Tag protein-dna_interaction [55 articles] Export

Recent papers classified by the tag protein-dna_interaction.

	Specificity of protein-DNA recognition revealed by structure-based potentials: symmetric/asymmetric and cognate/non-cognate binding. [My Copy] Journal of molecular biology, Vol. 322, No. 5. (4 October 2002), pp. 907-915. by Samuel Selvaraj, Hidetoshi Kono, Akinori Sarai posted to protein-dna_interaction by kaarsinogen on 2009-08-11 22:05:38 as
	Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. [My Copy] Nucleic Acids Res, Vol. 29, No. 13. (1 July 2001), pp. 2860-2874. by N. M. Luscombe, R. A. Laskowski, J. M. Thornton posted to protein-dna_interaction file-import-09-06-23 by semin on 2009-03-03 13:42:16 as along with 3 people and 8 groups kaarsinogen shantanu medic0747 structural_bioinformatics MathBio Biostatistics Bioinformatics microRNA Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology
	Protein-DNA interactions: a structural analysis [My Copy] Journal of Molecular Biology, Vol. 287, No. 5. (16 April 1999), pp. 877-896. by S. Jones, P. van Heyningen, H. M. Berman, J. M. Thornton posted to protein-dna_interaction file-import-09-06-23 by semin on 2009-03-03 13:41:28 as along with 3 people vingron kaarsinogen medic0747
	Learning to translate sequence and structure to function: identifying DNA binding and membrane binding proteins. [My Copy] Annals of biomedical engineering, Vol. 35, No. 6. (June 2007), pp. 1043-1052. by R. E. Langlois, M. B. Carson, N. Bhardwaj, H. Lu posted to dna_binding machine_learning protein-dna_interaction by kaarsinogen on 2008-08-12 18:54:34 as
	Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential [My Copy] Nucl. Acids Res., Vol. 33, No. 2. (26 January 2005), pp. 546-558. by Zhijie Liu, Fenglou Mao, Jun-tao Guo, et al.Bo Yan, Peng Wang, Youxing Qu, Ying Xu posted to protein-dna_interaction by kaarsinogen on 2008-03-20 17:50:53 as along with 2 people and 1 group nklee oannes Regulomics_UCHSC
	Protein-RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures. [My Copy] Bioinformatics (11 September 2006) by N Morozova, J Allers, J Myers, Y Shamoo posted to protein-dna_interaction by kaarsinogen on 2008-03-20 17:11:10 as along with 7 people and 3 groups balewis svozil semin yoonk marcius eckart_bindewald medic0747 Bioinformatics BioinfoCIPF SGU-CIPF
	Predicting rRNA-, RNA-, and DNA-binding proteins from primary structure with support vector machines [My Copy] Journal of Theoretical Biology, Vol. 240, No. 2. (21 May 2006), pp. 175-184. by Xiaojing Yu, Jianping Cao, Yudong Cai, Tieliu Shi, Yixue Li posted to protein-dna_interaction protein-rna svm by kaarsinogen on 2008-03-17 15:51:01 as along with 1 person balewis
	Residue-level prediction of DNA-binding sites and its application on DNA-binding protein predictions [My Copy] FEBS Letters, Vol. 581, No. 5. (6 March 2007), pp. 1058-1066. by Nitin Bhardwaj, Hui Lu posted to dna_binding protein-dna_interaction by kaarsinogen on 2008-03-07 19:15:28 as
	Prediction of DNA-binding residues from sequence [My Copy] Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i347-353. by Yanay Ofran, Venkatesh Mysore, Burkhard Rost posted to dna_binding protein-dna_interaction by kaarsinogen on 2008-03-07 19:03:24 as along with 3 people aalibes GustavoLacerda chrn
	BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences. [My Copy] Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006) by L. Wang, S. J. Brown posted to dna_binding protein-dna_interaction protein-rna by kaarsinogen on 2007-06-04 18:06:47 as
