441 related articles for article (PubMed ID: 18456842)
1. Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms.
Ding F; Sharma S; Chalasani P; Demidov VV; Broude NE; Dokholyan NV
RNA; 2008 Jun; 14(6):1164-73. PubMed ID: 18456842
[TBL] [Abstract][Full Text] [Related]
2. iFoldRNA: three-dimensional RNA structure prediction and folding.
Sharma S; Ding F; Dokholyan NV
Bioinformatics; 2008 Sep; 24(17):1951-2. PubMed ID: 18579566
[TBL] [Abstract][Full Text] [Related]
3. RNA folding on the 3D triangular lattice.
Gillespie J; Mayne M; Jiang M
BMC Bioinformatics; 2009 Nov; 10():369. PubMed ID: 19891777
[TBL] [Abstract][Full Text] [Related]
4. Ab initio folding of proteins with all-atom discrete molecular dynamics.
Ding F; Tsao D; Nie H; Dokholyan NV
Structure; 2008 Jul; 16(7):1010-8. PubMed ID: 18611374
[TBL] [Abstract][Full Text] [Related]
5. 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]
6. Prediction of RNA secondary structure by free energy minimization.
Mathews DH; Turner DH
Curr Opin Struct Biol; 2006 Jun; 16(3):270-8. PubMed ID: 16713706
[TBL] [Abstract][Full Text] [Related]
7. Prediction of consensus RNA secondary structures including pseudoknots.
Witwer C; Hofacker IL; Stadler PF
IEEE/ACM Trans Comput Biol Bioinform; 2004; 1(2):66-77. PubMed ID: 17048382
[TBL] [Abstract][Full Text] [Related]
8. SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.
Boniecki MJ; Lach G; Dawson WK; Tomala K; Lukasz P; Soltysinski T; Rother KM; Bujnicki JM
Nucleic Acids Res; 2016 Apr; 44(7):e63. PubMed ID: 26687716
[TBL] [Abstract][Full Text] [Related]
9. Crumple: a method for complete enumeration of all possible pseudoknot-free RNA secondary structures.
Bleckley S; Stone JW; Schroeder SJ
PLoS One; 2012; 7(12):e52414. PubMed ID: 23300665
[TBL] [Abstract][Full Text] [Related]
10. Physics-based de novo prediction of RNA 3D structures.
Cao S; Chen SJ
J Phys Chem B; 2011 Apr; 115(14):4216-26. PubMed ID: 21413701
[TBL] [Abstract][Full Text] [Related]
11. Simultaneous prediction of RNA secondary structure and helix coaxial stacking.
Shareghi P; Wang Y; Malmberg R; Cai L
BMC Genomics; 2012 Jun; 13 Suppl 3(Suppl 3):S7. PubMed ID: 22759616
[TBL] [Abstract][Full Text] [Related]
12. Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction.
Doshi KJ; Cannone JJ; Cobaugh CW; Gutell RR
BMC Bioinformatics; 2004 Aug; 5():105. PubMed ID: 15296519
[TBL] [Abstract][Full Text] [Related]
13. Prediction of RNA secondary structure with pseudoknots using integer programming.
Poolsap U; Kato Y; Akutsu T
BMC Bioinformatics; 2009 Jan; 10 Suppl 1(Suppl 1):S38. PubMed ID: 19208139
[TBL] [Abstract][Full Text] [Related]
14. Thermodynamic heuristics with case-based reasoning: combined insights for RNA pseudoknot secondary structure.
Al-Khatib RM; Rashid NA; Abdullah R
J Biomol Struct Dyn; 2011 Aug; 29(1):1-26. PubMed ID: 21696223
[TBL] [Abstract][Full Text] [Related]
15. [An iterative method for prediction of RNA secondary structures including pseudoknots based on minimum of free energy and covariance].
Wang ZX; Luo ZG; Guan NY; Yan FM; Jin X; Zhang W
Yi Chuan; 2007 Jul; 29(7):889-97. PubMed ID: 17646157
[TBL] [Abstract][Full Text] [Related]
16. Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations.
Xayaphoummine A; Bucher T; Thalmann F; Isambert H
Proc Natl Acad Sci U S A; 2003 Dec; 100(26):15310-5. PubMed ID: 14676318
[TBL] [Abstract][Full Text] [Related]
17. An RNA folding algorithm including pseudoknots based on dynamic weighted matching.
Liu H; Xu D; Shao J; Wang Y
Comput Biol Chem; 2006 Feb; 30(1):72-6. PubMed ID: 16321572
[TBL] [Abstract][Full Text] [Related]
18. Cotranscriptional Kinetic Folding of RNA Secondary Structures Including Pseudoknots.
Thanh VH; Korpela D; Orponen P
J Comput Biol; 2021 Sep; 28(9):892-908. PubMed ID: 33902324
[No Abstract] [Full Text] [Related]
19. 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]
20. Swellix: a computational tool to explore RNA conformational space.
Sloat N; Liu JW; Schroeder SJ
BMC Bioinformatics; 2017 Nov; 18(1):504. PubMed ID: 29157200
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
