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Items: 1 to 20 of 226

1.

Multidimensional virtual-system coupled canonical molecular dynamics to compute free-energy landscapes of peptide multimer assembly.

Hayami T, Higo J, Nakamura H, Kasahara K.

J Comput Chem. 2019 Jul 7. doi: 10.1002/jcc.26020. [Epub ahead of print]

PMID:
31282023
2.

Hydrogen bond donors and acceptors are generally depolarized in α-helices as revealed by a molecular tailoring approach.

Kondo HX, Kusaka A, Kitakawa CK, Onari J, Yamanaka S, Nakamura H, Takano Y.

J Comput Chem. 2019 Sep 5;40(23):2043-2052. doi: 10.1002/jcc.25859. Epub 2019 May 17.

PMID:
31099907
3.

Dietary Calcium Intake and Hypertension: Importance of Serum Concentrations of 25-Hydroxyvitamin D.

Nakamura H, Tsujiguchi H, Hara A, Kambayashi Y, Miyagi S, Thu Nguyen TT, Suzuki K, Tao Y, Sakamoto Y, Shimizu Y, Yamamoto N, Nakamura H.

Nutrients. 2019 Apr 23;11(4). pii: E911. doi: 10.3390/nu11040911.

4.

Relationship between the Intake of n-3 Polyunsaturated Fatty Acids and Depressive Symptoms in Elderly Japanese People: Differences According to Sex and Weight Status.

Tsujiguchi H, Thi Thu Nguyen T, Goto D, Miyagi S, Kambayashi Y, Hara A, Yamada Y, Nakamura H, Shimizu Y, Hori D, Suzuki F, Hayashi K, Tamai S, Nakamura H.

Nutrients. 2019 Apr 3;11(4). pii: E775. doi: 10.3390/nu11040775.

5.

Multimodal Structural Distribution of the p53 C-Terminal Domain upon Binding to S100B via a Generalized Ensemble Method: From Disorder to Extradisorder.

Iida S, Kawabata T, Kasahara K, Nakamura H, Higo J.

J Chem Theory Comput. 2019 Apr 9;15(4):2597-2607. doi: 10.1021/acs.jctc.8b01042. Epub 2019 Mar 22.

PMID:
30855964
6.

Association between Lower Intake of Minerals and Depressive Symptoms among Elderly Japanese Women but Not Men: Findings from Shika Study.

Thi Thu Nguyen T, Miyagi S, Tsujiguchi H, Kambayashi Y, Hara A, Nakamura H, Suzuki K, Yamada Y, Shimizu Y, Nakamura H.

Nutrients. 2019 Feb 13;11(2). pii: E389. doi: 10.3390/nu11020389.

7.

Relationship between saturated fatty acid intake and hypertension and oxidative stress.

Nakamura H, Tsujiguchi H, Kambayashi Y, Hara A, Miyagi S, Yamada Y, Nguyen TTT, Shimizu Y, Hori D, Nakamura H.

Nutrition. 2019 May;61:8-15. doi: 10.1016/j.nut.2018.10.020. Epub 2018 Oct 26.

PMID:
30682705
8.

Overall Introduction and Rationale, with View from Computational Biology.

Nakamura H.

Adv Exp Med Biol. 2018;1105:3-9. doi: 10.1007/978-981-13-2200-6_1. Review.

PMID:
30617819
9.

Relationship between Dietary n-6 Fatty Acid Intake and Hypertension: Effect of Glycated Hemoglobin Levels.

Nakamura H, Hara A, Tsujiguchi H, Thi Thu Nguyen T, Kambayashi Y, Miyagi S, Yamada Y, Suzuki K, Shimizu Y, Nakamura H.

Nutrients. 2018 Nov 24;10(12). pii: E1825. doi: 10.3390/nu10121825.

10.

Protein Data Bank: the single global archive for 3D macromolecular structure data.

wwPDB consortium .

Nucleic Acids Res. 2019 Jan 8;47(D1):D520-D528. doi: 10.1093/nar/gky949.

11.

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.

Young JY, Westbrook JD, Feng Z, Peisach E, Persikova I, Sala R, Sen S, Berrisford JM, Swaminathan GJ, Oldfield TJ, Gutmanas A, Igarashi R, Armstrong DR, Baskaran K, Chen L, Chen M, Clark AR, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PMS, Hudson BP, Ikegawa Y, Kengaku Y, Lawson CL, Liang Y, Mak L, Mukhopadhyay A, Narayanan B, Nishiyama K, Patwardhan A, Sahni G, Sanz-García E, Sato J, Sekharan MR, Shao C, Smart OS, Tan L, van Ginkel G, Yang H, Zhuravleva MA, Markley JL, Nakamura H, Kurisu G, Kleywegt GJ, Velankar S, Berman HM, Burley SK.

Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay002.

12.
13.

Molecular dynamics coupled with a virtual system for effective conformational sampling.

Hayami T, Kasahara K, Nakamura H, Higo J.

J Comput Chem. 2018 Jul 15;39(19):1291-1299. doi: 10.1002/jcc.25196. Epub 2018 Feb 21.

PMID:
29464736
14.

Prediction of Protein-compound Binding Energies from Known Activity Data: Docking-score-based Method and its Applications.

Fukunishi Y, Yamashita Y, Mashimo T, Nakamura H.

Mol Inform. 2018 Jul;37(6-7):e1700120. doi: 10.1002/minf.201700120. Epub 2018 Feb 14.

15.

Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state.

Kasahara K, Shiina M, Higo J, Ogata K, Nakamura H.

Nucleic Acids Res. 2018 Mar 16;46(5):2243-2251. doi: 10.1093/nar/gkx1297.

16.

Relationship between Vitamin Intake and Depressive Symptoms in Elderly Japanese Individuals: Differences with Gender and Body Mass Index.

Nguyen TTT, Tsujiguchi H, Kambayashi Y, Hara A, Miyagi S, Yamada Y, Nakamura H, Shimizu Y, Hori D, Suzuki F, Hayashi K, Nakamura H.

Nutrients. 2017 Dec 3;9(12). pii: E1319. doi: 10.3390/nu9121319.

17.

Validation of Structures in the Protein Data Bank.

Gore S, Sanz García E, Hendrickx PMS, Gutmanas A, Westbrook JD, Yang H, Feng Z, Baskaran K, Berrisford JM, Hudson BP, Ikegawa Y, Kobayashi N, Lawson CL, Mading S, Mak L, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Peisach E, Sahni G, Sekharan MR, Sen S, Shao C, Smart OS, Ulrich EL, Yamashita R, Quesada M, Young JY, Nakamura H, Markley JL, Berman HM, Burley SK, Velankar S, Kleywegt GJ.

Structure. 2017 Dec 5;25(12):1916-1927. doi: 10.1016/j.str.2017.10.009. Epub 2017 Nov 22.

18.

Multi-dimensional virtual system introduced to enhance canonical sampling.

Higo J, Kasahara K, Nakamura H.

J Chem Phys. 2017 Oct 7;147(13):134102. doi: 10.1063/1.4986129.

PMID:
28987097
19.

PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models.

Burley SK, Kurisu G, Markley JL, Nakamura H, Velankar S, Berman HM, Sali A, Schwede T, Trewhella J.

Structure. 2017 Sep 5;25(9):1317-1318. doi: 10.1016/j.str.2017.08.001.

20.

Density functional study of porphyrin distortion effects on redox potential of heme.

Imada Y, Nakamura H, Takano Y.

J Comput Chem. 2018 Jan 30;39(3):143-150. doi: 10.1002/jcc.25058. Epub 2017 Sep 2.

PMID:
28865080

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