Using non-Gaussian density functional fits to improve relative free energy calculations

2005 ◽  
Vol 122 (13) ◽  
pp. 134110 ◽  
Author(s):  
Hirsh Nanda ◽  
Nandou Lu ◽  
Thomas B. Woolf
Keyword(s):  
Free Energy ◽  
Density Functional ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Relative Free Energy ◽  
Gaussian Density ◽  
Non Gaussian

scholarly journals Computational Prediction of Mutational Effects on the SARS-CoV-2 Binding by Relative Free Energy Calculations

2020 ◽  
Author(s):  
Junjie Zou ◽  
Jian Yin ◽  
Lei Fang ◽  
Mingjun Yang ◽  
Tianyuan Wang ◽  
...  
Keyword(s):  
Free Energy ◽  
Computational Prediction ◽  
Free Energy Calculations ◽  
Alanine Scanning Mutagenesis ◽  
Angiotensin Converting Enzyme 2 ◽  
Energy Calculations ◽  
Relative Free Energy ◽  
Protein Interfaces ◽  
Computational Alanine Scanning ◽  
Entry Receptor

<p>The ability of coronaviruses to infect humans is invariably associated with their binding strengths to human receptor proteins. Both SARS-CoV-2, initially named 2019-nCoV, and SARS-CoV were reported to utilize angiotensin-converting enzyme 2 (ACE2) as an entry receptor in human cells. To better understand the interplay between SARS-CoV-2 and ACE2, we performed computational alanine scanning mutagenesis on the “hotspot” residues at protein-protein interfaces using relative free energy calculations. Our data suggest that the mutations in SARS-CoV-2 lead to a greater binding affinity relative to SARS-CoV. In addition, our free energy calculations provide insight into the infectious ability of viruses on a physical basis, and also provide useful information for the design of antiviral drugs.</p>

scholarly journals Computational Prediction of Mutational Effects on the SARS-CoV-2 Binding by Relative Free Energy Calculations

2020 ◽  
Author(s):  
Junjie Zou ◽  
Jian Yin ◽  
Lei Fang ◽  
Mingjun Yang ◽  
Tianyuan Wang ◽  
...  
Keyword(s):  
Free Energy ◽  
Computational Prediction ◽  
Free Energy Calculations ◽  
Alanine Scanning Mutagenesis ◽  
Angiotensin Converting Enzyme 2 ◽  
Energy Calculations ◽  
Relative Free Energy ◽  
Protein Interfaces ◽  
Computational Alanine Scanning ◽  
Entry Receptor

<p>The ability of coronaviruses to infect humans is invariably associated with their binding strengths to human receptor proteins. Both SARS-CoV-2, initially named 2019-nCoV, and SARS-CoV were reported to utilize angiotensin-converting enzyme 2 (ACE2) as an entry receptor in human cells. To better understand the interplay between SARS-CoV-2 and ACE2, we performed computational alanine scanning mutagenesis on the “hotspot” residues at protein-protein interfaces using relative free energy calculations. Our data suggest that the mutations in SARS-CoV-2 lead to a greater binding affinity relative to SARS-CoV. In addition, our free energy calculations provide insight into the infectious ability of viruses on a physical basis, and also provide useful information for the design of antiviral drugs.</p>

scholarly journals Computational Prediction of Mutational Effects on SARS-CoV-2 Binding by Relative Free Energy Calculations

2020 ◽  
Vol 60 (12) ◽  
pp. 5794-5802 ◽  
Author(s):  
Junjie Zou ◽  
Jian Yin ◽  
Lei Fang ◽  
Mingjun Yang ◽  
Tianyuan Wang ◽  
...  
Keyword(s):  
Free Energy ◽  
Computational Prediction ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Relative Free Energy

scholarly journals Using AMBER18 for Relative Free Energy Calculations

2019 ◽  
Vol 59 (7) ◽  
pp. 3128-3135 ◽  
Author(s):  
Lin Frank Song ◽  
Tai-Sung Lee ◽  
Chun Zhu ◽  
Darrin M. York ◽  
Kenneth M. Merz
Keyword(s):  
Free Energy ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Relative Free Energy

scholarly journals Computational Prediction of Mutational Effects on the SARS-CoV-2 Binding by Relative Free Energy Calculations

2020 ◽  
Author(s):  
Junjie Zou ◽  
Jian Yin ◽  
Lei Fang ◽  
Mingjun Yang ◽  
Tianyuan Wang ◽  
...  
Keyword(s):  
Free Energy ◽  
Computational Prediction ◽  
Free Energy Calculations ◽  
Alanine Scanning Mutagenesis ◽  
Angiotensin Converting Enzyme 2 ◽  
Energy Calculations ◽  
Relative Free Energy ◽  
Protein Interfaces ◽  
Computational Alanine Scanning ◽  
Entry Receptor

<p>The ability of coronaviruses to infect humans is invariably associated with their binding strengths to human receptor proteins. Both SARS-CoV-2, initially named 2019-nCoV, and SARS-CoV were reported to utilize angiotensin-converting enzyme 2 (ACE2) as an entry receptor in human cells. To better understand the interplay between SARS-CoV-2 and ACE2, we performed computational alanine scanning mutagenesis on the “hotspot” residues at protein-protein interfaces using relative free energy calculations. Our data suggest that the mutations in SARS-CoV-2 lead to a greater binding affinity relative to SARS-CoV. In addition, our free energy calculations provide insight into the infectious ability of viruses on a physical basis, and also provide useful information for the design of antiviral drugs.</p>

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