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Items: 1 to 50 of 401

1.

Force-field parametrization based on radial and energy distribution functions.

Chiba S, Okuno Y, Honma T, Ikeguchi M.

J Comput Chem. 2019 Jul 25. doi: 10.1002/jcc.26035. [Epub ahead of print]

PMID:
31343749
2.

How Does the Recently Discovered Peptide MIP Exhibit Much Higher Binding Affinity than an Anticancer Protein p53 for an Oncoprotein MDM2?

Yamada T, Hayashi T, Hikiri S, Kobayashi N, Yanagawa H, Ikeguchi M, Katahira M, Nagata T, Kinoshita M.

J Chem Inf Model. 2019 Aug 26;59(8):3533-3544. doi: 10.1021/acs.jcim.9b00226. Epub 2019 Jul 18.

PMID:
31282659
3.

In vitro assembly of Haemophilus influenzae adhesin transmembrane domain and studies on the electrostatic repulsion at the interface.

Aoki E, Ikeguchi M.

Biophys Rev. 2019 Jun;11(3):303-309. doi: 10.1007/s12551-019-00535-0. Epub 2019 May 9. Review.

4.

Mechanisms of ferritin assembly studied by time-resolved small-angle X-ray scattering.

Sato D, Ikeguchi M.

Biophys Rev. 2019 Jun;11(3):449-455. doi: 10.1007/s12551-019-00538-x. Epub 2019 May 8. Review.

5.

An accurate and rapid method for calculating hydration free energies of a variety of solutes including proteins.

Hikiri S, Hayashi T, Inoue M, Ekimoto T, Ikeguchi M, Kinoshita M.

J Chem Phys. 2019 May 7;150(17):175101. doi: 10.1063/1.5093110.

PMID:
31067910
6.

Structure, Function, Folding, and Aggregation of a Neuroferritinopathy-Related Ferritin Variant.

Kuwata T, Okada Y, Yamamoto T, Sato D, Fujiwara K, Fukumura T, Ikeguchi M.

Biochemistry. 2019 May 7;58(18):2318-2325. doi: 10.1021/acs.biochem.8b01068. Epub 2019 Apr 23.

PMID:
30986045
7.

Rotational Mechanism Model of the Bacterial V1 Motor Based on Structural and Computational Analyses.

Singharoy A, Chipot C, Ekimoto T, Suzuki K, Ikeguchi M, Yamato I, Murata T.

Front Physiol. 2019 Feb 5;10:46. doi: 10.3389/fphys.2019.00046. eCollection 2019. Review.

8.

Hybrid Methods for Modeling Protein Structures Using Molecular Dynamics Simulations and Small-Angle X-Ray Scattering Data.

Ekimoto T, Ikeguchi M.

Adv Exp Med Biol. 2018;1105:237-258. doi: 10.1007/978-981-13-2200-6_15. Review.

PMID:
30617833
9.

Elimination of Finite-Size Effects on Binding Free Energies via the Warp-Drive Method.

Ekimoto T, Yamane T, Ikeguchi M.

J Chem Theory Comput. 2018 Dec 11;14(12):6544-6559. doi: 10.1021/acs.jctc.8b00280. Epub 2018 Nov 21.

PMID:
30404450
10.

Statistical thermodynamics for the unexpectedly large difference between disaccharide stereoisomers in terms of solubility in water.

Hikiri S, Hayashi T, Ikeguchi M, Kinoshita M.

Phys Chem Chem Phys. 2018 Sep 19;20(36):23684-23693. doi: 10.1039/c8cp04377a.

PMID:
30191211
11.

Median arcuate ligament syndrome and aneurysm in the pancreaticoduodenal artery detected by retroperitoneal hemorrhage: A case report.

Hanaki T, Fukuta S, Okamoto M, Tsuda A, Yagyu T, Urushibara S, Endo K, Suzuki K, Nakamura S, Ikeguchi M.

Clin Case Rep. 2018 Jun 17;6(8):1496-1500. doi: 10.1002/ccr3.1643. eCollection 2018 Aug.

12.

β-Strand twisting/bending in soluble and transmembrane β-barrel structures.

Kikuchi N, Fujiwara K, Ikeguchi M.

Proteins. 2018 Dec;86(12):1231-1241. doi: 10.1002/prot.25576. Epub 2018 Nov 1.

PMID:
30019770
13.

Letter to the Editor on "Correlation between surgical site infection and preoperative immune nutrition of patients after surgery for colorectal perforation or obstruction".

Ikeguchi M.

Asian J Surg. 2018 Sep;41(5):517-518. doi: 10.1016/j.asjsur.2018.05.003. Epub 2018 Jul 11. No abstract available.

14.

