342 related articles for article (PubMed ID: 21413701)
1. 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]
2. Vfold: a web server for RNA structure and folding thermodynamics prediction.
Xu X; Zhao P; Chen SJ
PLoS One; 2014; 9(9):e107504. PubMed ID: 25215508
[TBL] [Abstract][Full Text] [Related]
3. Predicting loop-helix tertiary structural contacts in RNA pseudoknots.
Cao S; Giedroc DP; Chen SJ
RNA; 2010 Mar; 16(3):538-52. PubMed ID: 20100813
[TBL] [Abstract][Full Text] [Related]
4. Computing the conformational entropy for RNA folds.
Liu L; Chen SJ
J Chem Phys; 2010 Jun; 132(23):235104. PubMed ID: 20572741
[TBL] [Abstract][Full Text] [Related]
5. A Method to Predict the Structure and Stability of RNA/RNA Complexes.
Xu X; Chen SJ
Methods Mol Biol; 2016; 1490():63-72. PubMed ID: 27665593
[TBL] [Abstract][Full Text] [Related]
6. A Method to Predict the 3D Structure of an RNA Scaffold.
Xu X; Chen SJ
Methods Mol Biol; 2015; 1316():1-11. PubMed ID: 25967048
[TBL] [Abstract][Full Text] [Related]
7. Predicting RNA Structure with Vfold.
Zhao C; Xu X; Chen SJ
Methods Mol Biol; 2017; 1654():3-15. PubMed ID: 28986779
[TBL] [Abstract][Full Text] [Related]
8. Coarse-grained prediction of RNA loop structures.
Liu L; Chen SJ
PLoS One; 2012; 7(11):e48460. PubMed ID: 23144887
[TBL] [Abstract][Full Text] [Related]
9. Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal.
Cao S; Chen SJ
RNA; 2011 Dec; 17(12):2130-43. PubMed ID: 22028361
[TBL] [Abstract][Full Text] [Related]
10. Statistical mechanical modeling of RNA folding: from free energy landscape to tertiary structural prediction.
Cao S; Chen SJ
Nucleic Acids Mol Biol; 2012; 27():185-212. PubMed ID: 27293312
[TBL] [Abstract][Full Text] [Related]
11. 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]
12. Physics-based RNA structure prediction.
Xu X; Chen SJ
Biophys Rep; 2015; 1():2-13. PubMed ID: 26942214
[TBL] [Abstract][Full Text] [Related]
13. Predicting structures and stabilities for H-type pseudoknots with interhelix loops.
Cao S; Chen SJ
RNA; 2009 Apr; 15(4):696-706. PubMed ID: 19237463
[TBL] [Abstract][Full Text] [Related]
14. Tertiary structure prediction of RNA-RNA complexes using a secondary structure and fragment-based method.
Yamasaki S; Hirokawa T; Asai K; Fukui K
J Chem Inf Model; 2014 Feb; 54(2):672-82. PubMed ID: 24479711
[TBL] [Abstract][Full Text] [Related]
15. Conformational entropy of the RNA phosphate backbone and its contribution to the folding free energy.
Mak CH; Matossian T; Chung WY
Biophys J; 2014 Apr; 106(7):1497-507. PubMed ID: 24703311
[TBL] [Abstract][Full Text] [Related]
16. 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]
17. An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints.
Gaspin C; Westhof E
J Mol Biol; 1995 Nov; 254(2):163-74. PubMed ID: 7490740
[TBL] [Abstract][Full Text] [Related]
18. Secondary Structure Prediction of Single Sequences Using RNAstructure.
Xu ZZ; Mathews DH
Methods Mol Biol; 2016; 1490():15-34. PubMed ID: 27665590
[TBL] [Abstract][Full Text] [Related]
19. Secondary structure prediction of interacting RNA molecules.
Andronescu M; Zhang ZC; Condon A
J Mol Biol; 2005 Feb; 345(5):987-1001. PubMed ID: 15644199
[TBL] [Abstract][Full Text] [Related]
20. Vfold2D-MC: A Physics-Based Hybrid Model for Predicting RNA Secondary Structure Folding.
Cheng Y; Zhang S; Xu X; Chen SJ
J Phys Chem B; 2021 Sep; 125(36):10108-10118. PubMed ID: 34473508
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]