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Results: 1 to 20 of 256

1.

Force field validation for nucleic acid simulations: comparing energies and dynamics of a DNA dodecamer.

Jha S, Coveney PV, Laughton CA.

J Comput Chem. 2005 Nov 30;26(15):1617-27.

PMID:
16170796
[PubMed - indexed for MEDLINE]
2.

Simulations of nucleic acids and their complexes.

Giudice E, Lavery R.

Acc Chem Res. 2002 Jun;35(6):350-7. Review.

PMID:
12069619
[PubMed - indexed for MEDLINE]
3.

Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS.

Grindon C, Harris S, Evans T, Novik K, Coveney P, Laughton C.

Philos Trans A Math Phys Eng Sci. 2004 Jul 15;362(1820):1373-86.

PMID:
15306456
[PubMed - indexed for MEDLINE]
4.

Simulations of the molecular dynamics of nucleic acids.

Auffinger P, Westhof E.

Curr Opin Struct Biol. 1998 Apr;8(2):227-36. Review.

PMID:
9631298
[PubMed - indexed for MEDLINE]
5.

Molecular dynamics of DNA: comparison of force fields and terminal nucleotide definitions.

Ricci CG, de Andrade AS, Mottin M, Netz PA.

J Phys Chem B. 2010 Aug 5;114(30):9882-93. doi: 10.1021/jp1035663.

PMID:
20614923
[PubMed - indexed for MEDLINE]
6.

DNA sequence-dependent deformability--insights from computer simulations.

Lankas F.

Biopolymers. 2004 Feb 15;73(3):327-39. Review.

PMID:
14755569
[PubMed - indexed for MEDLINE]
7.

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]
8.

Molecular dynamics applied to nucleic acids.

Norberg J, Nilsson L.

Acc Chem Res. 2002 Jun;35(6):465-72. Review.

PMID:
12069632
[PubMed - indexed for MEDLINE]
9.

Theoretical methods for the simulation of nucleic acids.

Orozco M, PĂ©rez A, Noy A, Luque FJ.

Chem Soc Rev. 2003 Nov;32(6):350-64. Review.

PMID:
14671790
[PubMed - indexed for MEDLINE]
10.

Validation of the 53A6 GROMOS force field.

Oostenbrink C, Soares TA, van der Vegt NF, van Gunsteren WF.

Eur Biophys J. 2005 Jun;34(4):273-84. Epub 2005 Apr 1.

PMID:
15803330
[PubMed - indexed for MEDLINE]
11.

Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach.

Curuksu J, Zacharias M.

J Chem Phys. 2009 Mar 14;130(10):104110. doi: 10.1063/1.3086832.

PMID:
19292526
[PubMed - indexed for MEDLINE]
12.

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
13.

Comparison of protein force fields for molecular dynamics simulations.

Guvench O, MacKerell AD Jr.

Methods Mol Biol. 2008;443:63-88. doi: 10.1007/978-1-59745-177-2_4. Review.

PMID:
18446282
[PubMed - indexed for MEDLINE]
14.

Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations?

Rueda M, Cubero E, Laughton CA, Orozco M.

Biophys J. 2004 Aug;87(2):800-11.

PMID:
15298889
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

DNA dynamics in a water drop without counterions.

Mazur AK.

J Am Chem Soc. 2002 Dec 11;124(49):14707-15.

PMID:
12465982
[PubMed - indexed for MEDLINE]
16.

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
17.

Observation of an A-DNA to B-DNA transition in a nonhelical nucleic acid hairpin molecule using molecular dynamics.

Miller JL, Kollman PA.

Biophys J. 1997 Nov;73(5):2702-10.

PMID:
9370463
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Molecular dynamics simulation of a DNA containing a single strand break.

Yamaguchi H, Siebers JG, Furukawa A, Otagiri N, Osman R.

Radiat Prot Dosimetry. 2002;99(1-4):103-8.

PMID:
12194259
[PubMed - indexed for MEDLINE]
19.

Force field parameters for rotation around chi torsion axis in nucleic acids.

Ode H, Matsuo Y, Neya S, Hoshino T.

J Comput Chem. 2008 Nov 30;29(15):2531-42. doi: 10.1002/jcc.21006.

PMID:
18470965
[PubMed - indexed for MEDLINE]
20.

Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment.

Chocholousová J, Feig M.

J Phys Chem B. 2006 Aug 31;110(34):17240-51.

PMID:
16928023
[PubMed - indexed for MEDLINE]

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