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An overview of the structures of protein-DNA complexes
Nicholas M Luscombe, Susan E Austin, Helen M Berman , Janet M Thornton
Genome Biol. 2000; 1(1): reviews001.1–reviews001.37. Published online 2000 June 9.
PMCID:
PMC138832
Abstract Full Text PDF–14M
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 Is Cited by the Following 34 Articles in this Archive:
Exploiting a Reduced Set of Weighted Average Features to Improve Prediction of DNA-Binding Residues from 3D Structures
Yi Xiong, Junfeng Xia, Wen Zhang, Juan Liu
PLoS One. 2011; 6(12): e28440. Published online 2011 December 8. doi: 10.1371/journal.pone.0028440
PMCID:
PMC3234263
Abstract Full Text PDF–683K Supplementary Material
Experimental strategies for studying transcription factor–DNA binding specificities
Marcel Geertz, Sebastian J. Maerkl
Brief Funct Genomics. 2010 December; 9(5-6): 362–373. Published online 2010 September 23. doi: 10.1093/bfgp/elq023
PMCID:
PMC3080775
Abstract Full Text PDF–873K
Genomic repertoires of DNA-binding transcription factors across the tree of life
Varodom Charoensawan, Derek Wilson, Sarah A. Teichmann
Nucleic Acids Res. 2010 November; 38(21): 7364–7377. Published online 2010 July 30. doi: 10.1093/nar/gkq617
PMCID:
PMC2995046
Abstract Full Text PDF–2.4M Supplementary Material
Discovering protein–DNA binding sequence patterns using association rule mining
Kwong-Sak Leung, Ka-Chun Wong, Tak-Ming Chan, Man-Hon Wong, Kin-Hong Lee, Chi-Kong Lau, Stephen K. W. Tsui
Nucleic Acids Res. 2010 October; 38(19): 6324–6337. Published online 2010 June 6. doi: 10.1093/nar/gkq500
PMCID:
PMC2965231
Abstract Full Text PDF–9.2M Supplementary Material
The Protein-DNA Interface database
Tomás Norambuena, Francisco Melo
BMC Bioinformatics. 2010; 11: 262. Published online 2010 May 18. doi: 10.1186/1471-2105-11-262
PMCID:
PMC2885377
Abstract Full Text PDF–1.4M Supplementary Material
The developmental expression dynamics of Drosophila melanogaster transcription factors
Boris Adryan, Sarah A Teichmann
Genome Biol. 2010; 11(4): R40. Published online 2010 April 12. doi: 10.1186/gb-2010-11-4-r40
PMCID:
PMC2884543
Abstract Full Text PDF–1.3M Supplementary Material
Intrinsic flexibility of B-DNA: the experimental TRX scale
Brahim Heddi, Christophe Oguey, Christophe Lavelle, Nicolas Foloppe, Brigitte Hartmann
Nucleic Acids Res. 2010 January; 38(3): 1034–1047. Published online 2010 January. doi: 10.1093/nar/gkp962
PMCID:
PMC2817485
Abstract Full Text PDF–5.3M Supplementary Material
Three Dimensional Structure of the MqsR:MqsA Complex: A Novel TA Pair Comprised of a Toxin Homologous to RelE and an Antitoxin with Unique Properties
Breann L. Brown, Simina Grigoriu, Younghoon Kim, Jennifer M. Arruda, Andrew Davenport, Thomas K. Wood, Wolfgang Peti, Rebecca Page
PLoS Pathog. 2009 December; 5(12): e1000706. Published online 2009 December 24. doi: 10.1371/journal.ppat.1000706
PMCID:
PMC2791442
Abstract Full Text PDF–4.5M Supplementary Material
DNA-binding residues and binding mode prediction with binding-mechanism concerned models
Yu-Feng Huang, Chun-Chin Huang, Yu-Cheng Liu, Yen-Jen Oyang, Chien-Kang Huang
BMC Genomics. 2009; 10(Suppl 3): S23. Published online 2009 December 3. doi: 10.1186/1471-2164-10-S3-S23
