165 related articles for article (PubMed ID: 26575783)
1. Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings.
Cragnolini T; Laurin Y; Derreumaux P; Pasquali S
J Chem Theory Comput; 2015 Jul; 11(7):3510-22. PubMed ID: 26575783
[TBL] [Abstract][Full Text] [Related]
2. Coarse-grained simulations of RNA and DNA duplexes.
Cragnolini T; Derreumaux P; Pasquali S
J Phys Chem B; 2013 Jul; 117(27):8047-60. PubMed ID: 23730911
[TBL] [Abstract][Full Text] [Related]
3. Coarse-grained model for predicting RNA folding thermodynamics.
Denesyuk NA; Thirumalai D
J Phys Chem B; 2013 May; 117(17):4901-11. PubMed ID: 23527587
[TBL] [Abstract][Full Text] [Related]
4. HiRE-RNA: a high resolution coarse-grained energy model for RNA.
Pasquali S; Derreumaux P
J Phys Chem B; 2010 Sep; 114(37):11957-66. PubMed ID: 20795690
[TBL] [Abstract][Full Text] [Related]
5. Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations.
Bell DR; Cheng SY; Salazar H; Ren P
Sci Rep; 2017 Apr; 7():45812. PubMed ID: 28393861
[TBL] [Abstract][Full Text] [Related]
6. Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models.
Krokhotin A; Dokholyan NV
Methods Enzymol; 2015; 553():65-89. PubMed ID: 25726461
[TBL] [Abstract][Full Text] [Related]
7. The thermodynamics and kinetics of a nucleotide base pair.
Wang Y; Gong S; Wang Z; Zhang W
J Chem Phys; 2016 Mar; 144(11):115101. PubMed ID: 27004898
[TBL] [Abstract][Full Text] [Related]
8. Structural stability of tandemly occurring noncanonical basepairs within double helical fragments: molecular dynamics studies of functional RNA.
Halder S; Bhattacharyya D
J Phys Chem B; 2010 Nov; 114(44):14028-40. PubMed ID: 20945881
[TBL] [Abstract][Full Text] [Related]
9. Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations?
Svozil D; Hobza P; Sponer J
J Phys Chem B; 2010 Jan; 114(2):1191-203. PubMed ID: 20000584
[TBL] [Abstract][Full Text] [Related]
10. Ab initio RNA folding.
Cragnolini T; Derreumaux P; Pasquali S
J Phys Condens Matter; 2015 Jun; 27(23):233102. PubMed ID: 25993396
[TBL] [Abstract][Full Text] [Related]
11. Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 Model.
Zhang D; Chen SJ; Zhou R
J Phys Chem B; 2021 Nov; 125(43):11907-11915. PubMed ID: 34694128
[TBL] [Abstract][Full Text] [Related]
12. Discretized torsional dynamics and the folding of an RNA chain.
Fernández A; Salthú R; Cendra H
Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics; 1999 Aug; 60(2 Pt B):2105-19. PubMed ID: 11970003
[TBL] [Abstract][Full Text] [Related]
13. Sequence-dependent base-stacking stabilities guide tRNA folding energy landscapes.
Li R; Ge HW; Cho SS
J Phys Chem B; 2013 Oct; 117(42):12943-52. PubMed ID: 23841777
[TBL] [Abstract][Full Text] [Related]
14. A two-dimensional replica-exchange molecular dynamics method for simulating RNA folding using sparse experimental restraints.
Ebrahimi P; Kaur S; Baronti L; Petzold K; Chen AA
Methods; 2019 Jun; 162-163():96-107. PubMed ID: 31059830
[TBL] [Abstract][Full Text] [Related]
15. Estimating uncertainty in predicted folding free energy changes of RNA secondary structures.
Zuber J; Mathews DH
RNA; 2019 Jun; 25(6):747-754. PubMed ID: 30952689
[TBL] [Abstract][Full Text] [Related]
16. ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems.
Tosti Guerra F; Poppleton E; Šulc P; Rovigatti L
J Chem Phys; 2024 May; 160(20):. PubMed ID: 38814009
[TBL] [Abstract][Full Text] [Related]
17. Ant colony optimization for predicting RNA folding pathways.
Takitou S; Taneda A
Comput Biol Chem; 2019 Dec; 83():107118. PubMed ID: 31698162
[TBL] [Abstract][Full Text] [Related]
18. Understanding the kinetic mechanism of RNA single base pair formation.
Xu X; Yu T; Chen SJ
Proc Natl Acad Sci U S A; 2016 Jan; 113(1):116-21. PubMed ID: 26699466
[TBL] [Abstract][Full Text] [Related]
19. IsRNA: An Iterative Simulated Reference State Approach to Modeling Correlated Interactions in RNA Folding.
Zhang D; Chen SJ
J Chem Theory Comput; 2018 Apr; 14(4):2230-2239. PubMed ID: 29499114
[TBL] [Abstract][Full Text] [Related]
20. Coarse-grained modeling of RNA 3D structure.
Dawson WK; Maciejczyk M; Jankowska EJ; Bujnicki JM
Methods; 2016 Jul; 103():138-56. PubMed ID: 27125734
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
