Journal Article10.1016/S0009-2614(01)01416-6
Fragment molecular orbital method: use of approximate electrostatic potential
Tatsuya Nakano,Tsuguchika Kaminuma,Toshiyuki Sato,Kaori Fukuzawa,Yutaka Akiyama,Masami Uebayasi,Kazuo Kitaura +6 more
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TL;DR: The fragment molecular orbital (FMO) method as discussed by the authors has been proposed to reproduce ab initio total energies and geometries of molecules in good accuracy, but the most time consuming part in the method, the calculations of environmental electrostatic potentials, were speeded up by employing the Mulliken approximation for two-electron integrals and a fractional point charge approximation.
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About: This article is published in Chemical Physics Letters. The article was published on 17 Jan 2002. The article focuses on the topics: Fragment molecular orbital & Ab initio.
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Citations
Parallel Fock matrix construction with distributed shared memory model for the FMO-MO method.
Hiroaki Umeda,Yuichi Inadomi,Toshio Watanabe,Toshio Watanabe,Toru Yagi,Toru Yagi,Takayoshi Ishimoto,Takayoshi Ishimoto,Tsutomu Ikegami,Hiroto Tadano,Tetsuya Sakurai,Tetsuya Sakurai,Umpei Nagashima +12 more
TL;DR: A parallel Fock matrix construction program for FMO‐MO method has been developed with the distributed shared memory model and indicates that the parallelization efficiency of the matrix construction portion is as high as 93% at 1,024 processors.
26
Why does avian influenza A virus hemagglutinin bind to avian receptor stronger than to human receptor? Ab initio fragment molecular orbital studies.
Toshihiko Sawada,Tomohiro Hashimoto,Hirofumi Nakano,Tohru Suzuki,Hideharu Ishida,Makoto Kiso +5 more
TL;DR: The binding energy between avian H3 and avian receptor is 8.2kcal/mol larger than that of the avan H3-human receptor complex estimated at the FMO-HF/STO-3G level, which is a reason that avianH3 binds to avian receptors stronger than to human receptor.
26
Protein ligand interaction analysis against new CaMKK2 inhibitors by use of X-ray crystallography and the fragment molecular orbital (FMO) method.
Daisuke Takaya,Hideaki Niwa,Junko Mikuni,Kana Nakamura,Noriko Handa,Akiko Tanaka,Shigeyuki Yokoyama,Teruki Honma +7 more
TL;DR: The quantitative interaction analysis by the FMO method revealed that the dispersion interaction of inhibitors with hydrophobic residues, such as Ile171, Phe267, and Leu319, contributed highly to ligand binding; this was due to CH-π interactions with methoxy groups and/or aromatic rings contained in the authors' CaMKK2 inhibitor.
26
A Novel Potent and Highly Specific Inhibitor against Influenza Viral N1–N9 Neuraminidases: Insight into Neuraminidase–Inhibitor Interactions
Nongluk Sriwilaijaroen,Nongluk Sriwilaijaroen,Sadagopan Magesh,Akihiro Imamura,Hiromune Ando,Hideharu Ishida,Miho Sakai,Erika Ishitsubo,Takanori Hori,Setsuko Moriya,Takeshi Ishikawa,Kazuo Kuwata,Takato Odagiri,Masato Tashiro,Hiroaki Hiramatsu,Kenji Tsukamoto,Taeko Miyagi,Hiroaki Tokiwa,Makoto Kiso,Yasuo Suzuki +19 more
TL;DR: Broad efficacy of cPro-GUN against avian and human influenza viruses in cell cultures comparable to its sialidase inhibitory activities makes cPro -GUN ideal for further development for safe therapeutic or prophylactic use against both seasonal and pandemic influenza.
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Roles of K151 and D180 in L-2-haloacid dehalogenase from Pseudomonas sp. YL: analysis by molecular dynamics and ab initio fragment molecular orbital calculations.
Takashi Nakamura,Azusa Yamaguchi,Hirotaka Kondo,Hirofumi Watanabe,Tatsuo Kurihara,Nobuyoshi Esaki,Shuichi Hirono,Shigenori Tanaka +7 more
TL;DR: Analysis of the reaction mechanism of L‐DEX from Pseudomonas sp.
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References
Fragment molecular orbital method: an approximate computational method for large molecules
TL;DR: In this paper, an approximate molecular orbital (MO) method was proposed to calculate the total energy of a molecule by assigning the electrons of the molecules to fragments and calculating the MOs of fragments and fragment pairs.
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Fragment molecular orbital method: application to polypeptides
Tatsuya Nakano,Tsuguchika Kaminuma,Toshiyuki Sato,Yutaka Akiyama,Masami Uebayasi,Kazuo Kitaura +5 more
TL;DR: In this article, the fragment molecular orbital method (FMO) was applied to the model peptides of (Gly)n and (Ala)n (n=5-20), [Met5]enkephalin (YGGFM), and the synthetic designed peptide ALPHA-1 (acetyl-ELLKKLLEELKG) and the calculated total energies compare well with those from the conventional ab initio MO method.
358
Fragment molecular orbital method: analytical energy gradients
TL;DR: In this article, the fragment molecular orbital (FMO) method with the analytical energy gradient at the HF level of theory has been incorporated into the G aussian 94 (G94) package.
210
Centrosymmetric bilayers in the 0.75 A resolution structure of a designed alpha-helical peptide, D,L-Alpha-1.
TL;DR: The 0.75 Å crystal structure of a racemic mixture of the 12‐residue designed peptide “Alpha‐1” (Acetyl‐ELLKKLLEELKG) is reported, the L‐enantiomer of which is described in the accompanying paper.
Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin.
Christian Jelsch,Martha M. Teeter,Victor S. Lamzin,Virginie Pichon-Pesme,Robert H. Blessing,Claude Lecomte +5 more
TL;DR: The charge density distribution of a protein has been refined experimentally and the resulting electron density maps of redistributed valence electrons compare quantitatively well with a high-level quantum mechanical calculation performed on a monopeptide.