PMCID:
PMC2788376
Abstract Full Text PDF–553K
A Threading-Based Method for the Prediction of DNA-Binding Proteins with Application to the Human Genome
Mu Gao, Jeffrey Skolnick
PLoS Comput Biol. 2009 November; 5(11): e1000567. Published online 2009 November 13. doi: 10.1371/journal.pcbi.1000567
PMCID:
PMC2770119
Abstract Full Text PDF–657K
Crystal Structure of Porcine Reproductive and Respiratory Syndrome Virus Leader Protease Nsp1α
Yuna Sun, Fei Xue, Yu Guo, Ming Ma, Ning Hao, Xuejun C. Zhang, Zhiyong Lou, Xuemei Li, Zihe Rao
J Virol. 2009 November; 83(21): 10931–10940. Published online 2009 August 12. doi: 10.1128/JVI.02579-08
PMCID:
PMC2772781
Abstract Full Text PDF–2.3M
PDA: an automatic and comprehensive analysis program for protein-DNA complex structures
RyangGuk Kim, Jun-tao Guo
BMC Genomics. 2009; 10(Suppl 1): S13. Published online 2009 July 7. doi: 10.1186/1471-2164-10-S1-S13
PMCID:
PMC2709256
Abstract Full Text PDF–3.5M
Analysis of DNA Binding by a Eubacterial Zinc Finger Transcription Factor
Victor J. McAlister, Gail E. Christie
J Bacteriol. 2009 July; 191(14): 4513–4521. Published online 2009 May 15. doi: 10.1128/JB.00193-09
PMCID:
PMC2704732
Abstract Full Text PDF–1.6M
From Nonspecific DNA–Protein Encounter Complexes to the Prediction of DNA–Protein Interactions
Mu Gao, Jeffrey Skolnick
PLoS Comput Biol. 2009 April; 5(3): e1000341. Published online 2009 April 3. doi: 10.1371/journal.pcbi.1000341
PMCID:
PMC2659451
Abstract Full Text PDF–904K Supplementary Material
TFCat: the curated catalog of mouse and human transcription factors
Debra L Fulton, Saravanan Sundararajan, Gwenael Badis, Timothy R Hughes, Wyeth W Wasserman, Jared C Roach, Rob Sladek
Genome Biol. 2009; 10(3): R29. Published online 2009 March 12. doi: 10.1186/gb-2009-10-3-r29
PMCID:
PMC2691000
Abstract Full Text PDF–295K Supplementary Material
Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature
Jiansheng Wu, Hongde Liu, Xueye Duan, Yan Ding, Hongtao Wu, Yunfei Bai, Xiao Sun
Bioinformatics. 2009 January 1; 25(1): 30–35. Published online 2008 November 12. doi: 10.1093/bioinformatics/btn583
PMCID:
PMC2638931
Abstract Full Text PDF–136K Supplementary Material
Insights on protein-DNA recognition by coarse grain modelling
Pierre Poulain, Adrien Saladin, Brigitte Hartmann, Chantal Prévost
J Comput Chem. Author manuscript; available in PMC 2010 July 15.
Published in final edited form as: J Comput Chem. 2008 November; 29(15): 2582–2592. doi: 10.1002/jcc.21014
PMCID:
PMC2904573
Abstract Full Text PDF–1.0M
Computational Structural Analysis: Multiple Proteins Bound to DNA
Andrija Tomovic, Edward J. Oakeley
PLoS ONE. 2008; 3(9): e3243. Published online 2008 September 19. doi: 10.1371/journal.pone.0003243
PMCID:
PMC2532747
Abstract Full Text PDF–188K Supplementary Material
Insights into Protein–DNA Interactions through Structure Network Analysis
R. Sathyapriya, M. S. Vijayabaskar, Saraswathi Vishveshwara
PLoS Comput Biol. 2008 September; 4(9): e1000170. Published online 2008 September 5. doi: 10.1371/journal.pcbi.1000170
PMCID:
PMC2518215
Abstract Full Text PDF–679K Supplementary Material
The Phenomics and Expression Quantitative Trait Locus Mapping of Brain Transcriptomes Regulating Adaptive Divergence in Lake Whitefish Species Pairs (Coregonus sp.)
