109 related articles for article (PubMed ID: 31350881)
1. pourRNA-a time- and memory-efficient approach for the guided exploration of RNA energy landscapes.
Entzian G; Raden M
Bioinformatics; 2020 Jan; 36(2):462-469. PubMed ID: 31350881
[TBL] [Abstract][Full Text] [Related]
2. Memory-efficient RNA energy landscape exploration.
Mann M; Kucharík M; Flamm C; Wolfinger MT
Bioinformatics; 2014 Sep; 30(18):2584-91. PubMed ID: 24833804
[TBL] [Abstract][Full Text] [Related]
3. DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model.
Badelt S; Lorenz R; Hofacker IL
Bioinformatics; 2023 Jan; 39(1):. PubMed ID: 36655786
[TBL] [Abstract][Full Text] [Related]
4. Finding the direct optimal RNA barrier energy and improving pathways with an arbitrary energy model.
Takizawa H; Iwakiri J; Terai G; Asai K
Bioinformatics; 2020 Jul; 36(Suppl_1):i227-i235. PubMed ID: 32657400
[TBL] [Abstract][Full Text] [Related]
5. Basin Hopping Graph: a computational framework to characterize RNA folding landscapes.
Kucharík M; Hofacker IL; Stadler PF; Qin J
Bioinformatics; 2014 Jul; 30(14):2009-17. PubMed ID: 24648041
[TBL] [Abstract][Full Text] [Related]
6. RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes.
Entzian G; Hofacker IL; Ponty Y; Lorenz R; Tanzer A
Bioinformatics; 2021 Aug; 37(15):2126-2133. PubMed ID: 33538792
[TBL] [Abstract][Full Text] [Related]
7. A new heuristic method for approximating the number of local minima in partial RNA energy landscapes.
Albrecht AA; Day L; Abdelhadi Ep Souki O; Steinhöfel K
Comput Biol Chem; 2016 Feb; 60():43-52. PubMed ID: 26657221
[TBL] [Abstract][Full Text] [Related]
8. Pseudoknots in RNA folding landscapes.
Kucharík M; Hofacker IL; Stadler PF; Qin J
Bioinformatics; 2016 Jan; 32(2):187-94. PubMed ID: 26428288
[TBL] [Abstract][Full Text] [Related]
9. SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics.
Will S; Otto C; Miladi M; Möhl M; Backofen R
Bioinformatics; 2015 Aug; 31(15):2489-96. PubMed ID: 25838465
[TBL] [Abstract][Full Text] [Related]
10. Fast, approximate kinetics of RNA folding.
Senter E; Clote P
J Comput Biol; 2015 Feb; 22(2):124-44. PubMed ID: 25684201
[TBL] [Abstract][Full Text] [Related]
11. ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs.
Otto C; Möhl M; Heyne S; Amit M; Landau GM; Backofen R; Will S
BMC Bioinformatics; 2014 Dec; 15(1):404. PubMed ID: 25551362
[TBL] [Abstract][Full Text] [Related]
12. Efficient approximations of RNA kinetics landscape using non-redundant sampling.
Michálik J; Touzet H; Ponty Y
Bioinformatics; 2017 Jul; 33(14):i283-i292. PubMed ID: 28882001
[TBL] [Abstract][Full Text] [Related]
13. Atlasing of Assembly Landscapes using Distance Geometry and Graph Rigidity.
Prabhu R; Sitharam M; Ozkan A; Wu R
J Chem Inf Model; 2020 Oct; 60(10):4924-4957. PubMed ID: 32786706
[TBL] [Abstract][Full Text] [Related]
14. RNA folding kinetics using Monte Carlo and Gillespie algorithms.
Clote P; Bayegan AH
J Math Biol; 2018 Apr; 76(5):1195-1227. PubMed ID: 28780735
[TBL] [Abstract][Full Text] [Related]
15. 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]
16. RNApuzzler: efficient outerplanar drawing of RNA-secondary structures.
Wiegreffe D; Alexander D; Stadler PF; Zeckzer D
Bioinformatics; 2019 Apr; 35(8):1342-1349. PubMed ID: 30239566
[TBL] [Abstract][Full Text] [Related]
17. Approximating the set of local minima in partial RNA folding landscapes.
Sahoo S; Albrecht AA
Bioinformatics; 2012 Feb; 28(4):523-30. PubMed ID: 22210870
[TBL] [Abstract][Full Text] [Related]
18. LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search.
Huang L; Zhang H; Deng D; Zhao K; Liu K; Hendrix DA; Mathews DH
Bioinformatics; 2019 Jul; 35(14):i295-i304. PubMed ID: 31510672
[TBL] [Abstract][Full Text] [Related]
19. Computational design of RNAs with complex energy landscapes.
Höner zu Siederdissen C; Hammer S; Abfalter I; Hofacker IL; Flamm C; Stadler PF
Biopolymers; 2013 Dec; 99(12):1124-36. PubMed ID: 23818234
[TBL] [Abstract][Full Text] [Related]
20. RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory.
Garcia-Martin JA; Bayegan AH; Dotu I; Clote P
BMC Bioinformatics; 2016 Oct; 17(1):424. PubMed ID: 27756204
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