	Connecting protein structure with predictions of regulatory sites [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 17. (24 April 2007), pp. 7068-7073. by Alexandre V. Morozov, Eric D. Siggia posted to dna_binding protein-dna_interaction protein_structure transcription_factor by kaarsinogen on 2007-06-01 22:37:08 as along with 7 people and 2 groups vingron nklee maximilianh ana aalibes johncumbers lusk structural_bioinformatics Bioinformatics
	How do site-specific DNA-binding proteins find their targets? [My Copy] Nucl. Acids Res., Vol. 32, No. 10. (3 June 2004), pp. 3040-3052. by Stephen E. Halford, John F. Marko posted to dna_binding protein-dna_interaction transcription_factor by kaarsinogen on 2007-06-01 21:29:15 as along with 3 people and 1 group samjlord JintuRabha chrn moernerlab
	DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces [My Copy] Nucl. Acids Res., Vol. 35, No. 5. (12 March 2007), pp. 1465-1477. by Harianto Tjong, Huan-Xiang Zhou posted to dna_binding machine_learning protein-dna_interaction protein_descriptors protein_structure transcription_factor by kaarsinogen on 2007-06-01 21:15:06 as along with 1 person medic0747
	An overview of the structures of protein-DNA complexes [My Copy] Genome Biology, Vol. 1, No. 1. (2000) by Nicholas M. Luscombe, Susan E. Austin, Helen M. Berman, Janet M. Thornton posted to protein_structure protein-dna_interaction by kaarsinogen on 2007-02-02 20:11:01 as along with 5 people and 1 group agustinarce svozil indigoviolet medic0747 emptyhb EisenLab
	A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction [My Copy] Journal of Structural and Functional Genomics, Vol. 5, No. 4. (January 2005), pp. 255-265. by William Mclaughlin, Daniel Kulp, Joanna Cruz, Xiang-Jun Lu, Catherine Lawson, Helen Berman posted to protein_structure protein-dna_interaction dna_binding by kaarsinogen on 2007-01-22 06:42:38 as
	PSSM-based prediction of DNA binding sites in proteins. [My Copy] BMC Bioinformatics, Vol. 6 (2005) by S. Ahmad, A. Sarai posted to 2005_2006_dnabp dna_binding protein-dna_interaction pssm by kaarsinogen on 2006-11-03 23:08:37 as
	Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network. [My Copy] J Comput Chem, Vol. 25, No. 6. (30 April 2004), pp. 779-789. by M. Keil, T. E. Exner, J. Brickmann posted to machine_learning neural_network protein-dna_interaction by kaarsinogen on 2006-11-03 22:50:22 as along with 1 person nickolay
	Predicting DNA-binding sites of proteins from amino acid sequence. [My Copy] BMC Bioinformatics, Vol. 7 (2006) by C. Yan, M. Terribilini, F. Wu, R. L. Jernigan, D. Dobbs, V. Honavar posted to 2005_2006_dnabp dna_binding protein-dna_interaction protein_descriptors by kaarsinogen on 2006-11-03 20:47:02 as along with 3 people ameetsoni ezralanglois dandaman
	Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems [My Copy] PLoS Computational Biology, Vol. 2, No. 8. (1 August 2006), e101. by Erwin P. Gianchandani, Jason A. Papin, Nathan D. Price, Andrew R. Joyce, Bernhard O. Palsson posted to 2005_2006_dnabp gene_regulation protein-dna_interaction signaling_pathways transcription_factor by kaarsinogen on 2006-09-20 18:40:00 as along with 3 people and 1 group schwartzjmc jfr indigoviolet EisenLab
	Deciphering gene expression regulatory networks. [My Copy] Curr Opin Genet Dev, Vol. 12, No. 2. (April 2002), pp. 130-136. by J. J. Wyrick, R. A. Young posted to gene_regulation protein-dna_interaction by kaarsinogen on 2006-09-07 22:01:22 as
	Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins. [My Copy] Proteins, Vol. 64, No. 1. (1 July 2006), pp. 19-27. by I. B. Kuznetsov, Z. Gou, R. Li, S. Hwang posted to 2005_2006_dnabp dna_binding evolution protein-dna_interaction svm by kaarsinogen on 2006-07-29 00:36:37 as along with 1 person hplatero