Andrew R. Whiteley, Nicolas Derome, Sean M. Rogers, Jérôme St-Cyr, Jérôme Laroche, Aurélie Labbe, Arne Nolte, Sébastien Renaut, Julie Jeukens, Louis Bernatchez
Genetics. 2008 September; 180(1): 147–164. doi: 10.1534/genetics.108.089938
PMCID:
PMC2535670
Abstract Full Text PDF–609K
Classifying RNA-Binding Proteins Based on Electrostatic Properties
Shula Shazman, Yael Mandel-Gutfreund
PLoS Comput Biol. 2008 August; 4(8): e1000146. Published online 2008 August 8. doi: 10.1371/journal.pcbi.1000146
Correction in:
PLoS Comput Biol. 2008 August; 4(8): 10.1371/annotation/be4eb7dd-4092-49c1-a619-e8eeba40ed67.
PMCID:
PMC2518515
Abstract Full Text PDF–576K Supplementary Material Correction
Structural segments and residue propensities in protein-RNA interfaces: Comparison with protein-protein and protein-DNA complexes
Sumit Biswas, Mainak Guharoy, Pinak Chakrabarti
Bioinformation. 2008; 2(10): 422–427. Published online 2008 July 14.
PMCID:
PMC2561160
Abstract Full Text PDF–287K Supplementary Material
Trapping of Transcription Factors with Symmetrical DNA Using Thiol-Disulfide Exchange Chemistry
Markandeswar Panda, Daifeng Jiang, Harry W. Jarrett
J Chromatogr A. Author manuscript; available in PMC 2009 August 15.
Published in final edited form as: J Chromatogr A. 2008 August 15; 1202(1): 75–82. Published online 2008 June 22. doi: 10.1016/j.chroma.2008.06.020
PMCID:
PMC2538915
Abstract Full Text PDF–1.6M
Evolutionary conservation of DNA-contact residues in DNA-binding domains
Yao-Lin Chang, Huai-Kuang Tsai, Cheng-Yan Kao, Yung-Chian Chen, Yuh-Jyh Hu, Jinn-Moon Yang
BMC Bioinformatics. 2008; 9(Suppl 6): S3. Published online 2008 May 28. doi: 10.1186/1471-2105-9-S6-S3
PMCID:
PMC2423444
Abstract Full Text PDF–793K
FUNCTIONAL TRENDS IN STRUCTURAL CLASSES OF THE DNA BINDING DOMAINS OF REGULATORY TRANSCRIPTION FACTORS
RACHEL PATTON MCCORD, MARTHA L. BULYK
Pac Symp Biocomput. Author manuscript; available in PMC 2009 October 6.
Published in final edited form as: Pac Symp Biocomput. 2008: 441–452.
PMCID:
PMC2757920
Abstract Full Text PDF–856K Supplementary Material
Identification of DNA-binding proteins using support vector machines and evolutionary profiles
Manish Kumar, Michael M Gromiha, Gajendra PS Raghava
BMC Bioinformatics. 2007; 8: 463. Published online 2007 November 27. doi: 10.1186/1471-2105-8-463
PMCID:
PMC2216048
Abstract Full Text PDF–471K Supplementary Material
oPOSSUM: integrated tools for analysis of regulatory motif over-representation
Shannan J. Ho Sui, Debra L. Fulton, David J. Arenillas, Andrew T. Kwon, Wyeth W. Wasserman
Nucleic Acids Res. 2007 July; 35(Web Server issue): W245–W252. Published online 2007 July. doi: 10.1093/nar/gkm427
PMCID:
PMC1933229
Abstract Full Text PDF–1.9M Supplementary Material
Crystallization and preliminary X-ray analysis of phage Mu activator protein C in a complex with promoter DNA
Karthik K. Shanmuganatham, Manimekalai Ravichandran, Martha M. Howe, Hee-Won Park
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 July 1; 63(Pt 7): 620–623. Published online 2007 June 22. doi: 10.1107/S1744309107025286
PMCID:
PMC2335125
Abstract Full Text PDF–167K
Energetics of protein–DNA interactions
Jason E. Donald, William W. Chen, Eugene I. Shakhnovich
Nucleic Acids Res. 2007 February; 35(4): 1039–1047. Published online 2007 January 26. doi: 10.1093/nar/gkl1103
PMCID:
PMC1851630
Abstract Full Text PDF–2.7M Supplementary Material
Contribution of Invariant Residues to the Function of Rgg Family Transcription Regulators
Jennifer A. Loughman, Michael G. Caparon
J Bacteriol. 2007 January; 189(2): 650–655. Published online 2006 November 10. doi: 10.1128/JB.01437-06
PMCID:
PMC1797381
Abstract Full Text PDF–156K Supplementary Material
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