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Items: 1 to 20 of 43

1.

An Improved Reaction Coordinate for Nucleic Acid Base Flipping Studies.

Song K, Campbell AJ, Bergonzo C, de Los Santos C, Grollman AP, Simmerling C.

J Chem Theory Comput. 2009 Nov 10;5(11):3105-13. doi: 10.1021/ct9001575. Epub 2009 Oct 9.

PMID:
26609990
2.

Energetic and conformational aspects of A:T base-pair opening within the DNA double helix.

Giudice E, Várnai P, Lavery R.

Chemphyschem. 2001 Nov 19;2(11):673-7. doi: 10.1002/1439-7641(20011119)2:11<673::AID-CPHC673>3.0.CO;2-S.

PMID:
23686902
3.

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 1;2010(6):910-929.

4.

Free energy profile of RNA hairpins: a molecular dynamics simulation study.

Deng NJ, Cieplak P.

Biophys J. 2010 Feb 17;98(4):627-36. doi: 10.1016/j.bpj.2009.10.040.

5.

LOOS: an extensible platform for the structural analysis of simulations.

Romo TD, Grossfield A.

Conf Proc IEEE Eng Med Biol Soc. 2009;2009:2332-5. doi: 10.1109/IEMBS.2009.5335065.

PMID:
19965179
6.

RNA folding: thermodynamic and molecular descriptions of the roles of ions.

Draper DE.

Biophys J. 2008 Dec 15;95(12):5489-95. doi: 10.1529/biophysj.108.131813. Epub 2008 Oct 3. Review.

7.

Optimization by simulated annealing.

Kirkpatrick S, Gelatt CD Jr, Vecchi MP.

Science. 1983 May 13;220(4598):671-80.

PMID:
17813860
8.

In silico design of small RNA switches.

Avihoo A, Gabdank I, Shapira M, Barash D.

IEEE Trans Nanobioscience. 2007 Mar;6(1):4-11.

PMID:
17393844
9.

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.

10.

Convergence of molecular dynamics simulations of membrane proteins.

Grossfield A, Feller SE, Pitman MC.

Proteins. 2007 Apr 1;67(1):31-40.

PMID:
17243153
11.

Structures of RNA switches: insight into molecular recognition and tertiary structure.

Schwalbe H, Buck J, Fürtig B, Noeske J, Wöhnert J.

Angew Chem Int Ed Engl. 2007;46(8):1212-9. Review.

PMID:
17226886
12.

Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch.

Noeske J, Buck J, Fürtig B, Nasiri HR, Schwalbe H, Wöhnert J.

Nucleic Acids Res. 2007;35(2):572-83. Epub 2006 Dec 14.

13.
14.

Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pair.

Mathews DH, Case DA.

J Mol Biol. 2006 Apr 14;357(5):1683-93. Epub 2006 Feb 3.

PMID:
16487974
15.

Characterization of the TIP4P-Ew water model: vapor pressure and boiling point.

Horn HW, Swope WC, Pitera JW.

J Chem Phys. 2005 Nov 15;123(19):194504.

PMID:
16321097
16.

The Amber biomolecular simulation programs.

Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, Woods RJ.

J Comput Chem. 2005 Dec;26(16):1668-88.

17.

Incorporating variable dielectric environments into the generalized Born model.

Sigalov G, Scheffel P, Onufriev A.

J Chem Phys. 2005 Mar 1;122(9):094511.

PMID:
15836154
18.

Molecular dynamics simulations and free energy calculations of base flipping in dsRNA.

Hart K, Nyström B, Ohman M, Nilsson L.

RNA. 2005 May;11(5):609-18. Epub 2005 Apr 5.

19.

Solution structure of an RNA internal loop with three consecutive sheared GA pairs.

Chen G, Znosko BM, Kennedy SD, Krugh TR, Turner DH.

Biochemistry. 2005 Mar 1;44(8):2845-56.

PMID:
15723528
20.

Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases.

Rázga F, Koca J, Sponer J, Leontis NB.

Biophys J. 2005 May;88(5):3466-85. Epub 2005 Feb 18.

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