	Whole-genome discovery of transcription factor binding sites by network-level conservation. [My Copy] Genome research, Vol. 14, No. 1. (1 January 2004), pp. 99-108. by M. Pritsker, Y. C. Liu, M. A. Beer, S. Tavazoie posted to dna_binding e_coli gene_regulation genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-07-17 22:47:37 as along with 5 people alhufton Dulce aprasad koller xili03
	A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli. [My Copy] Genome Res, Vol. 14, No. 2. (February 2004), pp. 201-208. by M. L. Bulyk, A. M. McGuire, N. Masuda, G. M. Church posted to dna_binding e_coli gene_regulation genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-07-17 22:24:10 as along with 3 people wowalz LeightonP sconlan
	Adaptive evolution of transcription factor binding sites. [My Copy] BMC Evol Biol, Vol. 4, No. 1. (28 October 2004) by J. Berg, S. Willmann, M. Lässig posted to dna_binding e_coli protein-dna_interaction transcription_factor by kaarsinogen on 2006-07-17 19:07:37 as along with 4 people and 1 group bmajoros jjray discreteonyxorb cisevol cis-regulatory-evolution
	Sequencing and comparison of yeast species to identify genes and regulatory elements [My Copy] Nature, Vol. 423, No. 6937. (15 May 2003), pp. 241-254. by Manolis Kellis, Nick Patterson, Matthew Endrizzi, Bruce Birren, Eric S. Lander posted to gene_regulation genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-07-11 20:47:55 as along with 5 people viren4388 Dulce lyongu nklee kmdaily
	Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. [My Copy] Genome Res, Vol. 11, No. 7. (July 2001), pp. 1175-1186. by P. F. Cliften, L. W. Hillier, L. Fulton, et al.T. Graves, T. Miner, W. R. Gish, R. H. Waterston, M. Johnston posted to dna_binding genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-06-28 23:05:19 as along with 2 people evaf nklee
	DNA binding sites: representation and discovery [My Copy] Bioinformatics, Vol. 16, No. 1. (1 January 2000), pp. 16-23. by Gary D. Stormo posted to dna_binding protein-dna_interaction by kaarsinogen on 2006-06-28 23:00:52 as along with 6 people stharward Dulce austin_mcdonald ajbattle erdos emptyhb
	Genome-Wide Location and Function of DNA Binding Proteins [My Copy] Science, Vol. 290, No. 5500. (22 December 2000), pp. 2306-2309. by Bing Ren, Francois Robert, John J. Wyrick, et al.Oscar Aparicio, Ezra G. Jennings, Itamar Simon, Julia Zeitlinger, Jorg Schreiber, Nancy Hannett, Elenita Kanin, Thomas L. Volkert, Christopher J. Wilson, Stephen P. Bell, Richard A. Young posted to dna_binding genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-06-28 22:54:05 as along with 9 people TorstenWaldminghaus aprasad miguel johncumbers tvdbulck epigenetics yevishere kristallreiner dquest
	Computational prediction of transcription-factor binding site locations [My Copy] Genome Biology, Vol. 5, No. 1. (2003), 201. by Martha Bulyk posted to dna_binding genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-06-26 20:41:26 as along with 10 people and 1 group xubeisi Baschl marti tkmaia lusk Stew nklee yevishere xili03 aalibes EisenLab
	Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. [My Copy] Science, Vol. 265, No. 5170. (15 July 1994), pp. 346-355. by Y. Cho, S. Gorina, P. D. Jeffrey, N. P. Pavletich posted to dna_binding p53 protein-dna_interaction by kaarsinogen on 2006-03-08 17:49:17 as
	Definition of a consensus binding site for p53. [My Copy] Nat Genet, Vol. 1, No. 1. (April 1992), pp. 45-49. by W. S. el-Deiry, S. E. Kern, J. A. Pietenpol, K. W. Kinzler, B. Vogelstein posted to dna_binding p53 protein-dna_interaction by kaarsinogen on 2006-03-08 17:47:28 as
	Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity [My Copy] Cell, Vol. 124, No. 1. (13 January 2006), pp. 47-59. by O. Hallikas, K. Palin, N. Sinjushina, et al.R. Rautiainen, J. Partanen, E. Ukkonen, J. Taipale posted to 2005_2006_dnabp dna_binding genome protein-dna_interaction transcription_factor by kaarsinogen on 2006-01-30 19:48:04 as along with 16 people and 5 groups absterga xingxu cisstem Terkko tuck brant xwbcn dchughes nickluscombe olympos cabbagezs karfunkel maximilianh heliopais oelemento emptyhb Bioinformatics EisenLab G4ID EBI-regulation Genetics-of-Gambling
	A global map of p53 transcription-factor binding sites in the human genome. [My Copy] Cell, Vol. 124, No. 1. (13 January 2006), pp. 207-219. by C. L. Wei, Q. Wu, V. B. Vega, et al.K. P. Chiu, P. Ng, T. Zhang, A. Shahab, H. C. Yong, Y. Fu, Z. Weng, J. Liu, X. D. Zhao, J. L. Chew, Y. L. Lee, V. A. Kuznetsov, W. K. Sung, L. D. Miller, B. Lim, E. T. Liu, Q. Yu, H. H. Ng, Y. Ruan posted to 2005_2006_dnabp dna_binding genome p53 protein-dna_interaction transcription_factor by kaarsinogen on 2006-01-30 19:46:35 as along with 12 people and 1 group pick600 drestion jfr balajis tabu vega kengg jackjackjjj jtomasch karfunkel maralena bozdagd Plantandetc
	Structural features of protein-nucleic acid recognition sites. [My Copy] Biochemistry, Vol. 38, No. 7. (16 February 1999), pp. 1999-2017. by K. Nadassy, S. J. Wodak, J. Janin posted to dna_binding docking protein-dna_interaction protein_structure by kaarsinogen on 2006-01-25 23:39:26 as along with 2 people svozil medic0747
	Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. [My Copy] J Mol Biol, Vol. 320, No. 5. (26 July 2002), pp. 991-1009. by N. M. Luscombe, J. M. Thornton posted to dna_binding protein-dna_interaction by kaarsinogen on 2006-01-25 23:33:55 as along with 1 person medic0747
	Geometric analysis and comparison of protein-DNA interfaces: why is there no simple code for recognition? [My Copy] J Mol Biol, Vol. 301, No. 3. (18 August 2000), pp. 597-624. by C. O. Pabo, L. Nekludova posted to dna_binding docking protein-dna_interaction protein_structure by kaarsinogen on 2006-01-25 23:30:10 as along with 2 people yoonk medic0747
	Structure-based prediction of DNA target sites by regulatory proteins. [My Copy] Proteins, Vol. 35, No. 1. (1 April 1999), pp. 114-131. by H. Kono, A. Sarai posted to dna_binding protein-dna_interaction protein_structure transcription_factor by kaarsinogen on 2006-01-25 22:44:19 as along with 1 person medic0747
	A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. [My Copy] J Mol Biol, Vol. 284, No. 2. (27 November 1998), pp. 241-254. by K. Robison, A. M. McGuire, G. M. Church posted to dna_binding e_coli protein-dna_interaction by kaarsinogen on 2006-01-25 22:38:11 as along with 2 people medic0747 nklee
	Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites. [My Copy] Nucleic Acids Res, Vol. 26, No. 10. (15 May 1998), pp. 2306-2312. by Y. Mandel-Gutfreund, H. Margalit posted to dna_binding protein-dna_interaction protein_structure by kaarsinogen on 2006-01-25 22:35:43 as along with 2 people medic0747 roys
	Consistencies of individual DNA base-amino acid interactions in structures and sequences. [My Copy] Nucleic Acids Res, Vol. 23, No. 22. (25 November 1995), pp. 4707-4711. by B. Lustig, R. L. Jernigan posted to dna_binding protein-dna_interaction protein_descriptors protein_structure by kaarsinogen on 2006-01-25 22:32:32 as
	A simple physical model for the prediction and design of protein-DNA interactions. [My Copy] J Mol Biol, Vol. 344, No. 1. (12 November 2004), pp. 59-70. by J. J. Havranek, C. M. Duarte, D. Baker posted to dna_binding protein-dna_interaction by kaarsinogen on 2006-01-25 22:25:52 as along with 2 people aalibes medic0747
