scholarly journals Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

2010 ◽  
Vol 32 (5) ◽  
pp. 866-877 ◽  
Author(s):  
Tingjun Hou ◽  
Junmei Wang ◽  
Youyong Li ◽  
Wei Wang
Keyword(s):  
Molecular Mechanics ◽  
Surface Area ◽  
Generalized Born ◽  
Poisson Boltzmann

scholarly journals Using molecular dynamics simulations to evaluate active designs of cephradine hydrolase by molecular mechanics/Poisson–Boltzmann surface area and molecular mechanics/generalized Born surface area methods

RSC Advances ◽  
2019 ◽  
Vol 9 (24) ◽  
pp. 13868-13877 ◽  
Author(s):  
Jing Xue ◽  
Xiaoqiang Huang ◽  
Yushan Zhu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Mechanics ◽  
Surface Area ◽  
Assessment Method ◽  
Dynamics Simulation ◽  
Enzyme Design ◽  
Generalized Born ◽  
Computational Enzyme Design ◽  
Poisson Boltzmann ◽  
Dynamics Simulations

A quantitative assessment method for computational enzyme design was developed to rank the active designs of cephradine hydrolase based on molecular dynamics simulation.

scholarly journals Identification of a novel binding mechanism of quinoline based molecules with lactate dehydrogenase of Plasmodium falciparum

2019 ◽  
Author(s):  
Rahul Singh ◽  
Vijay Bhardwaj ◽  
Rituraj Purohit
Keyword(s):  
Plasmodium Falciparum ◽  
Molecular Docking ◽  
Molecular Mechanics ◽  
Surface Area ◽  
Binding Free Energy ◽  
Specific Inhibitor ◽  
Plasmodium Species ◽  
Ligand Efficiency ◽  
Surface Area Ratio ◽  
Poisson Boltzmann

Malaria remains a deadliest disease brought about by Plasmodium species, among one of these species, disease due to Plasmodium falciparum (Pf) is life-threatening. The structures of PfLDH and human LDH are very similar in terms of L-LDH activity, and their biological functions are also equivalent. Therefore, any treatment aiming blocking the functions of PfLDH can affect human LDH. Thus, the main objective of this study is to identify the molecule that exhibits selectivity towards PfLDH without a profound effect on human LDH. In this research, a set of 68 quinolines based molecules were used for molecular docking. From molecular docking, we selected molecules 3j, 4b, 4h, 4m based on their binding affinity, ligand efficiency, lipophilic ligand efficiency, and torsion with selectivity towards PfLDH. The stability of the docked molecules was compared to Chloroquine (reference inhibitor) by applying molecular dynamics simulations and molecular mechanics poisson boltzmann surface area calculations. All the selected molecules showed selectivity for PfLDH with stable dynamic behavior and high binding free energy in comparison to Chloroquine. After examining the molecular mechanics poisson boltzmann surface area ratio results, molecule 3j was reported as a potential and specific inhibitor for PfLDH with a novel mechanism of binding to PfLDH while the remaining molecules 4b, 4h, 4m could further be modified to be used as potent inhibitors against malarial infection.

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