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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
3rd International Scientific Conference Of Alkafeel University (iscku 2021)
Investigations for the critical vehicle velocities on a curved path
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􀀨􀀅􀀆􀀔􀀜􀀄􀀂􀀆􀀈􀀓􀀌􀀩􀀏􀀆􀀉􀀅􀀆􀀉􀀅􀀉􀀚􀀝􀀔􀀄􀀗􀀉􀀚􀀆􀀂􀀓􀀚􀀁􀀔􀀄􀀓􀀅􀀆􀀄􀀂􀀆􀀔􀀓􀀆􀀃􀀂􀀔􀀄􀀟􀀉􀀔􀀃􀀆􀀔􀀜􀀃􀀆􀀛􀀃􀀜􀀄􀀗􀀚􀀃􀀆􀀗􀀌􀀄􀀔􀀄􀀗􀀉􀀚􀀆􀀂􀀘􀀃􀀃􀀊􀀂􀀆􀀓􀀖􀀆􀀓􀀛􀀃􀀌􀀔􀀁􀀌􀀅􀀄􀀅􀀕􀀢􀀆􀀪􀀜􀀃􀀆􀀄􀀅􀀛􀀃􀀂􀀔􀀄􀀕􀀉􀀔􀀄􀀓􀀅􀀂􀀆 􀀉􀀌􀀃􀀆􀀙􀀉􀀂􀀃􀀊􀀆􀀓􀀅􀀆􀀉􀀁􀀔􀀓􀀟􀀓􀀙􀀄􀀚􀀃􀀆􀀚􀀉􀀔􀀃􀀌􀀉􀀚􀀆􀀂􀀘􀀉􀀗􀀃􀀆􀀟􀀄􀀊􀀂􀀔􀀆􀀔􀀜􀀃􀀆􀀗􀀃􀀅􀀔􀀃􀀌􀀚􀀄􀀅􀀃􀀂􀀆􀀓􀀖􀀆􀀔􀀜􀀃􀀆􀀙􀀉􀀂􀀃􀀆

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Publication Date
Fri Mar 01 2019
Journal Name
Al-khwarizmi Engineering Journal
A Finite Element Analysis for the Damaged Rotating Composite Blade
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In this paper, the finite element method is used to study the dynamic behavior of the damaged rotating composite blade. Three dimensional, finite element programs were developed using a nine node laminated shell as a discretization element for the blade structure (the same element type is used for damaged and non-damaged structure). In this analysis the initial stress effect (geometric stiffness) and other rotational effects except the carioles acceleration effect are included.  The investigation covers the effect speed of rotation, aspect ratio, skew angle, pre-twist angle, radius to length, layer lamination and fiber orientation of composite blade. After modeling a non-damaged rotating composite blade, the work procedure was to ap

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Publication Date
Mon Sep 03 2018
Journal Name
Al-academy
A new vision for the classic in contemporary fashion designResearch
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        fashion designers who have benefited greatly from the mobilization of ancient aesthetic ideas in the heritage of the people and guaranteed in their productions so that there is no change In the aesthetic value created by the designers of the research in the ancient heritage to find new signs that reflect the connection of man to the present as the aesthetic value of all the man created by the designs of fabrics and fashion through the ages      The problem of research was determined in the absence of a precise understanding of the nature of classical thought in fashion and the absence of a clear perception of the sustainability of this thought in contemporary fashion. He

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Publication Date
Fri Apr 01 2022
Journal Name
Baghdad Science Journal
Positive Definiteness of Symmetric Rank 1 (H-Version) Update for Unconstrained Optimization
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Several attempts have been made to modify the quasi-Newton condition in order to obtain rapid convergence with complete properties (symmetric and positive definite) of the inverse of  Hessian matrix (second derivative of the objective function). There are many unconstrained optimization methods that do not generate positive definiteness of the inverse of Hessian matrix. One of those methods is the symmetric rank 1( H-version) update (SR1 update), where this update satisfies the quasi-Newton condition and the symmetric property of inverse of Hessian matrix, but does not preserve the positive definite property of the inverse of Hessian matrix where the initial inverse of Hessian matrix is positive definiteness. The positive definite prope

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Publication Date
Mon Mar 08 2021
Journal Name
Baghdad Science Journal
EXTENSION OF HIGH REFLECTANCE BAND WIDTH FOR FAR INFRARED SPECTRAL REGION : (1)
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Extension of bandwidth for high reflectance zone for the spectral region (8-14pm) was studied adapting the concept of contiguous and overlapping high reflectance stacks. Computations was carried out using the modified characteristic matrix theory restricted to near-normal incidence of light on dielectric , homogenous and isotropic symmetrical stack. Certain precautions must be taken in the choice of stacks to avoid deep —reflectance minima from developing within the extended high reflectance region. Results illustrate that the techniques of extending the high reflectance regions are applicable not only to mirrors , but also to short-and long-edge filter and to narrow band pass filters.

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Publication Date
Sat Sep 30 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Effect of Heterogeneity on Recovery Factor for Carbonate Reservoirs. A Case Study for Mishrif Formation in West Qurna Oilfield, Southern Iraq
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Oil recovery could be impacted by the relation between vertical permeability (Kv) and horizontal permeability (Kh) (Kv/Kh). 4816 plugs that have been getting hold of 18 wells of Mishrif formation in the West Qurna oilfield were used. Kv/Kh data provided some scatter, but the mean is ~1. Kv/Kh =1 was used for the Petrel model before upscaling according to the heterogeneity of each layer.

Kv/Kh values for Mishrif Formation in West Qurna Oilfield are 0.8 for relatively homogeneous, 0.4 for heterogeneous rock, and 0.1 for cap rocks (CRII).

   Eclipse TM was used for reservoir simulation. PVT and SCAL data e

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Publication Date
Fri Jan 01 2016
Journal Name
Middle-east Journal Of Scientific Research
Question Classification Using Different Approach: A Whole Review
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Publication Date
Wed Jul 06 2022
Journal Name
Journal Of Al-qadisiyah For Computer Science And Mathematics
Image Compression using Polynomial Coding Techniques: A review
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Publication Date
Fri Jan 01 2016
Journal Name
Bio-inspired Computing – Theories And Applications
Image Segmentation Using Membrane Computing: A Literature Survey
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Publication Date
Sun Jul 09 2023
Journal Name
Journal Of Engineering
Improving IoT Applications Using a Proposed Routing Protocol
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The main objective of this work is to propose a new routing protocol for wireless sensor network employed to serve IoT systems. The routing protocol has to adapt with different requirements in order to enhance the performance of IoT applications. The link quality, node depth and energy are used as metrics to make routing decisions. Comparison with other protocols is essential to show the improvements achieved by this work, thus protocols designed to serve the same purpose such as AODV, REL and LABILE are chosen to compare the proposed routing protocol with. To add integrative and holistic, some of important features are added and tested such as actuating and mobility. These features are greatly required by some of IoT applications and im

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