Tag binding-site [37 articles] Export

Recent papers classified by the tag binding-site.

	Exhaustive search for over-represented DNA sequence motifs with CisFinder. [My Copy] DNA research : an international journal for rapid publication of reports on genes and genomes, Vol. 16, No. 5. (9 October 2009), pp. 261-273. by Alexei A. Sharov, Minoru S. Ko posted to word transcription-factor tf motif k-word ctcf consensus binding-site binding-motif binding by sebastien_vigneau to the group CTCF on 2009-10-28 22:59:36 as along with 2 people and 1 group operon polivares BergmanLab
	LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation [My Copy] BMC Structural Biology, Vol. 6, No. 1. (24 September 2006), 19. by Bingding Huang, Michael Schroeder posted to surface binding-site by superpyrin on 2009-08-24 08:41:23 as along with 6 people tomjad iaolier richardbickerton reyez tjimenez nickolay
	The josephin domain of ataxin-3 contains two distinct ubiquitin binding sites [My Copy] Biopolymers, Vol. 9999, No. 9999. (2009), NA. by Giuseppe Nicastro, Laura Masino, Veronica Esposito, et al.Rajesh P. Menon, Alfonso De Simone, Franca Fraternali, Annalisa Pastore posted to binding-site by carlosjavierna on 2009-08-05 06:39:19 as
	BSAlign: a rapid graph-based algorithm for detecting ligand-binding sites in protein structures. [My Copy] Genome informatics. International Conference on Genome Informatics, Vol. 21 (2008), pp. 65-76. by Zeyar Aung, Joo Chuan C. Tong posted to binding-site compare by dimka on 2009-07-30 18:12:55 as
	An A257V mutation in the Bacillus subtilis response regulator Spo0A prevents regulated expression of promoters with low consensus binding sites [My Copy] J. Bacteriol. (6 July 2009), JB.00590-09. by Steve D. Seredick, Barbara M. Seredick, David Baker, George B. Spiegelman posted to ala alanine binding-site binding-sites molecular-recognition mutagenesis val valine by carlosjavierna on 2009-07-08 17:54:52 as
	DNA binding site sequence directs glucocorticoid receptor structure and activity. [My Copy] Science (New York, N.Y.), Vol. 324, No. 5925. (17 April 2009), pp. 407-410. by Sebastiaan H. Meijsing, Miles A. Pufall, Alex Y. So, Darren L. Bates, Lin Chen, Keith R. Yamamoto posted to binding-site glucocorticoid-receptor gr by sebastien_vigneau on 2009-06-29 21:59:32 as along with 7 people and 1 group Annab JustinCrocker fenghezi absterga bpcusack jbhiatt djkt BenosLab
	Enhanced position weight matrices using mixture models. [My Copy] Bioinformatics (Oxford, England), Vol. 21 Suppl 1 (June 2005) by S. Hannenhalli, L. S. Wang posted to binding-motif binding-site positional-weight-matrix pwm subclass by sebastien_vigneau on 2009-06-29 21:57:20 as
	Critical DNA binding interactions of the insulator protein CTCF: a small number of zinc fingers mediate strong binding, and a single finger-DNA interaction controls binding at imprinted loci. [My Copy] The Journal of biological chemistry, Vol. 282, No. 46. (16 November 2007), pp. 33336-33345. by M. Renda, I. Baglivo, B. Burgess-Beusse, et al.S. Esposito, R. Fattorusso, G. Felsenfeld, P. V. Pedone posted to affinity assymetry binding binding-site cpg cpg-methylation ctcf dna-methylation h19 igf2 methylation orientation zing-finger by sebastien_vigneau to the group CTCF on 2009-06-18 23:25:55 as along with 1 person clearbluespring
	Fpocket: An open source platform for ligand pocket detection [My Copy] BMC Bioinformatics, Vol. 10 (02 June 2009), 168. by Vincent Le Guilloux, Peter Schmidtke, Pierre Tuffery posted to binding-site by superpyrin on 2009-06-07 13:35:05 as along with 2 people sobolevnrm reyez
	Using directed evolution to probe the substrate specificity of mandelamide hydrolase [My Copy] Protein Engineering, Design and Selection, Vol. 22, No. 2. (1 February 2009), pp. 103-110. by Pan-Fen Wang, Alejandra Yep, George L. Kenyon, Michael J. Mcleish posted to binding-site directed-evolution evolution protein protein-structure specificity by pauldobson on 2009-03-25 09:57:22 as
