priors and one double prior. In addition, a comparison is made for the performance of these estimators with respect to the numerical solution which are found using expansion method. The

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Publication Date
Sun Mar 31 2024
Journal Name
Association Of Arab Universities Journal Of Engineering Sciences
Using Solid Waste as A Substitute for Raw Materials in Construction: A Review.
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The main challenge is to protect the environment from future deterioration due to pollution and the lack of natural resources. Therefore, one of the most important things to pay attention to and get rid of its negative impact is solid waste. Solid waste is a double-edged sword according to the way it is dealt with, as neglecting it causes a serious environmental risk from water, air and soil pollution, while dealing with it in the right way makes it an important resource in preserving the environment. Accordingly, the proper management of solid waste and its reuse or recycling is the most important factor. Therefore, attention has been drawn to the use of solid waste in different ways, and the most common way is to use it as an alternative

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Publication Date
Sat Feb 28 2026
Journal Name
Journal Of Molecular Structure
Synthesis, Characterization, Molecular Docking and anti-corrosion activities of new Pyrimidine Derivatives
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Publication Date
Sun Mar 01 2026
Journal Name
Journal Of Molecular Structure
Synthesis, characterization, molecular docking and anti-corrosion activities of new pyrimidine derivatives
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In the present study, chalcone derivatives were synthesized via the Claisen-Schmidt condensation of 2-methyl acetanilide or 4-nitro acetanilide with p-dimethyl amino benzaldehyde in an ethanolic sodium hydroxide solution. The resulting chalcone reacted with urea or thiourea to produce several novel pyrimidine derivatives. All the synthesized compounds were characterized by FTIR, 1HNMR and 13CNMR spectroscopy. Before the synthesis process, molecular docking studies were performed to evaluate the potential of the synthesized molecules as drug candidates. Thus, molecular docking studies were performed using the CCDC GOLD suite (version 2025). The molecular docking results showed that the synthesized molecules had a noticeable affinity towards

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Publication Date
Mon Aug 01 2022
Journal Name
Inorganic Chemistry Communications
Study the application of new type green corrosion inhibitors for iron metal
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Density functional theory (DFT) calculations were used to evaluate the capability of Glutamine (Gln) and its derivative chemicals as inhibitors for the anti-corrosive behavior of iron. The current work is devoted to scrutinizing reactivity descriptors (both local and global) of Gln, two states of neutral and protonated. Also, the change of Gln upon the incorporation into dipeptides was investigated. Since the number of reaction centers has increased, an enhancement in dipeptides’ inhibitory effect was observed. Thus, the adsorption of small-scale peptides and glutamine amino acids on Fe surfaces (1 1 1) was performed, and characteristics such as adsorption energies and the configuration with the highest stability and lowest energy were ca

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Publication Date
Tue Sep 30 2025
Journal Name
Iraqi Journal Of Science
A Study on Using Molasses Production Waste Powder as a Green Adsorbent for Cu (II) Ions from its Aqueous Solution
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This study utilized low-cost agricultural waste (molasses production waste powder) to extract copper ions from aqueous solutions. The present investigation explored a range of factors that influence the adsorption process, including temperature, pH, ionic strength, contact time, quantity of adsorbent, and particle size. Spectrophotometric analysis was used to determine the solution's absorbance both before and after the adsorption procedure. The Langmuir and Freundlich adsorption models were used to match the equilibrium data. The Freundlich model was determined to be the best isotherm model using the linear regression coefficient R2=0.9868. Thermodynamic parameters, including enthalpy, entropy, and Gibbs free energy, were calculate

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Publication Date
Tue Jan 01 2019
Journal Name
Indian Journal Of Public Health Research & Development
Comparative Study of Hepcidin and Some Inflammatory Parameters in Pregnant Women at the Three Trimesters
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Publication Date
Sat Jul 04 2026
Journal Name
Journal Of Physical Education
A Comparative Study According to Angiotensin Genetic Diversity As Indicator for 30m Freestyle Swimming in Youth aged (15 – 16) Year Old
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