Book Chapter10.1007/978-981-15-9235-5_4
The ABINIT-MP Program
Yuji Mochizuki,Yuji Mochizuki,Tatsuya Nakano,Kota Sakakura,Yoshio Okiyama,Hiromasa Watanabe,Koichiro Kato,Yoshinobu Akinaga,Shinya Sato,Jun-inchi Yamamoto,Katsumi Yamashita,Tadashi Murase,Takeshi Ishikawa,Yuto Komeiji,Yuji Kato,Naoki Watanabe,Takashi Tsukamoto,Hirotoshi Mori,Koji Okuwaki,Shigenori Tanaka,Akifumi Kato,Chiduru Watanabe,Kaori Fukuzawa,Kaori Fukuzawa +23 more
- 01 Jan 2021
- pp 53-67
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TL;DR: The ABINIT-MP program as mentioned in this paper is an original code for the fragment molecular orbital (FMO) calculations and has several unique features such as a variety of efficient correlated methods and hybrid parallelism.
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Abstract: We have been developing the ABINIT-MP program system as an original code for the fragment molecular orbital (FMO) calculations. ABINIT-MP has several unique features such as a variety of efficient correlated methods and hybrid parallelism. Additionally, an associated graphical user interface (named as BioStation Viewer) has been provided for end-users. In this chapter, we summarize the current features of the ABINIT-MP program. Plans and activities of future developments are addressed as well.
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Citations
Protein–ligand binding affinity prediction of cyclin‐dependent kinase‐2 inhibitors by dynamically averaged fragment molecular orbital‐based interaction energy
Kenichiro Takaba,Chiduru Watanabe,Atsushi Tokuhisa,Yoshinobu Akinaga,Biao Ma,Ryo Kanada,Mitsugu Araki,Yasushi Okuno,Yusuke Kawashima,Hirotomo Moriwaki,Norihito Kawashita,Teruki Honma,Kaori Fukuzawa,Shigenori Tanaka +13 more
TL;DR: A dynamically averaged (DA) FMO‐based approach in which molecular dynamics simulations were used to generate multiple protein–ligand complex structures for FMO calculations, and the correlation between the experimental binding free energies and DA‐IFIEs of six CDK2 inhibitors whose net charges are zero was examined.
20
Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins.
Kaori Fukuzawa,Kaori Fukuzawa,Koichiro Kato,Chiduru Watanabe,Yusuke Kawashima,Yuma Handa,Ami Yamamoto,Kazuki Watanabe,Kazuki Watanabe,Tatsuya Ohyama,Kikuko Kamisaka,Daisuke Takaya,Teruki Honma +12 more
TL;DR: In this article, the authors have conducted studies based on the fragment molecular orbital (FMO) method for calculating the electronic structures of protein complexes and analyzing their quantitative molecular interactions, which enables them to extensively analyze the molecular interactions in residues or functional group units acting inside the protein complexes.
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Multi-level parallelization of quantum-chemical calculations.
Dmitri G. Fedorov,Buu Q. Pham +1 more
TL;DR: In this article , strategies for efficient load balancing on problems of increasing granularity are introduced and a four-level parallelization is developed based on a multi-level hierarchical grouping, and a high parallel efficiency is achieved on the Theta supercomputer using 131,072 OpenMP threads.
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Special feature of COVID-19 in FMODB: Fragment molecular orbital calculations and interaction energy analysis of SARS-CoV-2 related proteins
Kaori Fukuzawa,Koichiro Kato,Chiduru Watanabe,Yusuke Kawashima,Yuma Handa,Ami Yamamoto,Kazuki Watanabe,Tatsuya Ohyama,Kikuko Kamisaka,Daisuke Takaya,Teruki Honma +10 more
TL;DR: This work has performed several FMO calculations on the structures of SARS-CoV-2 related proteins registered in the protein data bank and published the results of 681 structures, including three structural proteins and eleven nonstructural proteins, on the COVID-19 special page.
Prediction of Binding Pose and Affinity of Nelfinavir, a SARS-CoV-2 Main Protease Repositioned Drug, by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations.
Yuma Handa,Koji Okuwaki,Yusuke Kawashima,Ryo Hatada,Yuji Mochizuki,Yuto Komeiji,Shigenori Tanaka,Takayuki Furuishi,Etsuo Yonemochi,Teruki Honma,Kaori Fukuzawa +10 more
TL;DR: In silico drug design procedure for predicting binding pose and affinity of Nelfinavir against SARS-CoV-2 Main Protease. The procedure combines docking, MD, and FMO calculations to predict binding structure and properties of Mpro for NFV. Several residues are important for ligand recognition, including Glu47, Asp48, Glu166, Asp187, and Gln189.
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