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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 Dec 30 2009
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Mass Transfer Correlations for a Rotating Cylinder Electrode under lsothermal and Controlled Heat Transfer Condition
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Mass transfer correlations for iron rotating cylinder electrode in chloride/sulphate solution, under isothermal and
controlled heat transfer conditions, were derived. Limiting current density values for the oxygen reduction reaction from
potentiostatic experiments at different bulk temperatures and various turbulent flow rates, under isothermal and heat
transfer conditions, were used for such derivation. The corelations were analogous to that obtained by Eisenberg et all
and other workers.

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Publication Date
Wed Dec 23 2020
Journal Name
Iraqi Journal For Electrical And Electronic Engineering
Heuristic and Meta-Heuristic Optimization Models for Task Scheduling in Cloud-Fog Systems: A Review
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Nowadays, cloud computing has attracted the attention of large companies due to its high potential, flexibility, and profitability in providing multi-sources of hardware and software to serve the connected users. Given the scale of modern data centers and the dynamic nature of their resource provisioning, we need effective scheduling techniques to manage these resources while satisfying both the cloud providers and cloud users goals. Task scheduling in cloud computing is considered as NP-hard problem which cannot be easily solved by classical optimization methods. Thus, both heuristic and meta-heuristic techniques have been utilized to provide optimal or near-optimal solutions within an acceptable time frame for such problems. In th

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Publication Date
Thu Jan 30 2020
Journal Name
Telecommunication Systems
Nature-inspired optimization algorithms for community detection in complex networks: a review and future trends
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Publication Date
Sun Jun 05 2022
Journal Name
Network
A Computationally Efficient Gradient Algorithm for Downlink Training Sequence Optimization in FDD Massive MIMO Systems
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Future wireless networks will require advance physical-layer techniques to meet the requirements of Internet of Everything (IoE) applications and massive communication systems. To this end, a massive MIMO (m-MIMO) system is to date considered one of the key technologies for future wireless networks. This is due to the capability of m-MIMO to bring a significant improvement in the spectral efficiency and energy efficiency. However, designing an efficient downlink (DL) training sequence for fast channel state information (CSI) estimation, i.e., with limited coherence time, in a frequency division duplex (FDD) m-MIMO system when users exhibit different correlation patterns, i.e., span distinct channel covariance matrices, is to date ve

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Publication Date
Wed Jul 20 2022
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
A new technique for solving fractional nonlinear equations by sumudu transform and adomian decomposition method
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A novel technique Sumudu transform Adomian decomposition method (STADM), is employed to handle some kinds of nonlinear time-fractional equations. We demonstrate that this method finds the solution without discretization or restrictive assumptions. This method is efficient, simple to implement, and produces good results. The fractional derivative is described in the Caputo sense. The solutions are obtained using STADM, and the results show that the suggested technique is valid and applicable and provides a more refined convergent series solution. The MATLAB software carried out all the computations and graphics. Moreover, a graphical representation was made for the solution of some examples. For integer and fractional order problems, solutio

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Publication Date
Fri Feb 08 2019
Journal Name
Iraqi Journal Of Laser
Fusion Splicing for a Large Mode Area Photonic Crystal Fiber with Conventional Single Mode Fiber
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In this paper the experimentally obtained conditions for the fusion splicing with photonic crystal fibers (PCF) having large mode areas were reported. The physical mechanism of the splice loss and the microhole collapse property of photonic crystal fiber (PCF) were studied. By controlling the arc-power and the arc-time of a conventional electric arc fusion splicer (FSM-60S), the minimum loss of splicing for fusion two conventional single mode fibers (SMF-28) was (0.00dB), which has similar mode field diameter. For splicing PCF (LMA-10) with a conventional single mode fiber (SMF-28), the loss was increased due to the mode field mismatch.

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Publication Date
Sun Sep 03 2017
Journal Name
Baghdad Science Journal
Gravity Field Interpretation for Major Fault Depth Detection in a Region Located SW- Qa’im / Iraq
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This research deals with the qualitative and quantitative interpretation of Bouguer gravity anomaly data for a region located to the SW of Qa’im City within Anbar province by using 2D- mapping methods. The gravity residual field obtained graphically by subtracting the Regional Gravity values from the values of the total Bouguer anomaly. The residual gravity field processed in order to reduce noise by applying the gradient operator and 1st directional derivatives filtering. This was helpful in assigning the locations of sudden variation in Gravity values. Such variations may be produced by subsurface faults, fractures, cavities or subsurface facies lateral variations limits. A major fault was predicted to extend with the direction NE-

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Publication Date
Mon Sep 01 2025
Journal Name
Microbial Biosystems
Harnessing cyanobacteria for a greener tomorrow: CO₂ mitigation and bioconversion to sustainable chemicals and fuels
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Publication Date
Fri Dec 01 2017
Journal Name
2017 Ieee 56th Annual Conference On Decision And Control (cdc)
Hierarchical non-singular terminal sliding mode controller for a single link flexible joint robot manipulator
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—This paper studies the control motion of a single link flexible joint robot by using a hierarchical non-singular terminal sliding mode controller (HNTSMC). In comparison to the conventional sliding mode controller (CSMC), the proposed algorithm (NTSMC) not only can conserve characteristics of the convention CSMC, such as easy implementation, guaranteed stability and good robustness against system uncertainties and external disturbances, but also can ensure a faster convergence rate of the systems states to zero in a finite time and singularity free. The flexible joint robot (FJR) is a two degree of freedom (2DOF) nonlinear and underactuated system. The system here is modeled as a fourth order system by using Lagrangian method. Based on t

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Publication Date
Tue Jan 17 2023
Journal Name
International Journal Of Online And Biomedical Engineering (ijoe)
An Image Feature Extraction to Generate a Key for Encryption in Cyber Security Medical Environments
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Cyber security is a term utilized for describing a collection of technologies, procedures, and practices that try protecting an online environment of a user or an organization. For medical images among most important and delicate data kinds in computer systems, the medical reasons require that all patient data, including images, be encrypted before being transferred over computer networks by healthcare companies. This paper presents a new direction of the encryption method research by encrypting the image based on the domain of the feature extracted to generate a key for the encryption process. The encryption process is started by applying edges detection. After dividing the bits of the edge image into (3×3) windows, the diffusions

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