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Results: 1 to 20 of 92

1.

Twenty-five years of nucleic acid simulations.

Cheatham TE 3rd, Case DA.

Biopolymers. 2013 Dec;99(12):969-77. doi: 10.1002/bip.22331.

PMID:
23784813
[PubMed - in process]
2.

Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations.

Jin H, Zheng S, Wang Z, Luo C, Shen J, Jiang H, Zhang L, Zhang L.

J Mol Model. 2006 Sep;12(6):781-91. Epub 2006 Feb 1.

PMID:
16450112
[PubMed - indexed for MEDLINE]
3.

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.

Pérez A, Marchán I, Svozil D, Sponer J, Cheatham TE 3rd, Laughton CA, Orozco M.

Biophys J. 2007 Jun 1;92(11):3817-29. Epub 2007 Mar 9.

PMID:
17351000
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Structural equilibrium of DNA represented with different force fields.

Feig M, Pettitt BM.

Biophys J. 1998 Jul;75(1):134-49.

PMID:
9649374
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in.

Ditzler MA, Otyepka M, Sponer J, Walter NG.

Acc Chem Res. 2010 Jan 19;43(1):40-7. doi: 10.1021/ar900093g.

PMID:
19754142
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations.

Pande V, Nilsson L.

Nucleic Acids Res. 2008 Mar;36(5):1508-16. doi: 10.1093/nar/gkm1182. Epub 2008 Jan 18.

PMID:
18203740
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Evaluation of DNA Force Fields in Implicit Solvation.

Gaillard T, Case DA.

J Chem Theory Comput. 2011 Oct 11;7(10):3181-3198.

PMID:
22043178
[PubMed]
Free PMC Article
8.

Toward a consensus view of duplex RNA flexibility.

Faustino I, Pérez A, Orozco M.

Biophys J. 2010 Sep 22;99(6):1876-85. doi: 10.1016/j.bpj.2010.06.061.

PMID:
20858433
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Recognition of RNA by amide modified backbone nucleic acids: molecular dynamics simulations of DNA-RNA hybrids in aqueous solution.

Nina M, Fonné-Pfister R, Beaudegnies R, Chekatt H, Jung PM, Murphy-Kessabi F, De Mesmaeker A, Wendeborn S.

J Am Chem Soc. 2005 Apr 27;127(16):6027-38.

PMID:
15839703
[PubMed - indexed for MEDLINE]
10.

Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration.

Beššeová I, Banáš P, Kührová P, Košinová P, Otyepka M, Šponer J.

J Phys Chem B. 2012 Aug 23;116(33):9899-916. doi: 10.1021/jp3014817. Epub 2012 Aug 9.

PMID:
22809319
[PubMed - indexed for MEDLINE]
11.

Molecular dynamics simulation of nucleic acids: successes, limitations, and promise.

Cheatham TE 3rd, Young MA.

Biopolymers. 2000-2001;56(4):232-56. Review.

PMID:
11754338
[PubMed - indexed for MEDLINE]
12.

RNA stability under different combinations of amber force fields and solvation models.

Gong Z, Xiao Y, Xiao Y.

J Biomol Struct Dyn. 2010 Dec;28(3):431-41.

PMID:
20919758
[PubMed - indexed for MEDLINE]
13.

Conformational flexibility influences degree of hydration of nucleic acid hybrids.

Pramanik S, Nagatoishi S, Saxena S, Bhattacharyya J, Sugimoto N.

J Phys Chem B. 2011 Dec 1;115(47):13862-72. doi: 10.1021/jp207856p. Epub 2011 Nov 9.

PMID:
21992117
[PubMed - indexed for MEDLINE]
14.

Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules.

Prabhu NV, Panda M, Yang Q, Sharp KA.

J Comput Chem. 2008 May;29(7):1113-30.

PMID:
18074338
[PubMed - indexed for MEDLINE]
15.

Computational study of the free energy landscape of the miniprotein CLN025 in explicit and implicit solvent.

Rodriguez A, Mokoema P, Corcho F, Bisetty K, Perez JJ.

J Phys Chem B. 2011 Feb 17;115(6):1440-9. doi: 10.1021/jp106475c. Epub 2011 Jan 21.

PMID:
21254763
[PubMed - indexed for MEDLINE]
16.

Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations.

Cino EA, Choy WY, Karttunen M.

J Chem Theory Comput. 2012 Aug 14;8(8):2725-2740. Epub 2012 Jun 19.

PMID:
22904695
[PubMed]
Free PMC Article
17.

Structural characteristics of 2'-O-(2-methoxyethyl)-modified nucleic acids from molecular dynamics simulations.

Lind KE, Mohan V, Manoharan M, Ferguson DM.

Nucleic Acids Res. 1998 Aug 15;26(16):3694-799.

PMID:
9685484
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Force field influences in beta-hairpin folding simulations.

Lwin TZ, Luo R.

Protein Sci. 2006 Nov;15(11):2642-55.

PMID:
17075138
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and DNA duplexes in solution.

Spacková N, Cheatham TE 3rd, Ryjácek F, Lankas F, Van Meervelt L, Hobza P, Sponer J.

J Am Chem Soc. 2003 Feb 19;125(7):1759-69.

PMID:
12580601
[PubMed - indexed for MEDLINE]
20.

DNA polymorphism: a comparison of force fields for nucleic acids.

Reddy SY, Leclerc F, Karplus M.

Biophys J. 2003 Mar;84(3):1421-49.

PMID:
12609851
[PubMed - indexed for MEDLINE]
Free PMC Article

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