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Items: 20

1.

TMB Library of Nucleosome Simulations.

Sun R, Li Z, Bishop TC.

J Chem Inf Model. 2019 Oct 28;59(10):4289-4299. doi: 10.1021/acs.jcim.9b00252. Epub 2019 Sep 24.

PMID:
31490686
2.

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA.

Pasi M, Maddocks JH, Beveridge D, Bishop TC, Case DA, Cheatham T 3rd, Dans PD, Jayaram B, Lankas F, Laughton C, Mitchell J, Osman R, Orozco M, Pérez A, Petkevičiūtė D, Spackova N, Sponer J, Zakrzewska K, Lavery R.

Nucleic Acids Res. 2014 Oct 29;42(19):12272-83. doi: 10.1093/nar/gku855. Epub 2014 Sep 26.

3.

Chromatin in 1, 2 and 3 dimensions: comment on "Cracking the chromatin code: precise rule of nucleosome positioning" by E.N. Trifonov.

Bishop TC.

Phys Life Rev. 2011 Mar;8(1):56-8; discussion 69-72. doi: 10.1016/j.plrev.2011.01.011. Epub 2011 Jan 31. No abstract available.

PMID:
21295530
4.

ICM Web: the interactive chromatin modeling web server.

Stolz RC, Bishop TC.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W254-61. doi: 10.1093/nar/gkq496. Epub 2010 Jun 11.

5.

Evaluation of elastic rod models with long range interactions for predicting nucleosome stability.

Sereda YV, Bishop TC.

J Biomol Struct Dyn. 2010 Jun;27(6):867-87.

PMID:
20232939
6.

Relaxation dynamics of nucleosomal DNA.

Ponomarev SY, Putkaradze V, Bishop TC.

Phys Chem Chem Phys. 2009 Dec 7;11(45):10633-43. doi: 10.1039/b910937b. Epub 2009 Sep 21.

PMID:
20145808
7.

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

Lavery R, Zakrzewska K, Beveridge D, Bishop TC, Case DA, Cheatham T 3rd, Dixit S, Jayaram B, Lankas F, Laughton C, Maddocks JH, Michon A, Osman R, Orozco M, Perez A, Singh T, Spackova N, Sponer J.

Nucleic Acids Res. 2010 Jan;38(1):299-313. doi: 10.1093/nar/gkp834. Epub 2009 Oct 22.

8.

VDNA: the virtual DNA plug-in for VMD.

Bishop TC.

Bioinformatics. 2009 Dec 1;25(23):3187-8. doi: 10.1093/bioinformatics/btp566. Epub 2009 Sep 29.

9.

The nucleosome family: dynamic and growing.

Zlatanova J, Bishop TC, Victor JM, Jackson V, van Holde K.

Structure. 2009 Feb 13;17(2):160-71. doi: 10.1016/j.str.2008.12.016. Review.

10.

Geometry of the nucleosomal DNA superhelix.

Bishop TC.

Biophys J. 2008 Aug;95(3):1007-17. doi: 10.1529/biophysj.107.122853. Epub 2008 Apr 18.

11.

Molecular dynamics simulations of a nucleosome and free DNA.

Bishop TC.

J Biomol Struct Dyn. 2005 Jun;22(6):673-86.

PMID:
15842172
12.

Identification of important residues in metal-chelate recognition by monoclonal antibodies.

Delehanty JB, Jones RM, Bishop TC, Blake DA.

Biochemistry. 2003 Dec 9;42(48):14173-83.

PMID:
14640685
13.

Enzymatic E-colicins bind to their target receptor BtuB by presentation of a small binding epitope on a coiled-coil scaffold.

Mohanty AK, Bishop CM, Bishop TC, Wimley WC, Wiener MC.

J Biol Chem. 2003 Oct 17;278(42):40953-8. Epub 2003 Aug 4.

14.

Mechanical model of the nucleosome and chromatin.

Bishop TC, Zhmudsky OO.

J Biomol Struct Dyn. 2002 Apr;19(5):877-87.

PMID:
11922842
15.

Homology modeling using multiple molecular dynamics simulations and docking studies of the human androgen receptor ligand binding domain bound to testosterone and nonsteroidal ligands.

Marhefka CA, Moore BM 2nd, Bishop TC, Kirkovsky L, Mukherjee A, Dalton JT, Miller DD.

J Med Chem. 2001 May 24;44(11):1729-40.

PMID:
11356108
16.

Binding of the estrogen receptor to DNA. The role of waters.

Kosztin D, Bishop TC, Schulten K.

Biophys J. 1997 Aug;73(2):557-70.

17.

How hormone receptor-DNA binding affects nucleosomal DNA: the role of symmetry.

Bishop TC, Kosztin D, Schulten K.

Biophys J. 1997 May;72(5):2056-67.

18.

Molecular dynamics study of glucocorticoid receptor-DNA binding.

Bishop TC, Schulten K.

Proteins. 1996 Jan;24(1):115-33.

PMID:
8628727
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