215 related articles for article (PubMed ID: 21349865)
1. All-atom knowledge-based potential for RNA structure prediction and assessment.
Capriotti E; Norambuena T; Marti-Renom MA; Melo F
Bioinformatics; 2011 Apr; 27(8):1086-93. PubMed ID: 21349865
[TBL] [Abstract][Full Text] [Related]
2. RNA structure alignment by a unit-vector approach.
Capriotti E; Marti-Renom MA
Bioinformatics; 2008 Aug; 24(16):i112-8. PubMed ID: 18689811
[TBL] [Abstract][Full Text] [Related]
3. Modeling Small Noncanonical RNA Motifs with the Rosetta FARFAR Server.
Yesselman JD; Das R
Methods Mol Biol; 2016; 1490():187-98. PubMed ID: 27665600
[TBL] [Abstract][Full Text] [Related]
4. Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure.
Reinharz V; Major F; Waldispühl J
Bioinformatics; 2012 Jun; 28(12):i207-14. PubMed ID: 22689763
[TBL] [Abstract][Full Text] [Related]
5. 3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures.
Wang J; Zhao Y; Zhu C; Xiao Y
Nucleic Acids Res; 2015 May; 43(10):e63. PubMed ID: 25712091
[TBL] [Abstract][Full Text] [Related]
6. Accurate prediction of RNA nucleotide interactions with backbone k-tree model.
Ding L; Xue X; LaMarca S; Mohebbi M; Samad A; Malmberg RL; Cai L
Bioinformatics; 2015 Aug; 31(16):2660-7. PubMed ID: 25886978
[TBL] [Abstract][Full Text] [Related]
7. RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data.
Yao J; Reinharz V; Major F; Waldispühl J
Nucleic Acids Res; 2017 Jul; 45(W1):W440-W444. PubMed ID: 28525607
[TBL] [Abstract][Full Text] [Related]
8. 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]
9. Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters.
Jonikas MA; Radmer RJ; Laederach A; Das R; Pearlman S; Herschlag D; Altman RB
RNA; 2009 Feb; 15(2):189-99. PubMed ID: 19144906
[TBL] [Abstract][Full Text] [Related]
10. Automated RNA 3D Structure Prediction with RNAComposer.
Biesiada M; Purzycka KJ; Szachniuk M; Blazewicz J; Adamiak RW
Methods Mol Biol; 2016; 1490():199-215. PubMed ID: 27665601
[TBL] [Abstract][Full Text] [Related]
11. WebRASP: a server for computing energy scores to assess the accuracy and stability of RNA 3D structures.
Norambuena T; Cares JF; Capriotti E; Melo F
Bioinformatics; 2013 Oct; 29(20):2649-50. PubMed ID: 23929030
[TBL] [Abstract][Full Text] [Related]
12. Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation.
Bernauer J; Huang X; Sim AY; Levitt M
RNA; 2011 Jun; 17(6):1066-75. PubMed ID: 21521828
[TBL] [Abstract][Full Text] [Related]
13. Optimized distance-dependent atom-pair-based potential DOOP for protein structure prediction.
Chae MH; Krull F; Knapp EW
Proteins; 2015 May; 83(5):881-90. PubMed ID: 25693513
[TBL] [Abstract][Full Text] [Related]
14. InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution.
Andreani J; Faure G; Guerois R
Bioinformatics; 2013 Jul; 29(14):1742-9. PubMed ID: 23652426
[TBL] [Abstract][Full Text] [Related]
15. Novel nonlinear knowledge-based mean force potentials based on machine learning.
Dong Q; Zhou S
IEEE/ACM Trans Comput Biol Bioinform; 2011; 8(2):476-86. PubMed ID: 20820079
[TBL] [Abstract][Full Text] [Related]
16. Development of a new meta-score for protein structure prediction from seven all-atom distance dependent potentials using support vector regression.
Shirota M; Ishida T; Kinoshita K
Genome Inform; 2009 Oct; 23(1):149-58. PubMed ID: 20180270
[TBL] [Abstract][Full Text] [Related]
17. Modeling and Predicting RNA Three-Dimensional Structures.
Reinharz V; Sarrazin-Gendron R; Waldispühl J
Methods Mol Biol; 2021; 2284():17-42. PubMed ID: 33835435
[TBL] [Abstract][Full Text] [Related]
18. TOUCHSTONE II: a new approach to ab initio protein structure prediction.
Zhang Y; Kolinski A; Skolnick J
Biophys J; 2003 Aug; 85(2):1145-64. PubMed ID: 12885659
[TBL] [Abstract][Full Text] [Related]
19. Modeling and predicting RNA three-dimensional structures.
Waldispühl J; Reinharz V
Methods Mol Biol; 2015; 1269():101-21. PubMed ID: 25577374
[TBL] [Abstract][Full Text] [Related]
20. All-atom four-body knowledge-based statistical potential to distinguish native tertiary RNA structures from nonnative folds.
Masso M
J Theor Biol; 2018 Sep; 453():58-67. PubMed ID: 29782930
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
