Large-scale FMO-MP3 calculations on the surface proteins of influenza virus, hemagglutinin (HA) and neuraminidase (NA)

Yuji Mochizuki; Katsumi Yamashita; Kaori Fukuzawa; Kazutomo Takematsu; Hirofumi Watanabe; Naoki Taguchi; Yoshio Okiyama; Misako Tsuboi; Tatsuya Nakano; Shigenori Tanaka

doi:10.1016/j.cplett.2010.05.034

Large-scale FMO-MP3 calculations on the surface proteins of influenza virus, hemagglutinin (HA) and neuraminidase (NA)

Yuji Mochizuki, Katsumi Yamashita, Kaori Fukuzawa, Kazutomo Takematsu, Hirofumi Watanabe, Naoki Taguchi, Yoshio Okiyama, Misako Tsuboi, Tatsuya Nakano, Shigenori Tanaka

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38 Citations (Scopus)

Abstract

Two proteins on the influenza virus surface have been well known. One is hemagglutinin (HA) associated with the infection to cells. The fragment molecular orbital (FMO) calculations were performed on a complex consisting of HA trimer and two Fab-fragments at the third-order Møller-Plesset perturbation (MP3) level. The numbers of residues and 6-31G basis functions were 2351 and 201276, and thus a massively parallel-vector computer was utilized to accelerate the processing. This FMO-MP3 job was completed in 5.8 h with 1024 processors. Another protein is neuraminidase (NA) involved in the escape from infected cells. The FMO-MP3 calculation was also applied to analyze the interactions between oseltamivir and surrounding residues in pharmacophore.

Original language	English
Pages (from-to)	346-352
Number of pages	7
Journal	Chemical Physics Letters
Volume	493
Issue number	4-6
DOIs	https://doi.org/10.1016/j.cplett.2010.05.034
Publication status	Published - 2010 Jun 25
Externally published	Yes

ASJC Scopus subject areas

Physics and Astronomy(all)
Physical and Theoretical Chemistry

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10.1016/j.cplett.2010.05.034

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title = "Large-scale FMO-MP3 calculations on the surface proteins of influenza virus, hemagglutinin (HA) and neuraminidase (NA)",

abstract = "Two proteins on the influenza virus surface have been well known. One is hemagglutinin (HA) associated with the infection to cells. The fragment molecular orbital (FMO) calculations were performed on a complex consisting of HA trimer and two Fab-fragments at the third-order M{\o}ller-Plesset perturbation (MP3) level. The numbers of residues and 6-31G basis functions were 2351 and 201276, and thus a massively parallel-vector computer was utilized to accelerate the processing. This FMO-MP3 job was completed in 5.8 h with 1024 processors. Another protein is neuraminidase (NA) involved in the escape from infected cells. The FMO-MP3 calculation was also applied to analyze the interactions between oseltamivir and surrounding residues in pharmacophore.",

author = "Yuji Mochizuki and Katsumi Yamashita and Kaori Fukuzawa and Kazutomo Takematsu and Hirofumi Watanabe and Naoki Taguchi and Yoshio Okiyama and Misako Tsuboi and Tatsuya Nakano and Shigenori Tanaka",

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AU - Mochizuki, Yuji

AU - Yamashita, Katsumi

AU - Fukuzawa, Kaori

AU - Takematsu, Kazutomo

AU - Watanabe, Hirofumi

AU - Taguchi, Naoki

AU - Okiyama, Yoshio

AU - Tsuboi, Misako

AU - Nakano, Tatsuya

AU - Tanaka, Shigenori

PY - 2010/6/25

Y1 - 2010/6/25

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AB - Two proteins on the influenza virus surface have been well known. One is hemagglutinin (HA) associated with the infection to cells. The fragment molecular orbital (FMO) calculations were performed on a complex consisting of HA trimer and two Fab-fragments at the third-order Møller-Plesset perturbation (MP3) level. The numbers of residues and 6-31G basis functions were 2351 and 201276, and thus a massively parallel-vector computer was utilized to accelerate the processing. This FMO-MP3 job was completed in 5.8 h with 1024 processors. Another protein is neuraminidase (NA) involved in the escape from infected cells. The FMO-MP3 calculation was also applied to analyze the interactions between oseltamivir and surrounding residues in pharmacophore.

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Large-scale FMO-MP3 calculations on the surface proteins of influenza virus, hemagglutinin (HA) and neuraminidase (NA)

Abstract

ASJC Scopus subject areas

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