	Predicting undesirable drug interactions with promiscuous proteins in silico [My Copy] Drug Discovery Today, Vol. 9, No. 6. (15 March 2004), pp. 276-285. by S. Ekins posted to binding-site cheminformatics drug drug-binding promiscuity protein by pauldobson on 2009-03-15 23:19:17 as along with 4 people pablocarb kuhn tomb girschick
	SuperPred: drug classification and target prediction. [My Copy] Nucleic acids research, Vol. 36, No. Web Server issue. (1 July 2008) by M. Dunkel, S. Günther, J. Ahmed, B. Wittig, R. Preissner posted to binding-site bioinformatics cheminformatics drug drug-binding machine-learning protein protein-function protein-structure by pauldobson on 2009-03-15 23:16:10 as along with 2 people reyez massivemayhem
	PocketMatch: A new algorithm to compare binding sites in protein structures [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008), 543. by Kalidas Yeturu, Nagasuma Chandra posted to binding-site bioinformatics cheminformatics drug drug-binding enzyme protein protein-function protein-structure by pauldobson on 2009-03-15 23:10:36 as along with 9 people and 1 group cdsouthan nanonan sobolevnrm jteyra kshameer reyez tny higueruelo druvus baker-group
	Computational Fragment-Based Approach at PDB Scale by Protein Local Similarity [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Fabrice Moriaud, Olivia Doppelt-Azeroual, Laetitia Martin, et al.Ksenia Oguievetskaia, Kerstin Koch, Artem Vorotyntsev, Stewart A. Adcock, François Delfaud posted to binding-site binding-sites by carlosjavierna on 2009-02-23 02:36:19 as along with 1 person sschurer
	Identifying and Characterizing Binding Sites and Assessing Druggability [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 2. (23 February 2009), pp. 377-389. by Thomas A. Halgren posted to binding-site by carlosjavierna on 2009-02-22 04:22:37 as along with 4 people and 1 group nickolay richardbickerton TonyIvetac timg McCammon
	Interfacial Properties of a Complex Multi-Domain 490 Amino Acid Peptide Derived from Apolipoprotein B (Residues 292−782) [My Copy] Langmuir, Vol. 25, No. 4. (17 February 2009), pp. 2322-2330. by Matthew A. Mitsche, Libo Wang, Gordon Z. Jiang, James C. Mcknight, Donald M. Small posted to alpha-helix beta-sheet beta-turn binding-mode binding-site by carlosjavierna on 2009-02-21 14:10:06 as
	Delineation of Alternative Conformational States in Escherichia coli Peptide Deformylase via Thermodynamic Studies for the Binding of Actinonin† [My Copy] Biochemistry, Vol. 48, No. 7. (24 February 2009), pp. 1584-1594. by Alexander K. Berg, D. K. Srivastava posted to binding binding-site conformational-states thermodynamic-studies by carlosjavierna on 2009-02-19 14:59:48 as
	Methylation and deamination of CpGs generate p53-binding sites on a genomic scale [My Copy] Trends in Genetics, Vol. 25, No. 2. (February 2009), pp. 63-66. by Tomasz Zemojtel, Szymon M. Kielbasa, Peter F. Arndt, Ho-Ryun Chung, Martin Vingron posted to binding-site cpg deamination dna-methylation mutation p53 review by rschulz on 2009-02-13 16:22:47 as along with 1 person djkt
	YY1's longer DNA-binding motifs. [My Copy] Genomics, Vol. 93, No. 2. (February 2009), pp. 152-158. by Jeong do Kim, Joomyeong Kim posted to binding-site imprinting inactivation peg3 x-chromosome xist yy1 by sebastien_vigneau to the group X-chromosome inactivation on 2009-02-11 20:45:14 as along with 2 people and 2 groups agonzale absterga Imprinting Epigenetics
