The ABINIT-MP Program

Mochizuki, Yuji; Nakano, Tatsuya; Sakakura, Kota; Okiyama, Yoshio; Watanabe, Hiromasa; Kato, Koichiro; Akinaga, Yoshinobu; Sato, Shinya; Yamamoto, Jun-inchi; Yamashita, Katsumi; Murase, Tadashi; Ishikawa, Takeshi; Komeiji, Yuto; Kato, Y.; Watanabe, Naoki; Tsukamoto, Takashi; Mori, Hirotoshi; Okuwaki, Koji; Tanaka, Shigenori; Kato, Akifumi; Watanabe, Chiduru; Fukuzawa, Kaori

doi:10.1007/978-981-15-9235-5_4

Cited by 20 publications

(18 citation statements)

References 123 publications

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“…We shall address these technical issues in the activities of the FMO drug design consortium (FMODD). , The last issue is the expansion of the FMO programs that are eligible for FMODB registration. Although the current FMODB includes only results calculated using the ABINIT-MP program, , some groups have performed FMO calculations for COVID-19-related proteins, such as Mpro , and S proteins, using the GAMESS program. − We currently improve FMODB so that the results of FMO calculations can be registered in GAMESS.…”

Section: Discussionmentioning

confidence: 99%

“…All calculations in the FMODB were performed using ABINIT-MP, , the FMO calculation software. We used supercomputers, including TSUBAME3.0 at the Tokyo Institute of Technology, Oakforest-PACS at JCAHPC, and Fugaku and HOKUSAI at RIKEN.…”

Section: Methodsmentioning

confidence: 99%

“… 17 , 18 As for QM calculation, the fragment molecular orbital (FMO) method 19 , 20 is one of the methods that can treat the entire protein with uniform accuracy. The FMO calculation for several specific SARS-CoV-2-related proteins, such as the S protein, 21 − 25 Mpro, 26 − 30 and RdRp, 31 have been performed using the ABINIT-MP program 32 , 33 and the GAMESS program. 34 − 36 The ABINIT-MP program used in this paper is capable of performing precise electron correlation calculations at the MP4 (SDQ) level for S proteins of up to 3300 residues using the Fugaku supercomputer.…”

Section: Introductionmentioning

confidence: 99%

“…In particular, many dynamical structural analysis studies have been performed, such as the movement of the open structure of the spike (S) protein, the evaluation of the effect of glycans, ,, the binding mechanism of the receptor-binding domain (RBD) of the S protein to the angiotensin-converting enzyme 2 (ACE2) or antibodies, the binding of the main protease (Mpro) to inhibitors, , and the apo and the remdesivir-binding structure of RNA-dependent RNA polymerase (RdRp). , As for QM calculation, the fragment molecular orbital (FMO) method , is one of the methods that can treat the entire protein with uniform accuracy. The FMO calculation for several specific SARS-CoV-2-related proteins, such as the S protein, − Mpro, − and RdRp, have been performed using the ABINIT-MP program , and the GAMESS program. − The ABINIT-MP program used in this paper is capable of performing precise electron correlation calculations at the MP4 (SDQ) level for S proteins of up to 3300 residues using the Fugaku supercomputer . On the other hand, the FMO-DFTB method included in GAMESS is suitable for screening owing to its much lower computational cost .…”

Section: Introductionmentioning

confidence: 99%

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Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins

Fukuzawa

Kato

Watanabe

et al. 2021

J. Chem. Inf. Model.

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SARS-CoV-2 is the causative agent of coronavirus (known as COVID-19), the virus causing the current pandemic. There are ongoing research studies to develop effective therapeutics and vaccines against COVID-19 using various methods and many results have been published. The structure-based drug design of SARS-CoV-2-related proteins is promising, however, reliable information regarding the structural and intra- and intermolecular interactions is required. We 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. This enables us to extensively analyze the molecular interactions in residues or functional group units acting inside the protein complexes. Such precise interaction data are available in the FMO database (FMODB) ( ). Since April 2020, we have performed several FMO calculations on the structures of SARS-CoV-2-related proteins registered in the Protein Data Bank. We have published the results of 681 structures, including three structural proteins and 11 nonstructural proteins, on the COVID-19 special page (as of June 8, 2021). In this paper, we describe the entire COVID-19 special page of the FMODB and discuss the calculation results for various proteins. These data not only aid the interpretation of experimentally determined structures but also the understanding of protein functions, which is useful for rational drug design for COVID-19.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins

Fukuzawa

Kato

Watanabe

et al. 2021

J. Chem. Inf. Model.

Self Cite

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“…In the subspace diagonalization, the screened Coulomb potential is calculated in the AO basis, and the product with a trial vector can be easily obtained using a standard linear-algebra module. The GW and GW/BSE methods were implemented into the locally modified version of the ABINIT-MP program. ,,, …”

Section: Methodsmentioning

confidence: 99%

Fragment-Based Excited-State Calculations Using the GW Approximation and the Bethe–Salpeter Equation

Fujita

Noguchi

2021

J. Phys. Chem. A

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Herein, we present a fragment-based approach for calculating the charged and neutral excited states in molecular systems, based on the many-body Green's function method within the GW approximation and the Bethe−Salpeter equation (BSE). The implementation relies on the many-body expansion of the total irreducible polarizability on the basis of fragment molecular orbitals. The GW quasi-particle energies in complex molecular environments are obtained by the GW calculation for the target fragment plus induced polarization contributions of the surrounding fragments at the static Coulomb-hole plus screened exchange level. In addition, we develop a large-scale GW/BSE method for calculating the delocalized excited states of molecular aggregates, based on the fragment molecular orbital method and the exciton model. The accuracy of fragment-based GW and GW/BSE methods was evaluated on molecular clusters and molecular crystals. We found that the accuracy of the total irreducible polarizability can be improved systematically by including two-body correction terms, and the fragment-based calculations can reasonably reproduce the results of the corresponding unfragmented calculations with a relative error of less than 100 meV. The proposed approach enables efficient excited-state calculations for large molecular systems with reasonable accuracy.

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Protein–ligand binding affinity prediction of cyclin‐dependent kinase‐2 inhibitors by dynamically averaged fragment molecular orbital‐based interaction energy

et al. 2022

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Fragment molecular orbital (FMO) method is a powerful computational tool for structure-based drug design, in which protein-ligand interactions can be described by the inter-fragment interaction energy (IFIE) and its pair interaction energy decomposition analysis (PIEDA). Here, we introduced a dynamically averaged (DA) FMO-based approach in which molecular dynamics simulations were used to generate multiple protein-ligand complex structures for FMO calculations. To assess this approach, we examined the correlation between the experimental binding free energies and DA-IFIEs of six CDK2 inhibitors whose net charges are zero. The correlation between the experimental binding free energies and snapshot IFIEs for X-ray crystal structures was R 2 = 0.75. Using the DA-IFIEs, the correlation significantly improved to 0.99. When an additional CDK2 inhibitor with net charge of À1 was added, the DA FMO-based scheme with the dispersion energies still achieved R 2 = 0.99, whereas R 2 decreased to 0.32 employing all the energy terms of PIEDA.

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The ABINIT-MP Program

Cited by 20 publications

References 123 publications

Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins

Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins

Fragment-Based Excited-State Calculations Using the GW Approximation and the Bethe–Salpeter Equation

Protein–ligand binding affinity prediction of cyclin‐dependent kinase‐2 inhibitors by dynamically averaged fragment molecular orbital‐based interaction energy

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