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8. Simple, yet powerful methodologies for conformational sampling of proteins. Harada R; Takano Y; Baba T; Shigeta Y Phys Chem Chem Phys; 2015 Mar; 17(9):6155-73. PubMed ID: 25659594 [TBL] [Abstract][Full Text] [Related]
9. Nontargeted Parallel Cascade Selection Molecular Dynamics Based on a Nonredundant Selection Rule for Initial Structures Enhances Conformational Sampling of Proteins. Harada R; Sladek V; Shigeta Y J Chem Inf Model; 2019 Dec; 59(12):5198-5206. PubMed ID: 31697897 [TBL] [Abstract][Full Text] [Related]
10. Ball-and-Stick Local Elevation Umbrella Sampling: Molecular Simulations Involving Enhanced Sampling within Conformational or Alchemical Subspaces of Low Internal Dimensionalities, Minimal Irrelevant Volumes, and Problem-Adapted Geometries. Hansen HS; Hünenberger PH J Chem Theory Comput; 2010 Sep; 6(9):2622-46. PubMed ID: 26616065 [TBL] [Abstract][Full Text] [Related]
11. Efficient Conformational Search Based on Structural Dissimilarity Sampling: Applications for Reproducing Structural Transitions of Proteins. Harada R; Shigeta Y J Chem Theory Comput; 2017 Mar; 13(3):1411-1423. PubMed ID: 28170260 [TBL] [Abstract][Full Text] [Related]
12. [Development of Membrane Permeability Coefficient by Means of Novel Molecular Dynamics Methods]. Harada R; Mitsuta Y; Shigeta Y Yakugaku Zasshi; 2024; 144(5):545-551. PubMed ID: 38692931 [TBL] [Abstract][Full Text] [Related]
13. Independent Nontargeted Parallel Cascade Selection Molecular Dynamics (Ino-PaCS-MD) to Enhance the Conformational Sampling of Proteins. Yasuda T; Morita R; Shigeta Y; Harada R J Chem Theory Comput; 2021 Sep; 17(9):5933-5943. PubMed ID: 34410106 [TBL] [Abstract][Full Text] [Related]
14. Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: application to the folding of a mini-protein, chignolin. Harada R; Takano Y; Shigeta Y J Comput Chem; 2015 Apr; 36(10):763-72. PubMed ID: 25691321 [TBL] [Abstract][Full Text] [Related]
15. Hybrid Cascade-Type Molecular Dynamics with a Markov State Model for Efficient Free Energy Calculations. Harada R; Shigeta Y J Chem Theory Comput; 2019 Jan; 15(1):680-687. PubMed ID: 30468705 [TBL] [Abstract][Full Text] [Related]