	Analysis of combinatorial cis-regulation in synthetic and genomic promoters [My Copy] Nature, Vol. 457, No. 7226. (23 November 2008), pp. 215-218. by Jason Gertz, Eric D. Siggia, Barak A. Cohen posted to binding-site promoter transcription-factor by sebastien_vigneau on 2009-01-08 21:51:55 as along with 17 people and 4 groups Vincent_Rouilly pcarbo emptyhb TRHvidsten rpatward jbhiatt lusk maximilianh roys dpollard druvus pengchy sandersl djkt siebert isimpson xianjun TranscriptionalRegulationWithThermodynamicModels RockmanLab cis-regulatory-evolution microbiology_nijmegen
	Modeling ChIP Sequencing In Silico with Applications [My Copy] PLoS Comput Biol, Vol. 4, No. 8. (22 August 2008), e1000158. by Zhengdong D. Zhang, Joel Rozowsky, Michael Snyder, Joseph Chang, Mark Gerstein posted to background binding-site chip-seq deep-seq prediction simulation stats-model transcription-factor by rschulz on 2008-12-06 10:58:45 as along with 10 people ewilban1 cassj WanderingAengus inesdesantiago aramesh2 djkt kengg Stew gdb caseybrown
	MSDmotif: exploring protein sites and motifs [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008), 312. by Adel Golovin, Kim Henrick posted to binding-site motifs by massivemayhem on 2008-07-21 11:32:41 as along with 6 people pansapiens HawkinsJohnC tjimenez reyez chad_davis Evangelia
	MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions. [My Copy] Nucleic Acids Res, Vol. 36 (8 May 2008), pp. 260-264. by Alexandra Shulman-Peleg, Maxim Shatsky, Ruth Nussinov, Haim J. J. Wolfson posted to binding-site by massivemayhem on 2008-06-11 14:24:40 as along with 2 people higueruelo reyez
	A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships. [My Copy] J Chem Inf Model, Vol. 46, No. 2. (r 2006), pp. 736-742. by N. D. Gold, R. M. Jackson posted to binding-site protein-ligand by massivemayhem on 2008-06-11 13:15:21 as along with 4 people and 1 group medic0747 caporaso blackbart reyez biomedical-nlp
	Identification of amino acid residues contributing to the ATP-binding site of a purinergic P2X receptor. [My Copy] J Biol Chem, Vol. 275, No. 44. (3 November 2000), pp. 34190-34196. by L. H. Jiang, F. Rassendren, A. Surprenant, R. A. North posted to binding-site p2x by Guerlet on 2008-02-21 16:15:49 as along with 1 person aspecht
	Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. [My Copy] EMBO J, Vol. 1, No. 8. (1982), pp. 945-951. by J. E. Walker, M. Saraste, M. J. Runswick, N. J. Gay posted to binding-site myosin by yalexeev on 2008-02-20 15:19:27 as along with 1 person laurabailey
	LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins [My Copy] Journal of Molecular Graphics and Modelling, Vol. 15, No. 6. (December 1997), pp. 359-363. by Manfred Hendlich, Friedrich Rippmann, Gerhard Barnickel posted to binding-site by massivemayhem on 2008-02-07 17:24:12 as along with 2 people tomjad trmr
	Fast prediction and visualization of protein binding pockets with PASS [My Copy] Journal of Computer-Aided Molecular Design, Vol. 14, No. 4. (1 May 2000), pp. 383-401. by Patrick G. Brady, Pieter F. Stouten posted to algorithm binding-site by massivemayhem on 2008-02-07 11:36:04 as
	A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology [My Copy] Journal of Molecular Biology, Vol. 323, No. 2. (18 October 2002), pp. 387-406. by Stefan Schmitt, Daniel Kuhn, Gerhard Klebe posted to binding-site ligands by massivemayhem on 2008-02-07 10:28:07 as
	Method for comparing the structures of protein ligand-binding sites and application for predicting protein-drug interactions [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA. by Ryoichi Minai, Yo Matsuo, Hiroyuki Onuki, Hiroshi Hirota posted to binding-site database prediction protein-drug protein-ligand by massivemayhem on 2008-01-24 12:06:30 as along with 6 people reyez ramensky tjimenez jteyra mingzhi higueruelo