Comprehensive analysis of the mouse cytochrome P450 family responsible for omega-3 epoxidation of eicosapentaenoic acid.

Isobe Y, Itagaki M, Ito Y, Naoe S, Kojima K, Ikeguchi M, Arita M.

Sci Rep. 2018 May 21;8(1):7954. doi: 10.1038/s41598-018-26325-4.

15.

Ionic scattering factors of atoms that compose biological molecules.

Yonekura K, Matsuoka R, Yamashita Y, Yamane T, Ikeguchi M, Kidera A, Maki-Yonekura S.

IUCrJ. 2018 Apr 27;5(Pt 3):348-353. doi: 10.1107/S2052252518005237. eCollection 2018 May 1.

16.

Physical Origin of Thermostabilization by a Quadruple Mutation for the Adenosine A2a Receptor in the Active State.

Kajiwara Y, Yasuda S, Hikiri S, Hayashi T, Ikeguchi M, Murata T, Kinoshita M.

J Phys Chem B. 2018 Apr 26;122(16):4418-4427. doi: 10.1021/acs.jpcb.8b00443. Epub 2018 Apr 13.

PMID:
29617137
17.

Energetics and conformational pathways of functional rotation in the multidrug transporter AcrB.

Matsunaga Y, Yamane T, Terada T, Moritsugu K, Fujisaki H, Murakami S, Ikeguchi M, Kidera A.

Elife. 2018 Mar 6;7. pii: e31715. doi: 10.7554/eLife.31715.

18.

The attenuation value of preoperative computed tomography as a novel predictor for pancreatic fistula after pancreaticoduodenectomy.

Hanaki T, Uejima C, Amisaki M, Yosuke A, Tokuyasu N, Honjo S, Sakamoto T, Saito H, Ikeguchi M, Fujiwara Y.

Surg Today. 2018 Jun;48(6):598-608. doi: 10.1007/s00595-018-1626-y. Epub 2018 Jan 30.

PMID:
29383597
19.

Optimization of Haemophilus influenzae adhesin transmembrane domain expression in Escherichia coli.

Aoki E, Fujiwara K, Shimizu A, Takase-Yoden S, Ikeguchi M.

Protein Expr Purif. 2018 May;145:19-24. doi: 10.1016/j.pep.2017.12.009. Epub 2017 Dec 25.

PMID:
29284141
20.

Multiscale molecular dynamics simulations of rotary motor proteins.

Ekimoto T, Ikeguchi M.

Biophys Rev. 2018 Apr;10(2):605-615. doi: 10.1007/s12551-017-0373-4. Epub 2017 Dec 4. Review.

21.

Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance.

Ishiyama S, Nishiyama A, Saeki Y, Moritsugu K, Morimoto D, Yamaguchi L, Arai N, Matsumura R, Kawakami T, Mishima Y, Hojo H, Shimamura S, Ishikawa F, Tajima S, Tanaka K, Ariyoshi M, Shirakawa M, Ikeguchi M, Kidera A, Suetake I, Arita K, Nakanishi M.

Mol Cell. 2017 Oct 19;68(2):350-360.e7. doi: 10.1016/j.molcel.2017.09.037.

22.

Effect of Gold Nanoparticle Distribution in TiO2 on the Optical and Electrical Characteristics of Dye-Sensitized Solar Cells.

Mayumi S, Ikeguchi Y, Nakane D, Ishikawa Y, Uraoka Y, Ikeguchi M.

Nanoscale Res Lett. 2017 Aug 29;12(1):513. doi: 10.1186/s11671-017-2285-4.

23.

C-Reactive Protein/Albumin Ratio and Prognostic Nutritional Index Are Strong Prognostic Indicators of Survival in Resected Pancreatic Ductal Adenocarcinoma.

Ikeguchi M, Hanaki T, Endo K, Suzuki K, Nakamura S, Sawata T, Shimizu T.

J Pancreat Cancer. 2017 Jul 1;3(1):31-36. doi: 10.1089/pancan.2017.0006. eCollection 2017.

24.

Itinerary profiling to analyze a large number of protein-folding trajectories.

Ota M, Ikeguchi M, Kidera A.

Biophys Physicobiol. 2016 Nov 18;13:295-304. doi: 10.2142/biophysico.13.0_295. eCollection 2016.

25.

Electrostatic Repulsion between Unique Arginine Residues Is Essential for the Efficient in Vitro Assembly of the Transmembrane Domain of a Trimeric Autotransporter.

Aoki E, Sato D, Fujiwara K, Ikeguchi M.

Biochemistry. 2017 Apr 18;56(15):2139-2148. doi: 10.1021/acs.biochem.6b01130. Epub 2017 Apr 10.

PMID:
28357859
26.

