249 related articles for article (PubMed ID: 25005281)
1. Principal component analysis of molecular dynamics: on the use of Cartesian vs. internal coordinates.
Sittel F; Jain A; Stock G
J Chem Phys; 2014 Jul; 141(1):014111. PubMed ID: 25005281
[TBL] [Abstract][Full Text] [Related]
2. Contact- and distance-based principal component analysis of protein dynamics.
Ernst M; Sittel F; Stock G
J Chem Phys; 2015 Dec; 143(24):244114. PubMed ID: 26723658
[TBL] [Abstract][Full Text] [Related]
3. Dihedral angle principal component analysis of molecular dynamics simulations.
Altis A; Nguyen PH; Hegger R; Stock G
J Chem Phys; 2007 Jun; 126(24):244111. PubMed ID: 17614541
[TBL] [Abstract][Full Text] [Related]
4. Energy landscape of a small peptide revealed by dihedral angle principal component analysis.
Mu Y; Nguyen PH; Stock G
Proteins; 2005 Jan; 58(1):45-52. PubMed ID: 15521057
[TBL] [Abstract][Full Text] [Related]
5. Free-energy landscape of RNA hairpins constructed via dihedral angle principal component analysis.
Riccardi L; Nguyen PH; Stock G
J Phys Chem B; 2009 Dec; 113(52):16660-8. PubMed ID: 20028141
[TBL] [Abstract][Full Text] [Related]
6. Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis.
Altis A; Otten M; Nguyen PH; Hegger R; Stock G
J Chem Phys; 2008 Jun; 128(24):245102. PubMed ID: 18601386
[TBL] [Abstract][Full Text] [Related]
7. Latent dynamics of a protein molecule observed in dihedral angle space.
Omori S; Fuchigami S; Ikeguchi M; Kidera A
J Chem Phys; 2010 Mar; 132(11):115103. PubMed ID: 20331318
[TBL] [Abstract][Full Text] [Related]
8. Reconstructing the free-energy landscape of Met-enkephalin using dihedral principal component analysis and well-tempered metadynamics.
Sicard F; Senet P
J Chem Phys; 2013 Jun; 138(23):235101. PubMed ID: 23802984
[TBL] [Abstract][Full Text] [Related]
9. Are there non-trivial dynamic cross-correlations in proteins?
Abseher R; Nilges M
J Mol Biol; 1998 Jun; 279(4):911-20. PubMed ID: 9654442
[TBL] [Abstract][Full Text] [Related]
10. Internal coordinate molecular dynamics: a foundation for multiscale dynamics.
Vaidehi N; Jain A
J Phys Chem B; 2015 Jan; 119(4):1233-42. PubMed ID: 25517406
[TBL] [Abstract][Full Text] [Related]
11. Principal component analysis on a torus: Theory and application to protein dynamics.
Sittel F; Filk T; Stock G
J Chem Phys; 2017 Dec; 147(24):244101. PubMed ID: 29289136
[TBL] [Abstract][Full Text] [Related]
12. Backbone conformational preferences of an intrinsically disordered protein in solution.
Espinoza-Fonseca LM; Ilizaliturri-Flores I; Correa-Basurto J
Mol Biosyst; 2012 Jun; 8(6):1798-805. PubMed ID: 22506277
[TBL] [Abstract][Full Text] [Related]
13. Microsecond scale replica exchange molecular dynamic simulation of villin headpiece: an insight into the folding landscape.
Jani V; Sonavane UB; Joshi R
J Biomol Struct Dyn; 2011 Jun; 28(6):845-60. PubMed ID: 21469746
[TBL] [Abstract][Full Text] [Related]
14. How many atoms are required to characterize accurately trajectory fluctuations of a protein?
Cukier RI
J Chem Phys; 2010 Jun; 132(24):245101. PubMed ID: 20590215
[TBL] [Abstract][Full Text] [Related]
15. Free energy landscape of a biomolecule in dihedral principal component space: sampling convergence and correspondence between structures and minima.
Maisuradze GG; Leitner DM
Proteins; 2007 May; 67(3):569-78. PubMed ID: 17348026
[TBL] [Abstract][Full Text] [Related]
16. Protein simulations using techniques suitable for very large systems: the cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics.
Mathiowetz AM; Jain A; Karasawa N; Goddard WA
Proteins; 1994 Nov; 20(3):227-47. PubMed ID: 7892172
[TBL] [Abstract][Full Text] [Related]
17. Hierarchical Biomolecular Dynamics: Picosecond Hydrogen Bonding Regulates Microsecond Conformational Transitions.
Buchenberg S; Schaudinnus N; Stock G
J Chem Theory Comput; 2015 Mar; 11(3):1330-6. PubMed ID: 26579778
[TBL] [Abstract][Full Text] [Related]
18. Conformational analysis in a multidimensional energy landscape: study of an arginylglutamate repeat.
Campos SR; Baptista AM
J Phys Chem B; 2009 Dec; 113(49):15989-6001. PubMed ID: 19778072
[TBL] [Abstract][Full Text] [Related]
19. Comment on: "Energy landscape of a small peptide revealed by dihedral angle principal component analysis".
Hinsen K
Proteins; 2006 Aug; 64(3):795-7; discussion 798-9. PubMed ID: 16456860
[TBL] [Abstract][Full Text] [Related]
20. JEDi: java essential dynamics inspector - a molecular trajectory analysis toolkit.
David CC; Avery CS; Jacobs DJ
BMC Bioinformatics; 2021 May; 22(1):226. PubMed ID: 33932974
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]