	Divergence of Transcription Factor Binding Sites Across Related Yeast Species [My Copy] Science, Vol. 317, No. 5839. (10 August 2007), pp. 815-819. by Anthony R. Borneman, Tara A. Gianoulis, Zhengdong D. Zhang, et al.Haiyuan Yu, Joel Rozowsky, Michael R. Seringhaus, Lu Y. Wang, Mark Gerstein, Michael Snyder posted to binding-site divergence yeast by sujaikumar on 2007-08-17 08:16:06 as along with 22 people and 2 groups pradiptaray gdb fenghezi dbensasson caseybrown bryankr aalibes chad_davis dpollard djkt mikaelhuss lusk cjeans zwang GustavoLacerda Jporci maximilianh cisevol njcitulike emptyhb nklee anka EisenLab cis-regulatory-evolution
	How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding. [My Copy] J Mol Biol (29 September 2006) by Kannan Gunasekaran, Ruth Nussinov posted to flexibility-descriptor binding-site by dgruiz on 2007-01-18 12:20:56 as along with 10 people and 1 group aqeel reyez BragilMassoud radestock lna yongzhao choonpeng weisblum higueruelo nickolay TSRI_MGL
	The Evolution of Word Composition in Metazoan Promoter Sequence [My Copy] PLoS Computational Biology, Vol. preprint, No. 2006. (1 September 2006) by Eliot C. Bush, Bruce T. Lahn posted to binding-site promoter by JAShapiro on 2006-10-05 18:48:05 as
	Ligand-induced changes in the binding sites of proteins. [My Copy] Bioinformatics, Vol. 18, No. 7. (July 2002), pp. 939-948. by X. Fradera, X. De La Cruz, C. H. Silva, J. L. Gelpí, F. J. Luque, M. Orozco posted to binding-site flexible-receptor by dgruiz on 2005-07-14 12:58:36 as along with 1 person blackbart
	Binding site characteristics in structure-based virtual screening: evaluation of current docking tools [My Copy] Journal of Molecular Modeling, Vol. 9, No. 1. (February 2003), pp. 47-57. by Tanja Schulz-Gasch, Martin Stahl posted to pl-docking docking-tools-evaluation binding-site by dgruiz on 2005-07-04 10:51:52 as along with 1 person LamBras
	Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis. [My Copy] Protein science : a publication of the Protein Society, Vol. 14, No. 4. (April 2005), pp. 1104-1114. by M. I. Zavodszky, L. A. Kuhn posted to pl-docking flexible-receptor docking-flexible binding-site by dgruiz on 2005-04-07 11:23:04 as along with 9 people and 2 groups fl ramensky BragilMassoud yongzhao nknii blackbart kazemi rsantana LamBras TCR_Signaling TSRI_MGL
	Testing a flexible-receptor docking algorithm in a model binding site. [My Copy] J Mol Biol, Vol. 337, No. 5. (9 April 2004), pp. 1161-1182. by B. Q. Wei, L. H. Weaver, A. M. Ferrari, B. W. Matthews, B. K. Shoichet posted to binding-site docking-flexible flexible-receptor by dgruiz on 2005-01-31 13:33:52 as along with 2 people apaydin blackbart

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binding	5
transcription-factor	5
ctcf	4
imprinting	4
inactivation	4
peg3	4
protein	4
protein-structure	4
x-chromosome	4
xist	4
yy1	4
binding-motif	3
cheminformatics	3
cpg	3
dna-methylation	3
drug	3
drug-binding	3
flexible-receptor	3
prediction	3
affinity	2
assymetry	2
background	2
binding-sites	2
bioinformatics	2
chip-seq	2
consensus	2
cpg-methylation	2
deep-seq	2
docking-flexible	2
h19	2
igf2	2
k-word	2
methylation	2
motif	2
orientation	2
pl-docking	2
promoter	2
protein-function	2
protein-ligand	2
simulation	2
stats-model	2
surface	2
tf	2
word	2
zing-finger	2
ala	1
alanine	1
algorithm	1
alpha-helix	1
beta-sheet	1
beta-turn	1
binding-mode	1
compare	1
conformational-states	1
database	1
deamination	1
directed-evolution	1
divergence	1
docking-tools-evaluation	1
enzyme	1
evolution	1
flexibility-descriptor	1
glucocorticoid-receptor	1
gr	1
ligands	1
machine-learning	1
molecular-recognition	1
motifs	1
mutagenesis	1
mutation	1
myosin	1
p2x	1
p53	1
positional-weight-matrix	1
promiscuity	1
protein-drug	1
pwm	1
review	1
specificity	1
subclass	1
thermodynamic-studies	1
val	1
valine	1
yeast	1

Tag binding-site [37 articles] Export

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