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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
Tue Dec 30 2014
Journal Name
College Of Islamic Sciences
Investigations in the sanctity of divine texts and their composition: (Comparative study between the Quran and the Torah)
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The research deals with an important issue that many people are working on, namely the sanctification of the texts on which the timings of the time and the different conditions of the place took place. Do not live up to the ranks of perfection and perfection, and every effort has explanations according to the mind machine, which is not protected by infallibility from error. The great downfall is to put these intellectual efforts in the Bible without separating them from the Word of God. The situation and the place on the adherents of a religion and mixed with the trick of the average individual only to be subject to the words of the teachers of Sharia and docility.

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Publication Date
Mon Jun 30 2025
Journal Name
Ingénierie Des Systèmes D Information
Comparative Analysis of Four Programming Languages for Machine Learning
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Publication Date
Wed Jan 31 2024
Journal Name
Journal Of The Faculty Of Medicine Baghdad (jfacmed Baghdad)
The Role of Activin A levels, Body Mass Index and Beta-Human Chorionic Gonadotropin in Ectopic Pregnancies and Missed Abortions – A Study on a Group of Iraqi Women
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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
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
Thu Sep 01 2022
Journal Name
Precision Radiation Oncology
Assessment of dose‐volume histogram statistics using three‐dimensional conformal techniques in breast cancer adjuvant radiotherapy treatment
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Abstract<sec><title>Objective

Breast cancer (BC) is first of the top 10 malignancies in Iraq. Dose‐volume histograms (DVHs) are most commonly used as a plan evaluation tool. This study aimed to assess DVH statistics using three‐dimensional conformal radiotherapies in BC in an adjuvant setting.

Methods

A retrospective study of 70 histologically confirmed women diagnosed with BC was reviewed. The study was conducted between November 2020 and May 2021, planning for treatment with adjuvant three‐dimensional conformal radiotherapies. The treatment plan used for each woman was based on an analysis of the volumetric dose, inclu

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Publication Date
Wed Dec 30 2015
Journal Name
College Of Islamic Sciences
Arrows of Kurdish scholars in the service of the Sunnah of Imam Majd al-Din Ibn al-Atheer al-Jazari (544_606): A model
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This research is a modest effort to talk about the great world of ancient lineage, Imam Majd al-Din Abu Saadat, known as Ibn al-Atheer island, through the statement of his name, surname, nickname, family, elders and his pupils and his most important works.
It also deals with the modern research on his famous book in the field of modern science called (the end in the strange talk and impact), which is one of the most wonderful books of modern and especially the strange talk, through the scientific effort of the Imam and the importance of the book and methodology, and the most prominent aspects of the service and care of Ibn Al Atheer For the modern stranger, which boils down to two aspects:
First: the linguistic rooting of the stran

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Publication Date
Mon Jun 01 2009
Journal Name
Journal Of Economics And Administrative Sciences
Use of lower squares and restricted boxes In the estimation of the first-order self-regression parameter AR (1) (simulation study)
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Use of lower squares and restricted boxes
In the estimation of the first-order self-regression parameter
AR (1) (simulation study)

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Publication Date
Fri Jan 30 2026
Journal Name
Journal Mustansiriyah Of Sports Science
The effect of using Daniel's model for people with two types of brain control (left and right) to learn the skill of the Cartwheel in artistic gymnastics for second-stage students
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The research problem focused through the researcher's experience in the gymnastics game and the lack of use of educational models that give the student an important role in the educational process, so it became necessary to identify the type of prevailing style for students, and the need for diversity in the use of educational models based on scientific theories, including the Daniel Document model. Based on three theories of learning, which are structural, behavioral, and meaningful learning. The research aimed to identify the effect of using the Daniel model for people with two types of brain control (left and right) to learn the skill of the Cartwheel in artistic gymnastics for students of the second stage. The researcher used the experi

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Publication Date
Mon Jun 28 2021
Journal Name
Journal Of The College Of Education For Women
The Style of Prophet's Civilized Dialogue in the Glorious Qur'an: The HUD (PBUH)-Aad Dialogue as a Sample: طلال خليفة سلمان العبيدي
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The present paper focuses on examining the style of both the civilized dialogue of Prophet Hud (PBUH) in the Glorious Qur'an, and the debated dialogue of Aad’s people. The study consists of an introduction which shows the importance of the civilized dialogue and its significant impact on containing, accepting, and persuading the other in peaceful ways without intolerance and violence. Then, the conditions and techniques of the civilized dialogue and its types have been mentioned. This is followed by the practical side of the study, which involves examining stylistically the techniques used in Hud’s (PBUH) civilized dialogue to be invested later in people’s future conversations. It is also concerned with investigating stylistically

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