186 related articles for article (PubMed ID: 25967048)
1. 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]
2. 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]
3. Predicting RNA Scaffolds with a Hybrid Method of Vfold3D and VfoldLA.
Xu X; Chen SJ
Methods Mol Biol; 2021; 2323():1-11. PubMed ID: 34086269
[TBL] [Abstract][Full Text] [Related]
4. 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]
5. 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]
6. 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]
7. 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]
8. RNA 3D Structure Modeling by Combination of Template-Based Method ModeRNA, Template-Free Folding with SimRNA, and Refinement with QRNAS.
Piatkowski P; Kasprzak JM; Kumar D; Magnus M; Chojnowski G; Bujnicki JM
Methods Mol Biol; 2016; 1490():217-35. PubMed ID: 27665602
[TBL] [Abstract][Full Text] [Related]
9. VfoldLA: A web server for loop assembly-based prediction of putative 3D RNA structures.
Xu X; Zhao C; Chen SJ
J Struct Biol; 2019 Sep; 207(3):235-240. PubMed ID: 31173857
[TBL] [Abstract][Full Text] [Related]
10. The Multiscale Ernwin/SPQR RNA Structure Prediction Pipeline.
Thiel BC; Poblete S; Hofacker IL
Methods Mol Biol; 2024; 2726():377-399. PubMed ID: 38780739
[TBL] [Abstract][Full Text] [Related]
11. GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization.
Boudard M; Barth D; Bernauer J; Denise A; Cohen J
Bioinformatics; 2017 Aug; 33(16):2479-2486. PubMed ID: 28398456
[TBL] [Abstract][Full Text] [Related]
12. 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]
13. Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction.
Bayrak CS; Kim N; Schlick T
Nucleic Acids Res; 2017 May; 45(9):5414-5422. PubMed ID: 28158755
[TBL] [Abstract][Full Text] [Related]
14. FR3D: finding local and composite recurrent structural motifs in RNA 3D structures.
Sarver M; Zirbel CL; Stombaugh J; Mokdad A; Leontis NB
J Math Biol; 2008 Jan; 56(1-2):215-52. PubMed ID: 17694311
[TBL] [Abstract][Full Text] [Related]
15. Hierarchical Assembly of RNA Three-Dimensional Structures Based on Loop Templates.
Xu X; Chen SJ
J Phys Chem B; 2018 May; 122(21):5327-5335. PubMed ID: 29258305
[TBL] [Abstract][Full Text] [Related]
16. DotAligner: identification and clustering of RNA structure motifs.
Smith MA; Seemann SE; Quek XC; Mattick JS
Genome Biol; 2017 Dec; 18(1):244. PubMed ID: 29284541
[TBL] [Abstract][Full Text] [Related]
17. Computational prediction of riboswitch tertiary structures including pseudoknots by RAGTOP: a hierarchical graph sampling approach.
Kim N; Zahran M; Schlick T
Methods Enzymol; 2015; 553():115-35. PubMed ID: 25726463
[TBL] [Abstract][Full Text] [Related]
18. Classification and Identification of Non-canonical Base Pairs and Structural Motifs.
Sarrazin-Gendron R; WaldispĆ¼hl J; Reinharz V
Methods Mol Biol; 2024; 2726():143-168. PubMed ID: 38780731
[TBL] [Abstract][Full Text] [Related]
19. 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]
20. Vfold-Pipeline: a web server for RNA 3D structure prediction from sequences.
Li J; Zhang S; Zhang D; Chen SJ
Bioinformatics; 2022 Aug; 38(16):4042-4043. PubMed ID: 35758624
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]