Evaluation on the performance of MM/PBSA in nucleic acid-protein systems

2021 ◽  
Author(s):  
Yuan-Qiang Chen ◽  
Yan-Jing Sheng ◽  
Hong-Ming Ding ◽  
Yu-Qiang Ma
Keyword(s):  
Nucleic Acid ◽  
Binding Energy ◽  
Molecular Mechanics ◽  
Pearson Correlation ◽  
Electrostatic Energy ◽  
Pearson Correlation Coefficient ◽  
Acid Protein ◽  
Poisson Boltzmann ◽  
Protein Nucleic Acid ◽  
Better Than

Abstract The molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method has been widely used in predicting the binding affinity among the ligands, the proteins and the nucleic acids. However, the accuracy of the predicted binding energy by the standard MM/PBSA is not always good, especially in highly charged systems. In this work, we take the protein-nucleic acid complexes as an example, and showed that the use of screening electrostatic energy (instead of coulomb electrostatic energy) in molecular mechanics can greatly improve the performance of MM/PBSA. In particular, the Pearson correlation coefficient of dataset II in the modified MM/PBSA (i.e., screening MM/PBSA) is about 0.52, much better than that (<0.33) in the standard MM/PBSA. Further, we also evaluate the effect of the solute dielectric constant and the salt concentration on the performance of the screening MM/PBSA. The present study highlights the potential power of the screening MM/PBSA for predicting the binding energy in highly charged bio-systems.

scholarly journals PROTEIN-NUCLEIC ACID INTERFACE (PNAI) INHIBITOR DRUG MOLECULES FOR SARS-COV-2

2020 ◽  
Author(s):  
Hamdullah Khadim Sheikh ◽  
Tanzila Arshad ◽  
Zainab Sher Mohammad ◽  
Iqra Arshad ◽  
Mohtasheemul Hassan
Keyword(s):  
Nucleic Acid ◽  
Binding Energy ◽  
Protease Inhibitors ◽  
Atomic Structure ◽  
Molecular Structures ◽  
Drug Molecules ◽  
Protein Nucleic Acid ◽  
Inhibitor Drug

<p>In this research we used the structure of SARS-CoV-2 related, recently mapped, atomic structure of nsp10/16 proteins for docking with some known drug molecular structures at pH 7 and 5. Chosen molecules were azo -N=N- and -COOH derivatives. It was revealed that the molecules showed good binding energy with nsp10/16 protein at both pH. These molecules can act as protein-nucleic acid interface (PNAI) inhibitor drug molecules. Such molecules can be used in combination with polymerase and protease inhibitors for treatment of SARS-CoV-2. </p>

Imperialist Competitive Algorithm with Updated Assimilation for the Solution of Real Valued Optimization Problems

2018 ◽  
Vol 27 (02) ◽  
pp. 1850005
Author(s):  
Zhavat Sherinov ◽  
Ahmet Ünveren ◽  
Adnan Acan
Keyword(s):  
Euclidean Distance ◽  
Optimization Problems ◽  
State Of The Art ◽  
Pearson Correlation ◽  
Imperialist Competitive Algorithm ◽  
Benchmark Problems ◽  
Pearson Correlation Coefficient ◽  
Competitive Algorithm ◽  
Imperialistic Competitive Algorithm ◽  
Better Than

In this paper, an improved imperialistic competitive algorithm is presented for real-valued optimization problems. A new method is introduced for the movement of colonies towards their imperialist, which is called assimilation. The proposed method uses Euclidean distance along with Pearson correlation coefficient as an operator for assimilating colonies with respect to their imperialists. Applications of the proposed algorithm to classical and recently published hard benchmark problems, and statistical analysis associated with the corresponding experimental results illustrated that the achieved success is significantly better than a number of state-of-the art methods.

Chemical control of biomolecular interaction modules

2009 ◽  
Vol 81 (2) ◽  
pp. 273-284 ◽  
Author(s):  
Frank Altenbrunn ◽  
Tom N. Grossmann ◽  
Christian Haase ◽  
Franziska Mende ◽  
Lars Röglin ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Chemical Synthesis ◽  
Mutual Recognition ◽  
Protein Domains ◽  
Synthesis Methods ◽  
Acid Protein ◽  
Hybrid Molecules ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions ◽  
And Control

The mutual recognition of biomacromolecules often is mediated by dedicated interaction modules. We take two main approaches in order to recognize and control nucleic acid-nucleic acid, protein-protein, and protein-nucleic acid interactions. In one, the rules that govern the formation of nucleic acid structures are used to design molecules that respond to the presence of nucleic acid or protein targets by showing changes of conformation or reactivity. For example, hybrid molecules can transduce changes of nucleic acid structure to changes of peptide structure, and vice versa. The other approach takes advantage of protein domains that once may form the basis of sensor materials and control elements. However, the current chemical synthesis methods have still not reached the level of maturity required to provide routine access to folded protein domains. In this article, we also describe recent progress that may facilitate the chemical synthesis of protein interaction domains.

scholarly journals PROTEIN-NUCLEIC ACID INTERFACE (PNAI) INHIBITOR DRUG MOLECULES FOR SARS-COV-2

2020 ◽  
Author(s):  
Hamdullah Khadim Sheikh ◽  
Tanzila Arshad ◽  
Zainab Sher Mohammad ◽  
Iqra Arshad ◽  
Mohtasheemul Hassan
Keyword(s):  
Nucleic Acid ◽  
Binding Energy ◽  
Protease Inhibitors ◽  
Atomic Structure ◽  
Molecular Structures ◽  
Drug Molecules ◽  
Protein Nucleic Acid ◽  
Inhibitor Drug

