| Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes J Higo, J Ikebe, N Kamiya, H Nakamura Biophysical reviews 4, 27-44, 2012 | 73 | 2012 |
| Accessibility of the histone H3 tail in the nucleosome for binding of paired readers J Gatchalian, X Wang, J Ikebe, KL Cox, AH Tencer, Y Zhang, NL Burge, ... Nature communications 8 (1), 1489, 2017 | 72 | 2017 |
| Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water J Ikebe, K Umezawa, N Kamiya, T Sugihara, Y Yonezawa, Y Takano, ... Journal of computational chemistry 32 (7), 1286-1297, 2011 | 63 | 2011 |
| H3 histone tail conformation within the nucleosome and the impact of K14 acetylation studied using enhanced sampling simulation J Ikebe, S Sakuraba, H Kono PLoS computational biology 12 (3), e1004788, 2016 | 55 | 2016 |
| Covalent modifications of histone H3K9 promote binding of CHD3 AH Tencer, KL Cox, L Di, JB Bridgers, J Lyu, X Wang, JK Sims, ... Cell reports 21 (2), 455-466, 2017 | 46 | 2017 |
| Simulation study on the disordered state of an Alzheimer's β amyloid peptide Aβ (12–36) in water consisting of random‐structural, β‐structural, and helical clusters J Ikebe, N Kamiya, JI Ito, H Shindo, J Higo Protein science 16 (8), 1596-1608, 2007 | 34 | 2007 |
| Enhanced sampling simulations to construct free-energy landscape of protein–partner substrate interaction J Ikebe, K Umezawa, J Higo Biophysical reviews 8, 45-62, 2016 | 27 | 2016 |
| Ab initio simulation of a 57‐residue protein in explicit solvent reproduces the native conformation in the lowest free‐energy cluster J Ikebe, DM Standley, H Nakamura, J Higo Protein Science 20 (1), 187-196, 2011 | 25 | 2011 |
| Conformational ensembles of an intrinsically disordered protein pKID with and without a KIX domain in explicit solvent investigated by all-atom multicanonical molecular dynamics K Umezawa, J Ikebe, M Takano, H Nakamura, J Higo Biomolecules 2 (1), 104-121, 2012 | 20 | 2012 |
| Adaptive lambda square dynamics simulation: An efficient conformational sampling method for biomolecules J Ikebe, S Sakuraba Biophysical Journal 106 (2), 405a, 2014 | 16 | 2014 |
| Conformational sampling of a 40-residue protein consisting of α and β secondary-structure elements in explicit solvent J Ikebe, N Kamiya, H Shindo, H Nakamura, J Higo Chemical physics letters 443 (4-6), 364-368, 2007 | 16 | 2007 |
| Structure dependency of a 24-residue peptide humanin on solvent and preferential solvation by trifluoroethanol studied by multicanonical sampling R Yagisawa, N Kamiya, J Ikebe, K Umezawa, J Higo Chemical Physics Letters 455 (4-6), 293-296, 2008 | 7 | 2008 |
| Enzyme modification using mutation site prediction method for enhancing the regioselectivity of substrate reaction sites J Ikebe, M Suzuki, A Komori, K Kobayashi, T Kameda Scientific reports 11 (1), 19004, 2021 | 6 | 2021 |
| Conformational sampling of unmodified and acetylated H3 histone tails on a nucleosome by all-atom model molecular dynamics simulations J Ikebe, S Sakuraba, H Kono Biophysical Journal 108 (2), 540a-541a, 2015 | 2 | 2015 |
| Conformational requirement on peptides to exert laminin's activities and search for protein segments with laminin's activities K Umezawa, J Ikebe, M Nomizu, H Nakamura, J Higo Peptide Science: Original Research on Biomolecules 92 (2), 124-131, 2009 | 2 | 2009 |
| Impact of histone variant and post-translational modification on nucleosome H Kono, J Ikebe, S Sakuraba, H Ishida Biophysical Journal 110 (3), 69a, 2016 | 1 | 2016 |
| Author Correction: Enzyme modification using mutation site prediction method for enhancing the regioselectivity of substrate reaction sites J Ikebe, M Suzuki, A Komori, K Kobayashi, T Kameda Scientific Reports 12 (1), 8059, 2022 | | 2022 |
| Enzyme modification using mutation site prediction method for enhancing the regioselectivity of substrate reaction sites (vol 11, 19004, 2021) J Ikebe, M Suzuki, A Komori, K Kobayashi, T Kameda SCIENTIFIC REPORTS 12 (1), 2022 | | 2022 |
| Exhaustive Sampling of Intrinsically Disordered Protein Docking Conformation with ALSD Simulation HK Jinzen Ikebe HPCI Research Report 7 (1), 23-32, 2022 | | 2022 |
| Development of P450-BM3 using molecular dynamics simulations-A tribute to the late Professor Hideaki Yamada S Ishihara, S Koikeda, J Ikebe, T Kameda, SB Park, J Ogawa, S Kishino, ... | | 2022 |