Rotation Mechanism of Molecular Motor V1-ATPase Studied by Multiscale Molecular Dynamics Simulation.

Isaka Y, Ekimoto T, Kokabu Y, Yamato I, Murata T, Ikeguchi M.

Biophys J. 2017 Mar 14;112(5):911-920. doi: 10.1016/j.bpj.2017.01.029.

27.

Dissection of the angle of single fluorophore attached to the nucleotide in corkscrewing microtubules.

Fujimura S, Ito Y, Ikeguchi M, Adachi K, Yajima J, Nishizaka T.

Biochem Biophys Res Commun. 2017 Apr 8;485(3):614-620. doi: 10.1016/j.bbrc.2017.01.165. Epub 2017 Feb 28.

PMID:
28257843
28.

Evaluation of prognostic markers for patients with curatively resected thoracic esophageal squamous cell carcinomas.

Ikeguchi M, Kouno Y, Kihara K, Suzuki K, Endo K, Nakamura S, Sawada T, Shimizu T, Matsunaga T, Fukumoto Y, Saito H.

Mol Clin Oncol. 2016 Dec;5(6):767-772. doi: 10.3892/mco.2016.1073. Epub 2016 Nov 2.

29.

Computational Methods for Configurational Entropy Using Internal and Cartesian Coordinates.

Hikiri S, Yoshidome T, Ikeguchi M.

J Chem Theory Comput. 2016 Dec 13;12(12):5990-6000. Epub 2016 Dec 2.

30.

Isolated port-site metastasis of hepatocellular carcinoma after laparoscopic liver resection.

Kihara K, Endo K, Suzuki K, Nakamura S, Sawata T, Shimizu T, Ikeguchi M, Tokuyasu Y, Nakamoto S.

Asian J Endosc Surg. 2017 May;10(2):191-193. doi: 10.1111/ases.12339. Epub 2016 Oct 17.

PMID:
27748057
31.

Intra-Abdominal Complications after Curative Gastrectomies Worsen Prognoses of Patients with Stage II-III Gastric Cancer.

A T M Abdul K, Murakami Y, Yoshimoto M, Onishi K, Kuroda H, Matsunaga T, Fukumoto Y, Takano S, Tokuyasu N, Osaki T, Saito H, Ikeguchi M.

Yonago Acta Med. 2016 Sep 12;59(3):210-216. eCollection 2016 Sep.

32.

Prognostic Benefits of Thoracoscopic Esophagectomy for Thoracic Esophageal Squamous Cell Carcinomas.

Ikeguchi M, Fukumoto Y; -.

Chirurgia (Bucur). 2016 Jul-Aug;111(4):313-7.

33.

Apo- and Antagonist-Binding Structures of Vitamin D Receptor Ligand-Binding Domain Revealed by Hybrid Approach Combining Small-Angle X-ray Scattering and Molecular Dynamics.

Anami Y, Shimizu N, Ekimoto T, Egawa D, Itoh T, Ikeguchi M, Yamamoto K.

J Med Chem. 2016 Sep 8;59(17):7888-900. doi: 10.1021/acs.jmedchem.6b00682. Epub 2016 Aug 26.

PMID:
27535484
34.

Carbohydrate-binding domain of the POMGnT1 stem region modulates O-mannosylation sites of α-dystroglycan.

Kuwabara N, Manya H, Yamada T, Tateno H, Kanagawa M, Kobayashi K, Akasaka-Manya K, Hirose Y, Mizuno M, Ikeguchi M, Toda T, Hirabayashi J, Senda T, Endo T, Kato R.

Proc Natl Acad Sci U S A. 2016 Aug 16;113(33):9280-5. doi: 10.1073/pnas.1525545113. Epub 2016 Aug 4.

35.

Predictive factors for recurrence in T2N0 and T3N0 gastric cancer patients.

Saito H, Murakami Y, Miyatani K, Kuroda H, Matsunaga T, Fukumoto Y, Osaki T, Ikeguchi M.

Langenbecks Arch Surg. 2016 Sep;401(6):823-8. doi: 10.1007/s00423-016-1480-6. Epub 2016 Jul 27.

PMID:
27460840
36.

Nicotine enhances the malignant potential of human pancreatic cancer cells via activation of atypical protein kinase C.

Hanaki T, Horikoshi Y, Nakaso K, Nakasone M, Kitagawa Y, Amisaki M, Arai Y, Tokuyasu N, Sakamoto T, Honjo S, Saito H, Ikeguchi M, Yamashita K, Ohno S, Matsura T.

Biochim Biophys Acta. 2016 Nov;1860(11 Pt A):2404-2415. doi: 10.1016/j.bbagen.2016.07.008. Epub 2016 Jul 15.

PMID:
27424921
37.
38.

Solution structure of the isolated histone H2A-H2B heterodimer.

