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Items: 1 to 20 of 24

1.

Predicting target DNA sequences of DNA-binding proteins based on unbound structures.

Chen CY, Chien TY, Lin CK, Lin CW, Weng YZ, Chang DT.

PLoS One. 2012;7(2):e30446. doi: 10.1371/journal.pone.0030446. Epub 2012 Feb 1.

2.

AH-DB: collecting protein structure pairs before and after binding.

Chang DT, Yao TJ, Fan CY, Chiang CY, Bai YH.

Nucleic Acids Res. 2012 Jan;40(Database issue):D472-8. doi: 10.1093/nar/gkr940. Epub 2011 Nov 13.

3.

Improved similarity scores for comparing motifs.

Tanaka E, Bailey T, Grant CE, Noble WS, Keich U.

Bioinformatics. 2011 Jun 15;27(12):1603-9. doi: 10.1093/bioinformatics/btr257. Epub 2011 May 4.

4.
5.

The Protein Data Bank (PDB), its related services and software tools as key components for in silico guided drug discovery.

Kirchmair J, Markt P, Distinto S, Schuster D, Spitzer GM, Liedl KR, Langer T, Wolber G.

J Med Chem. 2008 Nov 27;51(22):7021-40. doi: 10.1021/jm8005977. No abstract available.

PMID:
18975926
6.

DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions.

Gao M, Skolnick J.

Nucleic Acids Res. 2008 Jul;36(12):3978-92. doi: 10.1093/nar/gkn332. Epub 2008 May 31.

7.

Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach.

Liu Z, Guo JT, Li T, Xu Y.

Proteins. 2008 Sep;72(4):1114-24. doi: 10.1002/prot.22002.

PMID:
18320590
8.

TFmodeller: comparative modelling of protein-DNA complexes.

Contreras-Moreira B, Branger PA, Collado-Vides J.

Bioinformatics. 2007 Jul 1;23(13):1694-6. Epub 2007 Apr 25.

PMID:
17459960
9.

Connecting protein structure with predictions of regulatory sites.

Morozov AV, Siggia ED.

Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7068-73. Epub 2007 Apr 16.

10.

Energetics of protein-DNA interactions.

Donald JE, Chen WW, Shakhnovich EI.

Nucleic Acids Res. 2007;35(4):1039-47. Epub 2007 Jan 26.

11.

Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility.

van Dijk M, van Dijk AD, Hsu V, Boelens R, Bonvin AM.

Nucleic Acids Res. 2006 Jul 4;34(11):3317-25. Print 2006.

12.

A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data.

Macisaac KD, Gordon DB, Nekludova L, Odom DT, Schreiber J, Gifford DK, Young RA, Fraenkel E.

Bioinformatics. 2006 Feb 15;22(4):423-9. Epub 2005 Dec 6.

PMID:
16332710
13.

Protein-DNA binding specificity predictions with structural models.

Morozov AV, Havranek JJ, Baker D, Siggia ED.

Nucleic Acids Res. 2005 Oct 24;33(18):5781-98. Print 2005.

14.

Improved detection of DNA motifs using a self-organized clustering of familial binding profiles.

Mahony S, Golden A, Smith TJ, Benos PV.

Bioinformatics. 2005 Jun;21 Suppl 1:i283-91.

PMID:
15961468
15.

TM-align: a protein structure alignment algorithm based on the TM-score.

Zhang Y, Skolnick J.

Nucleic Acids Res. 2005 Apr 22;33(7):2302-9. Print 2005.

16.

A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes.

Zhang C, Liu S, Zhu Q, Zhou Y.

J Med Chem. 2005 Apr 7;48(7):2325-35.

PMID:
15801826
17.

Computational methods for transcriptional regulation.

Siggia ED.

Curr Opin Genet Dev. 2005 Apr;15(2):214-21. Review.

PMID:
15797205
18.

Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential.

Liu Z, Mao F, Guo JT, Yan B, Wang P, Qu Y, Xu Y.

Nucleic Acids Res. 2005 Jan 26;33(2):546-58. Print 2005.

19.

Transcription factor binding site identification using the self-organizing map.

Mahony S, Hendrix D, Golden A, Smith TJ, Rokhsar DS.

Bioinformatics. 2005 May 1;21(9):1807-14. Epub 2005 Jan 12.

PMID:
15647296
20.

Toward an atomistic model for predicting transcription-factor binding sites.

Endres RG, Schulthess TC, Wingreen NS.

Proteins. 2004 Nov 1;57(2):262-8.

PMID:
15340913

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