157 related articles for article (PubMed ID: 32179130)
21. Structural variations of single and tandem mismatches in RNA duplexes: a joint MD simulation and crystal structure database analysis.
Halder S; Bhattacharyya D
J Phys Chem B; 2012 Oct; 116(39):11845-56. PubMed ID: 22953716
[TBL] [Abstract][Full Text] [Related]
22. Structural and evolutionary classification of G/U wobble basepairs in the ribosome.
Mokdad A; Krasovska MV; Sponer J; Leontis NB
Nucleic Acids Res; 2006; 34(5):1326-41. PubMed ID: 16522645
[TBL] [Abstract][Full Text] [Related]
23. Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAs.
Burkard ME; Kierzek R; Turner DH
J Mol Biol; 1999 Jul; 290(5):967-82. PubMed ID: 10438596
[TBL] [Abstract][Full Text] [Related]
24. Energy hyperspace for stacking interaction in AU/AU dinucleotide step: Dispersion-corrected density functional theory study.
Mukherjee S; Kailasam S; Bansal M; Bhattacharyya D
Biopolymers; 2014 Jan; 101(1):107-20. PubMed ID: 23722519
[TBL] [Abstract][Full Text] [Related]
25. Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations?
Svozil D; Hobza P; Sponer J
J Phys Chem B; 2010 Jan; 114(2):1191-203. PubMed ID: 20000584
[TBL] [Abstract][Full Text] [Related]
26. An innate twist between Crick's wobble and Watson-Crick base pairs.
Ananth P; Goldsmith G; Yathindra N
RNA; 2013 Aug; 19(8):1038-53. PubMed ID: 23861536
[TBL] [Abstract][Full Text] [Related]
27. Diversity of base-pair conformations and their occurrence in rRNA structure and RNA structural motifs.
Lee JC; Gutell RR
J Mol Biol; 2004 Dec; 344(5):1225-49. PubMed ID: 15561141
[TBL] [Abstract][Full Text] [Related]
28. Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5'-d(GCGAAGC)-3' hairpin: Complete basis set calculations at the MP2 and CCSD(T) levels.
Dabkowska I; Gonzalez HV; Jurecka P; Hobza P
J Phys Chem A; 2005 Feb; 109(6):1131-6. PubMed ID: 16833422
[TBL] [Abstract][Full Text] [Related]
29. The crystal structure of the octamer [r(guauaca)dC]2 with six Watson-Crick base-pairs and two 3' overhang residues.
Shi K; Biswas R; Mitra SN; Sundaralingam M
J Mol Biol; 2000 May; 299(1):113-22. PubMed ID: 10860726
[TBL] [Abstract][Full Text] [Related]
30. Physico-chemical profiles of the wobble ↔ Watson-Crick G*·2AP(w) ↔ G·2AP(WC) and A·2AP(w) ↔ A*·2AP(WC) tautomerisations: a QM/QTAIM comprehensive survey.
Brovarets' OO; Voiteshenko IS; Hovorun DM
Phys Chem Chem Phys; 2017 Dec; 20(1):623-636. PubMed ID: 29227488
[TBL] [Abstract][Full Text] [Related]
31. Can modified DNA base pairs with chalcogen bonding expand the genetic alphabet? A combined quantum chemical and molecular dynamics simulation study.
Sharma KD; Kathuria P; Wetmore SD; Sharma P
Phys Chem Chem Phys; 2020 Nov; 22(41):23754-23765. PubMed ID: 33063082
[TBL] [Abstract][Full Text] [Related]
32. Analysis of stacking overlap in nucleic acid structures: algorithm and application.
Pingali PK; Halder S; Mukherjee D; Basu S; Banerjee R; Choudhury D; Bhattacharyya D
J Comput Aided Mol Des; 2014 Aug; 28(8):851-67. PubMed ID: 24990628
[TBL] [Abstract][Full Text] [Related]
33. An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN Internal Loops Studied by Molecular Dynamics Methods.
Réblová K; Střelcová Z; Kulhánek P; Beššeová I; Mathews DH; Van Nostrand K; Yildirim I; Turner DH; Šponer J
J Chem Theory Comput; 2010 Mar; 6(3):910-29. PubMed ID: 26613316
[TBL] [Abstract][Full Text] [Related]
34. Zipper-like Watson-Crick base-pairs.
Chou SH; Chin KH
J Mol Biol; 2001 Sep; 312(4):753-68. PubMed ID: 11575930
[TBL] [Abstract][Full Text] [Related]
35. An RNA molecular switch: Intrinsic flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN internal loops studied by molecular dynamics methods.
Réblová K; Střelcová Z; Kulhánek P; Beššeová I; Mathews DH; Nostrand KV; Yildirim I; Turner DH; Sponer J
J Chem Theory Comput; 2010 Jan; 2010(6):910-929. PubMed ID: 21132104
[TBL] [Abstract][Full Text] [Related]
36. π-Cooperativity effect on the base stacking interactions in DNA: is there a novel stabilization factor coupled with base pairing H-bonds?
Karabıyık H; Sevinçek R; Karabıyık H
Phys Chem Chem Phys; 2014 Aug; 16(29):15527-38. PubMed ID: 24953339
[TBL] [Abstract][Full Text] [Related]
37. RNABPDB: Molecular Modeling of RNA Structure-From Base Pair Analysis in Crystals to Structure Prediction.
Mukherjee D; Maiti S; Gouda PK; Sharma R; Roy P; Bhattacharyya D
Interdiscip Sci; 2022 Sep; 14(3):759-774. PubMed ID: 35705797
[TBL] [Abstract][Full Text] [Related]
38. Trans Hoogsteen/sugar edge base pairing in RNA. Structures, energies, and stabilities from quantum chemical calculations.
Mládek A; Sharma P; Mitra A; Bhattacharyya D; Sponer J; Sponer JE
J Phys Chem B; 2009 Feb; 113(6):1743-55. PubMed ID: 19152254
[TBL] [Abstract][Full Text] [Related]
39. RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs.
Bhattacharyya D; Halder S; Basu S; Mukherjee D; Kumar P; Bansal M
J Comput Aided Mol Des; 2017 Feb; 31(2):219-235. PubMed ID: 28102461
[TBL] [Abstract][Full Text] [Related]
40. GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing.
Gerlach W; Giegerich R
Bioinformatics; 2006 Mar; 22(6):762-4. PubMed ID: 16403789
[TBL] [Abstract][Full Text] [Related]
[Previous] [Next] [New Search]