136 related articles for article (PubMed ID: 34410106)
1. 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]
2. Enhanced Conformational Sampling Method Based on Anomaly Detection Parallel Cascade Selection Molecular Dynamics: ad-PaCS-MD.
Harada R; Yamaguchi K; Shigeta Y
J Chem Theory Comput; 2020 Oct; 16(10):6716-6725. PubMed ID: 32926622
[TBL] [Abstract][Full Text] [Related]
3. 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]
4. Efficient Conformational Sampling of Collective Motions of Proteins with Principal Component Analysis-Based Parallel Cascade Selection Molecular Dynamics.
Yasuda T; Shigeta Y; Harada R
J Chem Inf Model; 2020 Aug; 60(8):4021-4029. PubMed ID: 32786508
[TBL] [Abstract][Full Text] [Related]
5. Nontargeted Parallel Cascade Selection Molecular Dynamics for Enhancing the Conformational Sampling of Proteins.
Harada R; Kitao A
J Chem Theory Comput; 2015 Nov; 11(11):5493-502. PubMed ID: 26574337
[TBL] [Abstract][Full Text] [Related]
6. Selection rules on initial structures in parallel cascade selection molecular dynamics affect conformational sampling efficiency.
Harada R; Shigeta Y
J Mol Graph Model; 2018 Oct; 85():153-159. PubMed ID: 30205290
[TBL] [Abstract][Full Text] [Related]
7. On-the-Fly Specifications of Reaction Coordinates in Parallel Cascade Selection Molecular Dynamics Accelerate Conformational Transitions of Proteins.
Harada R; Shigeta Y
J Chem Theory Comput; 2018 Jun; 14(6):3332-3341. PubMed ID: 29727581
[TBL] [Abstract][Full Text] [Related]
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. Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid docking.
Harada R; Yoshino R; Nishizawa H; Shigeta Y
J Mol Graph Model; 2019 Nov; 92():94-99. PubMed ID: 31344548
[TBL] [Abstract][Full Text] [Related]
10. Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins.
Harada R; Shigeta Y
J Comput Chem; 2017 Dec; 38(31):2671-2674. PubMed ID: 28861895
[TBL] [Abstract][Full Text] [Related]
11. Ligand Binding Path Sampling Based on Parallel Cascade Selection Molecular Dynamics: LB-PaCS-MD.
Aida H; Shigeta Y; Harada R
Materials (Basel); 2022 Feb; 15(4):. PubMed ID: 35208030
[TBL] [Abstract][Full Text] [Related]
12. Parallel Cascade Selection Molecular Dynamics (PaCS-MD) to generate conformational transition pathway.
Harada R; Kitao A
J Chem Phys; 2013 Jul; 139(3):035103. PubMed ID: 23883057
[TBL] [Abstract][Full Text] [Related]
13. Nontargeted Parallel Cascade Selection Molecular Dynamics Using Time-Localized Prediction of Conformational Transitions in Protein Dynamics.
Harada R; Sladek V; Shigeta Y
J Chem Theory Comput; 2019 Sep; 15(9):5144-5153. PubMed ID: 31411882
[TBL] [Abstract][Full Text] [Related]
14. How low-resolution structural data predict the conformational changes of a protein: a study on data-driven molecular dynamics simulations.
Harada R; Shigeta Y
Phys Chem Chem Phys; 2018 Jul; 20(26):17790-17798. PubMed ID: 29922770
[TBL] [Abstract][Full Text] [Related]
15. Molecular Simulation to Investigate Open-Close Motion of a Flagellar Export Apparatus Protein FlhA
Kitao A
Methods Mol Biol; 2023; 2646():27-34. PubMed ID: 36842103
[TBL] [Abstract][Full Text] [Related]
16. Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins.
Takaba K; Tran DP; Kitao A
J Chem Phys; 2020 Jun; 152(22):225101. PubMed ID: 32534517
[TBL] [Abstract][Full Text] [Related]
17. 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]
18. PaCS-Toolkit: Optimized Software Utilities for Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Simulations and Subsequent Analyses.
Ikizawa S; Hori T; Wijaya TN; Kono H; Bai Z; Kimizono T; Lu W; Tran DP; Kitao A
J Phys Chem B; 2024 Apr; 128(15):3631-3642. PubMed ID: 38578072
[TBL] [Abstract][Full Text] [Related]
19. Free-Energy Profiles for Membrane Permeation of Compounds Calculated Using Rare-Event Sampling Methods.
Harada R; Morita R; Shigeta Y
J Chem Inf Model; 2023 Jan; 63(1):259-269. PubMed ID: 36574612
[TBL] [Abstract][Full Text] [Related]
20. Structural dissimilarity sampling with dynamically self-guiding selection.
Harada R; Shigeta Y
J Comput Chem; 2017 Aug; 38(22):1921-1929. PubMed ID: 28558119
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]