Moriwaki Y, Yamane T, Ohtomo H, Ikeguchi M, Kurita J, Sato M, Nagadoi A, Shimojo H, Nishimura Y.

Sci Rep. 2016 May 16;6:24999. doi: 10.1038/srep24999.

39.

Residual structures in the unfolded state of starch-binding domain of glucoamylase revealed by near-UV circular dichroism and protein engineering techniques.

Ota C, Ikeguchi M, Tanaka A, Hamada D.

Biochim Biophys Acta. 2016 Oct;1864(10):1464-72. doi: 10.1016/j.bbapap.2016.05.002. Epub 2016 May 6.

PMID:
27164491
40.

Role of Surgery in the Management for Gastric Cancer with Synchronous Distant Metastases.

Ikeguchi M, Miyatani K, Takaya S, Matsunaga T, Fukumoto Y, Osaki T, Saito H, Wakatsuki T.

Indian J Surg Oncol. 2016 Mar;7(1):32-6. doi: 10.1007/s13193-015-0428-6. Epub 2015 Jul 1.

41.

A high number of IgG4-positive cells in gastric cancer tissue is associated with tumor progression and poor prognosis.

Miyatani K, Saito H, Murakami Y, Watanabe J, Kuroda H, Matsunaga T, Fukumoto Y, Osaki T, Nakayama Y, Umekita Y, Ikeguchi M.

Virchows Arch. 2016 May;468(5):549-57. doi: 10.1007/s00428-016-1914-0. Epub 2016 Mar 7.

PMID:
26951261
42.

New Prognostic Indicator is Useful for Predicting the Survival of Patients with Unresectable Advanced Colorectal Cancer.

Ikeguchi M, Ashida K, Saito H.

Hepatogastroenterology. 2015 Jun;62(140):859-62.

PMID:
26902016
43.

Perioperative Outcomes after Pancreaticoduodenectomy in Elderly Patients.

Watanabe J, Hanaki T, Arai Y, Tokuyasu N, Sakamoto T, Honjo S, Otani S, Ikeguchi M.

Hepatogastroenterology. 2015 May;62(139):590-4.

PMID:
26897934
44.

Prognostic indicators based on inflammatory and nutritional factors after pancreaticoduodenectomy for pancreatic cancer.

Watanabe J, Otani S, Sakamoto T, Arai Y, Hanaki T, Amisaki M, Tokuyasu N, Honjo S, Ikeguchi M.

Surg Today. 2016 Nov;46(11):1258-67. doi: 10.1007/s00595-016-1308-6. Epub 2016 Feb 11.

PMID:
26869184
45.

An increased number of PD-1+ and Tim-3+ CD8+ T cells is involved in immune evasion in gastric cancer.

Takano S, Saito H, Ikeguchi M.

Surg Today. 2016 Nov;46(11):1341-7. doi: 10.1007/s00595-016-1305-9. Epub 2016 Jan 22.

PMID:
26801344
46.

Usefulness of Preoperative Assessment of Perigastric Vascular Anatomy by Dynamic Computed Tomography for Laparoscopic Gastrectomy.

Osaki T, Saito H, Murakami Y, Miyatani K, Kuroda H, Matsunaga T, Fukumoto Y, Ikeguchi M.

Yonago Acta Med. 2015 Dec;58(4):157-64. Epub 2015 Dec 18.

47.

Electrostatic Repulsion during Ferritin Assembly and Its Screening by Ions.

Sato D, Takebe S, Kurobe A, Ohtomo H, Fujiwara K, Ikeguchi M.

Biochemistry. 2016 Jan 26;55(3):482-8. doi: 10.1021/acs.biochem.5b01197. Epub 2016 Jan 8.

PMID:
26716350
48.

Ferritin Assembly Revisited: A Time-Resolved Small-Angle X-ray Scattering Study.

Sato D, Ohtomo H, Yamada Y, Hikima T, Kurobe A, Fujiwara K, Ikeguchi M.

Biochemistry. 2016 Jan 19;55(2):287-93. doi: 10.1021/acs.biochem.5b01152. Epub 2016 Jan 5.

PMID:
26690025
49.

Finite-size effect on the charging free energy of protein in explicit solvent.

Ekimoto T, Matubayasi N, Ikeguchi M.

J Chem Theory Comput. 2015 Jan 13;11(1):215-23. doi: 10.1021/ct5008394.

PMID:
26574219
50.

TSLP Expression and High Serum TSLP Level Indicate a Poor Prognosis in Gastric Cancer Patients.

Watanabe J, Saito H, Miyatani K, Ikeguchi M, Umekita Y.

Yonago Acta Med. 2015 Sep;58(3):137-43. Epub 2015 Oct 14.

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