224 related articles for article (PubMed ID: 27125734)
21. 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]
22. Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings.
Cragnolini T; Laurin Y; Derreumaux P; Pasquali S
J Chem Theory Comput; 2015 Jul; 11(7):3510-22. PubMed ID: 26575783
[TBL] [Abstract][Full Text] [Related]
23. 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]
24. Modeling RNA topological structures using small angle X-ray scattering.
Bhandari YR; Jiang W; Stahlberg EA; Stagno JR; Wang YX
Methods; 2016 Jul; 103():18-24. PubMed ID: 27090001
[TBL] [Abstract][Full Text] [Related]
25. Coarse-Grained Protein Models and Their Applications.
Kmiecik S; Gront D; Kolinski M; Wieteska L; Dawid AE; Kolinski A
Chem Rev; 2016 Jul; 116(14):7898-936. PubMed ID: 27333362
[TBL] [Abstract][Full Text] [Related]
26. All-atom Monte Carlo simulation of GCAA RNA folding.
Nivón LG; Shakhnovich EI
J Mol Biol; 2004 Nov; 344(1):29-45. PubMed ID: 15504400
[TBL] [Abstract][Full Text] [Related]
27. Computational modeling of RNA 3D structures, with the aid of experimental restraints.
Magnus M; Matelska D; Lach G; Chojnowski G; Boniecki MJ; Purta E; Dawson W; Dunin-Horkawicz S; Bujnicki JM
RNA Biol; 2014; 11(5):522-36. PubMed ID: 24785264
[TBL] [Abstract][Full Text] [Related]
28. Coarse-graining methods for computational biology.
Saunders MG; Voth GA
Annu Rev Biophys; 2013; 42():73-93. PubMed ID: 23451897
[TBL] [Abstract][Full Text] [Related]
29. Fast flexible modeling of RNA structure using internal coordinates.
Flores SC; Sherman MA; Bruns CM; Eastman P; Altman RB
IEEE/ACM Trans Comput Biol Bioinform; 2011; 8(5):1247-57. PubMed ID: 21778523
[TBL] [Abstract][Full Text] [Related]
30. IsRNA1:
Zhang D; Li J; Chen SJ
J Chem Theory Comput; 2021 Mar; 17(3):1842-1857. PubMed ID: 33560836
[TBL] [Abstract][Full Text] [Related]
31. Bridging the gap in RNA structure prediction.
Shapiro BA; Yingling YG; Kasprzak W; Bindewald E
Curr Opin Struct Biol; 2007 Apr; 17(2):157-65. PubMed ID: 17383172
[TBL] [Abstract][Full Text] [Related]
32. Coarse-grained model for predicting RNA folding thermodynamics.
Denesyuk NA; Thirumalai D
J Phys Chem B; 2013 May; 117(17):4901-11. PubMed ID: 23527587
[TBL] [Abstract][Full Text] [Related]
33. Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding.
Denesyuk NA; Hori N; Thirumalai D
J Phys Chem B; 2018 Dec; 122(50):11860-11867. PubMed ID: 30468380
[TBL] [Abstract][Full Text] [Related]
34. Coarse-Grained Modeling of Nucleic Acids Using Anisotropic Gay-Berne and Electric Multipole Potentials.
Li G; Shen H; Zhang D; Li Y; Wang H
J Chem Theory Comput; 2016 Feb; 12(2):676-93. PubMed ID: 26717419
[TBL] [Abstract][Full Text] [Related]
35. Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered molecular dynamics.
Poblete S; Bottaro S; Bussi G
Biochem Biophys Res Commun; 2018 Mar; 498(2):352-358. PubMed ID: 29248728
[TBL] [Abstract][Full Text] [Related]
36. Advancing RNA 3D structure prediction: Exploring hierarchical and hybrid approaches in CASP15.
Li J; Zhang S; Chen SJ
Proteins; 2023 Dec; 91(12):1779-1789. PubMed ID: 37615235
[TBL] [Abstract][Full Text] [Related]
37. RNA and protein 3D structure modeling: similarities and differences.
Rother K; Rother M; Boniecki M; Puton T; Bujnicki JM
J Mol Model; 2011 Sep; 17(9):2325-36. PubMed ID: 21258831
[TBL] [Abstract][Full Text] [Related]
38. Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models.
Jonikas MA; Radmer RJ; Altman RB
Bioinformatics; 2009 Dec; 25(24):3259-66. PubMed ID: 19812110
[TBL] [Abstract][Full Text] [Related]
39. Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 Model.
Zhang D; Chen SJ; Zhou R
J Phys Chem B; 2021 Nov; 125(43):11907-11915. PubMed ID: 34694128
[TBL] [Abstract][Full Text] [Related]
40. 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]
[Previous] [Next] [New Search]
