scholarly journals High-Precision Atomic Charge Prediction for Protein Systems Using Fragment Molecular Orbital Calculation and Machine Learning

2020 ◽  
Vol 60 (7) ◽  
pp. 3361-3368
Author(s):  
Koichiro Kato ◽  
Tomohide Masuda ◽  
Chiduru Watanabe ◽  
Naoki Miyagawa ◽  
Hideo Mizouchi ◽  
...  
Keyword(s):  
Machine Learning ◽  
Molecular Orbital ◽  
High Precision ◽  
Atomic Charge ◽  
Molecular Orbital Calculation ◽  
Fragment Molecular Orbital

Fragment molecular orbital calculation using the RI-MP2 method

2009 ◽  
Vol 474 (1-3) ◽  
pp. 195-198 ◽  
Author(s):  
Takeshi Ishikawa ◽  
Kazuo Kuwata
Keyword(s):  
Molecular Orbital ◽  
Molecular Orbital Calculation ◽  
Fragment Molecular Orbital ◽  
Mp2 Method

scholarly journals Intermolecular Interaction Among Remdesivir, RNA and RNA-Dependent RNA Polymerase of SARS-CoV-2 Analyzed by Fragment Molecular Orbital Calculation

2020 ◽  
Author(s):  
Koichiro Kato ◽  
Teruki Honma ◽  
Kaori Fukuzawa
Keyword(s):  
Rna Polymerase ◽  
Molecular Orbital ◽  
Antiviral Drug ◽  
Molecular Orbital Calculation ◽  
Data Bank ◽  
Rna Dependent Rna Polymerase ◽  
Fragment Molecular Orbital ◽  
Global Pandemic ◽  
The World ◽  
Primer Rna

<p>COVID-19, a disease caused by a new strain of coronavirus (SARS-CoV-2) originating from Wuhan, China, has now spread around the world, triggering a global pandemic, leaving the public eagerly awaiting the development of a specific medicine and vaccine. In response, aggressive efforts are underway around the world to overcome COVID-19. In this study, referencing the data published on the Protein Data Bank (PDB ID: 7BV2) on April 22, we conducted a detailed analysis of the interaction between the complex structures of the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 and Remdesivir, an antiviral drug, from the quantum chemical perspective based on the fragment molecular orbital (FMO) method. In addition to the hydrogen bonding and intra-strand stacking between complementary strands as seen in normal base pairs, Remdesivir bound to the terminus of an primer-RNA strand was further stabilized by diagonal π-π stacking with the -1A base of the complementary strand and an additional hydrogen bond with an intra-strand base, due to the effect of chemically modified functional group. Moreover, stable OH/π interaction is also formed with Thr687 of the RdRp. We quantitatively revealed the exhaustive interaction within the complex among Remdesivir, template-primer-RNA, RdRp and co-factors, and published the results in the FMODB database.</p>

scholarly journals Intermolecular Interaction Among Remdesivir, RNA and RNA-Dependent RNA Polymerase of SARS-CoV-2 Analyzed by Fragment Molecular Orbital Calculation

2020 ◽  
Author(s):  
Koichiro Kato ◽  
Teruki Honma ◽  
Kaori Fukuzawa
Keyword(s):  
Rna Polymerase ◽  
Molecular Orbital ◽  
Antiviral Drug ◽  
Molecular Orbital Calculation ◽  
Data Bank ◽  
Rna Dependent Rna Polymerase ◽  
Fragment Molecular Orbital ◽  
Global Pandemic ◽  
The World ◽  
Primer Rna

<p>COVID-19, a disease caused by a new strain of coronavirus (SARS-CoV-2) originating from Wuhan, China, has now spread around the world, triggering a global pandemic, leaving the public eagerly awaiting the development of a specific medicine and vaccine. In response, aggressive efforts are underway around the world to overcome COVID-19. In this study, referencing the data published on the Protein Data Bank (PDB ID: 7BV2) on April 22, we conducted a detailed analysis of the interaction between the complex structures of the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 and Remdesivir, an antiviral drug, from the quantum chemical perspective based on the fragment molecular orbital (FMO) method. In addition to the hydrogen bonding and intra-strand stacking between complementary strands as seen in normal base pairs, Remdesivir bound to the terminus of an primer-RNA strand was further stabilized by diagonal π-π stacking with the -1A base of the complementary strand and an additional hydrogen bond with an intra-strand base, due to the effect of chemically modified functional group. Moreover, stable OH/π interaction is also formed with Thr687 of the RdRp. We quantitatively revealed the exhaustive interaction within the complex among Remdesivir, template-primer-RNA, RdRp and co-factors, and published the results in the FMODB database.</p>

Antigen–antibody interactions of influenza virus hemagglutinin revealed by the fragment molecular orbital calculation

2011 ◽  
Vol 130 (4-6) ◽  
pp. 1197-1202 ◽  
Author(s):  
Akio Yoshioka ◽  
Kazutomo Takematsu ◽  
Ikuo Kurisaki ◽  
Kaori Fukuzawa ◽  
Yuji Mochizuki ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Molecular Orbital ◽  
Molecular Orbital Calculation ◽  
Fragment Molecular Orbital ◽  
Influenza Virus Hemagglutinin ◽  
Antigen Antibody ◽  
Antibody Interactions
Sign in / Sign up

Export Citation Format

Share Document