	Identifying DNA-binding proteins using structural motifs and the electrostatic potential. [My Copy] Nucleic Acids Res, Vol. 32, No. 16. (2004), pp. 4732-4741. by H. P. Shanahan, M. A. Garcia, S. Jones, J. M. Thornton posted to electrostatic_potential protein-dna_interaction protein_structure by kaarsinogen on 2006-01-25 22:21:47 as along with 3 people sriram_s medic0747 ezralanglois
	Structural analysis of conserved base pairs in protein-DNA complexes. [My Copy] Nucleic Acids Res, Vol. 30, No. 7. (1 April 2002), pp. 1704-1711. by L. A. Mirny, M. S. Gelfand posted to protein-dna_interaction protein_structure by kaarsinogen on 2006-01-25 22:17:46 as
	Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. [My Copy] J Mol Biol, Vol. 311, No. 2. (10 August 2001), pp. 395-408. by P. Aloy, E. Querol, F. X. Aviles, M. J. Sternberg posted to docking protein-dna_interaction by kaarsinogen on 2006-01-25 22:14:43 as along with 6 people ramiro2k chrn bicko chad_davis sriram_s cjeans
	Global analysis of protein activities using proteome chips. [My Copy] Science (New York, N.Y.), Vol. 293, No. 5537. (14 September 2001), pp. 2101-2105. by H. Zhu, M. Bilgin, R. Bangham, et al.D. Hall, A. Casamayor, P. Bertone, N. Lan, R. Jansen, S. Bidlingmaier, T. Houfek, T. Mitchell, P. Miller, R. A. Dean, M. Gerstein, M. Snyder posted to dna_binding protein-dna_interaction protein_chips by kaarsinogen on 2006-01-23 19:46:22 as along with 2 people Buntworthy selrac
	Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites. [My Copy] Nat Biotechnol, Vol. 21, No. 4. (April 2003), pp. 435-439. by Z. S. Qin, L. A. McCue, W. Thompson, L. Mayerhofer, C. E. Lawrence, J. S. Liu posted to bayesian_network dna_binding protein-dna_interaction by kaarsinogen on 2005-11-11 20:05:51 as along with 3 people balajis nklee wenhan
	Annotating nucleic acid-binding function based on protein structure. [My Copy] J Mol Biol, Vol. 326, No. 4. (28 February 2003), pp. 1065-1079. by E. W. Stawiski, L. M. Gregoret, Y. Mandel-Gutfreund posted to dna_binding protein-dna_interaction by kaarsinogen on 2005-11-11 19:30:49 as along with 1 person marti
	rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation. [My Copy] Nucleic Acids Res, Vol. 31, No. 1. (1 January 2003), pp. 118-121. by J. V. Ponomarenko, T. I. Merkulova, G. V. Orlova, et al.O. N. Fokin, E. V. Gorshkova, A. S. Frolov, V. P. Valuev, M. P. Ponomarenko posted to dna_binding protein-dna_interaction transcription transcription_factor by kaarsinogen on 2005-10-14 20:57:18 as
	Correlated Evolutionary Pressure at Interacting Transcription Factors and DNA Response Elements Can Guide the Rational Engineering of DNA Binding Specificity [My Copy] Journal of Molecular Biology, Vol. 350, No. 3. (15 July 2005), pp. 402-415. by Michele Raviscioni, Peili Gu, Minawar Sattar, Austin J. Cooney, Olivier Lichtarge posted to 2005_2006_dnabp dna_binding evolution protein-dna_interaction by kaarsinogen on 2005-09-23 18:42:10 as along with 4 people mdimmic chrn lulab cjeans
	Automatic methods for predicting functionally important residues. [My Copy] J Mol Biol, Vol. 326, No. 4. (28 February 2003), pp. 1289-1302. by A. del Sol Mesa, F. Pazos, A. Valencia posted to protein-dna_interaction by kaarsinogen on 2005-09-12 19:34:11 as along with 2 people nickolay tjimenez

Note: You may cite this page as: http://www.citeulike.org/tag/protein-dna_interaction

Result page: 1 2 Next

dna_binding	39
transcription_factor	15
protein_structure	12
genome	8
2005_2006_dnabp	7
gene_regulation	5
e_coli	4
docking	3
machine_learning	3
p53	3
protein_descriptors	3
evolution	2
file-import-09-06-23	2
protein-rna	2
svm	2
bayesian_network	1
electrostatic_potential	1
entropy	1
hydrogen_bonding	1
neural_network	1
protein_chips	1
pssm	1
sequence_alignment	1
signaling_pathways	1
transcription	1

Tag protein-dna_interaction [55 articles] Export

Related Tags