Literature DB >> 24740821

Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems.

Shigenori Tanaka1, Yuji Mochizuki, Yuto Komeiji, Yoshio Okiyama, Kaori Fukuzawa.   

Abstract

Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.

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Year:  2014        PMID: 24740821     DOI: 10.1039/c4cp00316k

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  20 in total

1.  The GTP responsiveness of PI5P4Kβ evolved from a compromised trade-off between activity and specificity.

Authors:  Koh Takeuchi; Yoshiki Ikeda; Miki Senda; Ayaka Harada; Koji Okuwaki; Kaori Fukuzawa; So Nakagawa; Hong Yang Yu; Lisa Nagase; Misaki Imai; Mika Sasaki; Yu-Hua Lo; Doshun Ito; Natsuki Osaka; Yuki Fujii; Atsuo T Sasaki; Toshiya Senda
Journal:  Structure       Date:  2022-05-02       Impact factor: 5.871

2.  N-Benzyl Substitution of Polyhydroxypyrrolidines: The Way to Selective Inhibitors of Golgi α-Mannosidase II.

Authors:  Sergej Šesták; Maroš Bella; Tomáš Klunda; Soňa Gurská; Petr Džubák; Florian Wöls; Iain B H Wilson; Vladimir Sladek; Marián Hajdúch; Monika Poláková; Juraj Kóňa
Journal:  ChemMedChem       Date:  2018-02-06       Impact factor: 3.466

3.  Identification of Novel Natural Product Inhibitors against Matrix Metalloproteinase 9 Using Quantum Mechanical Fragment Molecular Orbital-Based Virtual Screening Methods.

Authors:  Hocheol Lim; Hansol Hong; Seonik Hwang; Song Ja Kim; Sung Yum Seo; Kyoung Tai No
Journal:  Int J Mol Sci       Date:  2022-04-18       Impact factor: 6.208

4.  Newly characterized interaction stabilizes DNA structure: oligoethylene glycols stabilize G-quadruplexes CH-π interactions.

Authors:  Hisae Tateishi-Karimata; Tatsuya Ohyama; Takahiro Muraoka; Peter Podbevsek; Adam M Wawro; Shigenori Tanaka; Shu-Ichi Nakano; Kazushi Kinbara; Janez Plavec; Naoki Sugimoto
Journal:  Nucleic Acids Res       Date:  2017-07-07       Impact factor: 16.971

5.  Identification of correlated inter-residue interactions in protein complex based on the fragment molecular orbital method.

Authors:  Shigenori Tanaka; Chiduru Watanabe; Teruki Honma; Kaori Fukuzawa; Kazue Ohishi; Tadashi Maruyama
Journal:  J Mol Graph Model       Date:  2020-07-09       Impact factor: 2.518

6.  Accurate high-throughput screening based on digital protein synthesis in a massively parallel femtoliter droplet array.

Authors:  Yi Zhang; Yoshihiro Minagawa; Hiroto Kizoe; Kentaro Miyazaki; Ryota Iino; Hiroshi Ueno; Kazuhito V Tabata; Yasuhiro Shimane; Hiroyuki Noji
Journal:  Sci Adv       Date:  2019-08-21       Impact factor: 14.136

7.  Structural Basis of Activin Receptor-Like Kinase 2 (R206H) Inhibition by Bis-heteroaryl Pyrazole-Based Inhibitors for the Treatment of Fibrodysplasia Ossificans Progressiva Identified by the Integration of Ligand-Based and Structure-Based Drug Design Approaches.

Authors:  Tomohiro Sato; Katsuhiko Sekimata; Naoki Sakai; Hisami Watanabe; Chiemi Mishima-Tsumagari; Tomonori Taguri; Takehisa Matsumoto; Yoshifumi Fujii; Noriko Handa; Akiko Tanaka; Mikako Shirouzu; Shigeyuki Yokoyama; Yoshinobu Hashizume; Kohei Miyazono; Hiroo Koyama; Teruki Honma
Journal:  ACS Omega       Date:  2020-05-12

8.  Computational Analysis of the Interaction Energies between Amino Acid Residues of the Measles Virus Hemagglutinin and Its Receptors.

Authors:  Fengqi Xu; Shigenori Tanaka; Hirofumi Watanabe; Yasuhiro Shimane; Misako Iwasawa; Kazue Ohishi; Tadashi Maruyama
Journal:  Viruses       Date:  2018-05-03       Impact factor: 5.048

9.  An integrated approach to unravel a crucial structural property required for the function of the insect steroidogenic Halloween protein Noppera-bo.

Authors:  Kotaro Koiwai; Kazue Inaba; Kana Morohashi; Sora Enya; Reina Arai; Hirotatsu Kojima; Takayoshi Okabe; Yuuta Fujikawa; Hideshi Inoue; Ryunosuke Yoshino; Takatsugu Hirokawa; Koichiro Kato; Kaori Fukuzawa; Yuko Shimada-Niwa; Akira Nakamura; Fumiaki Yumoto; Toshiya Senda; Ryusuke Niwa
Journal:  J Biol Chem       Date:  2020-04-02       Impact factor: 5.157

10.  Towards good correlation between fragment molecular orbital interaction energies and experimental IC50 for ligand binding: A case study of p38 MAP kinase.

Authors:  Yinglei Sheng; Hirofumi Watanabe; Keiya Maruyama; Chiduru Watanabe; Yoshio Okiyama; Teruki Honma; Kaori Fukuzawa; Shigenori Tanaka
Journal:  Comput Struct Biotechnol J       Date:  2018-10-13       Impact factor: 7.271

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