<p>In this research we used the structure of SARS-CoV-2 related, recently mapped, atomic structure of nsp10/16 proteins for docking with some known drug molecular structures at pH 7 and 5. Chosen molecules were azo -N=N- and -COOH derivatives. It was revealed that the molecules showed good binding energy with nsp10/16 protein at both pH. These molecules can act as protein-nucleic acid interface (PNAI) inhibitor drug molecules. Such molecules can be used in combination with polymerase and protease inhibitors for treatment of SARS-CoV-2. </p>

Snapshot blotting: The transfer of nucleic acids and nucleoprotein complexes from electrophoresis gels to EM grids

1992 ◽  
Vol 50 (1) ◽  
pp. 762-763
Author(s):  
Stephen D. Jett
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Nucleic Acid Binding ◽  
Mobility Shift ◽  
Carbon Coated ◽  
Nucleoprotein Complexes ◽  
Mobility Shift Assay ◽  
Protein Nucleic Acid ◽  
Gel Mobility Shift ◽  
Nucleic Acid Interactions

The electrophoresis gel mobility shift assay is a popular method for the study of protein-nucleic acid interactions. The binding of proteins to DNA is characterized by a reduction in the electrophoretic mobility of the nucleic acid. Binding affinity, stoichiometry, and kinetics can be obtained from such assays; however, it is often desirable to image the various species in the gel bands using TEM. Present methods for isolation of nucleoproteins from gel bands are inefficient and often destroy the native structure of the complexes. We have developed a technique, called “snapshot blotting,” by which nucleic acids and nucleoprotein complexes in electrophoresis gels can be electrophoretically transferred directly onto carbon-coated grids for TEM imaging.

Pengaruh Kotbah, Musik Gereja Dan Fasilitas Gereja Terhadap Tingkat Kehadiran Jemaat

2016 ◽  
Vol 1 (1) ◽  
pp. 1-15
Author(s):  
Frederich Oscar Lontoh
Keyword(s):  
Regression Analysis ◽  
Multiple Regression Analysis ◽  
Church Music ◽  
Pearson Correlation ◽  
Descriptive Analysis ◽  
Target Population ◽  
The Other ◽  
Pearson Correlation Coefficient ◽  
Christian Church ◽  
The City

This research is titled " The influence of sermon, church music and church facilities on the level of attendance”. The purpose of research is to identify and analyze whether sermon, church music and church facilities have influence on the the level of attendance. The target population in this study is a Christian church members who live in the city of Surabaya.. Sample required is equal to 47 respondents. Through sampling stratified Random techniques.These influence was measured using Pearson correlation coefficient and multiple regression analysis, t-test and analysis of variance. Descriptive  analysis  were taken to analyze the level of attendance according to demographic groups.The hypothesis in this study are the sermon, church music and church facilities have positive and significant on the level of attendance. The results showed that collectively, there are positive and significant correlation among the sermon, church music and church facilities on the level of attendance  96,2%. It means that 96,2 % of level of attendance influenced by sermon, church music and church facilities and the other 28,9% by others. All of the variable partially have significant correlation to level of attendance.

Genome-Wide Nucleic Acid/Protein Interaction in Breast Cancer

2005 ◽  
Author(s):  
Pamela A. Silver
Keyword(s):  
Breast Cancer ◽  
Nucleic Acid ◽  
Protein Interaction ◽  
Genome Wide ◽  
Acid Protein

Relationship between Invasive and Non-Invasive Hemodynamic Measures in Experimental Pulmonary Hypertension

2020 ◽  
Vol 16 (1) ◽  
pp. 47-53
Author(s):  
Vicente Benavides-Córdoba ◽  
Mauricio Palacios Gómez
Keyword(s):  
Heart Rate ◽  
Pulmonary Hypertension ◽  
Ejection Fraction ◽  
Right Ventricle ◽  
Correlation Coefficient ◽  
Pearson Correlation ◽  
Systolic Pressure ◽  
Control Group ◽  
Pearson Correlation Coefficient ◽  
Non Invasive

Introduction: Animal models have been used to understand the pathophysiology of pulmonary hypertension, to describe the mechanisms of action and to evaluate promising active ingredients. The monocrotaline-induced pulmonary hypertension model is the most used animal model. In this model, invasive and non-invasive hemodynamic variables that resemble human measurements have been used. Aim: To define if non-invasive variables can predict hemodynamic measures in the monocrotaline-induced pulmonary hypertension model. Materials and Methods: Twenty 6-week old male Wistar rats weighing between 250-300g from the bioterium of the Universidad del Valle (Cali - Colombia) were used in order to establish that the relationships between invasive and non-invasive variables are sustained in different conditions (healthy, hypertrophy and treated). The animals were organized into three groups, a control group who was given 0.9% saline solution subcutaneously (sc), a group with pulmonary hypertension induced with a single subcutaneous dose of Monocrotaline 30 mg/kg, and a group with pulmonary hypertension with 30 mg/kg of monocrotaline treated with Sildenafil. Right ventricle ejection fraction, heart rate, right ventricle systolic pressure and the extent of hypertrophy were measured. The functional relation between any two variables was evaluated by the Pearson correlation coefficient. Results: It was found that all correlations were statistically significant (p <0.01). The strongest correlation was the inverse one between the RVEF and the Fulton index (r = -0.82). The Fulton index also had a strong correlation with the RVSP (r = 0.79). The Pearson correlation coefficient between the RVEF and the RVSP was -0.81, meaning that the higher the systolic pressure in the right ventricle, the lower the ejection fraction value. Heart rate was significantly correlated to the other three variables studied, although with relatively low correlation. Conclusion: The correlations obtained in this study indicate that the parameters evaluated in the research related to experimental pulmonary hypertension correlate adequately and that the measurements that are currently made are adequate and consistent with each other, that is, they have good predictive capacity.

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