hryk's library 167 articles Export

	Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. [My Copy] Genome research (13 October 2009) by Gemma C. Langridge, Minh-Duy D. Phan, Daniel J. Turner, et al.Timothy T. Perkins, Leopold Parts, Jana Haase, Ian Charles, Duncan J. Maskell, Sarah E. Peters, Gordon Dougan, John Wain, Julian Parkhill, A. Keith Turner posted to transposon_insertion salmonella_typhi essential by hryk on 2009-11-09 15:55:13 as along with 2 people Annab jjturner
	An aPKC-Exocyst Complex Controls Paxillin Phosphorylation and Migration through Localised JNK1 Activation [My Copy] PLoS Biol, Vol. 7, No. 11. (3 November 2009), e1000235. by Carine Rosse, Etienne Formstecher, Katrina Boeckeler, et al.Yingming Zhao, Joachim Kremerskothen, Michael D. White, Jacques H. Camonis, Peter J. Parker posted to protein-structure programming molecular_dynamics maximum-likelifood by hryk on 2009-11-06 09:15:04 as along with 1 person renatomilani
	Structure of IL-33 and Its Interaction with the ST2 and IL-1RAcP ReceptorsInsight into Heterotrimeric IL-1 Signaling Complexes [My Copy] Vol. 17, No. 10. (14 October 2009), pp. 1398-1410. by Andreas Lingel, Thomas M. Weiss, Marc Niebuhr, et al.Borlan Pan, Brent A. Appleton, Christian Wiesmann, J. Fernando Bazan, Wayne J. Fairbrother posted to protein_structure il-1 cytokine by hryk on 2009-10-24 09:31:56 as
	Protein-binding site prediction based on three-dimensional protein modeling [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 77, No. S9. (2009), pp. 152-156. by Mina Oh, Keehyoung Joo, Jooyoung Lee posted to protein_structure prediction model ligand_binding casp by hryk on 2009-10-24 09:07:00 as along with 2 people and 1 group AliC reyez Orengo Group Journal Picks
	Dynamic interactions of proteins in complex networks: a more structured view [My Copy] FEBS Journal, Vol. 276, No. 19. (2009), pp. 5390-5405. by Amelie Stein, Roland A. Pache, Pau Bernadó, Miquel Pons, Patrick Aloy posted to protein-structure by hryk on 2009-10-21 12:11:38 as
	The structural analysis of protein-protein interactions by NMR spectroscopy [My Copy] PROTEOMICS, Vol. 9999, No. 999A. (2009), NA. by Mitchell R. O' Connell, Roland Gamsjaeger, Joel P. Mackay posted to ppi nmr by hryk on 2009-10-20 03:21:49 as
	Three-dimensional computation of atom depth in complex molecular structures [My Copy] Bioinformatics, Vol. 21, No. 12. (15 June 2005), pp. 2856-2860. by Daniele Varrazzo, Andrea Bernini, Ottavia Spiga, et al.Arianna Ciutti, Stefano Chiellini, Vincenzo Venditti, Luisa Bracci, Neri Niccolai posted to software protein_structures atom_depth accessible_surface_area by hryk on 2009-10-17 05:57:54 as
	Quantifying the relationship of protein burying depth and sequence [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 70, No. 2. (2008), pp. 509-516. by Zheng Yuan, Zhi-Xin Wang posted to solvent_accessible_surface protein_surface protein_structures accessible_surface_area by hryk on 2009-10-17 05:52:49 as
	Atom Depth as a Descriptor of the Protein Interior [My Copy] Biophysical Journal, Vol. 84, No. 4. (April 2003), pp. 2553-2561. by A. Pintar posted to protein_structures dpx atoms by hryk on 2009-10-17 05:42:34 as
	Predicting protein-protein binding sites in membrane proteins. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (2009), 312. by Andrew J. Bordner posted to prediction ppi by hryk on 2009-10-13 03:19:44 as along with 4 people and 1 group sillitoe niallhaslam reyez neils Orengo Group Journal Picks
	Enumeration of condition-dependent dense modules in protein interaction networks [My Copy] Bioinformatics, Vol. 25, No. 7. (1 April 2009), pp. 933-940. by Elisabeth Georgii, Sabine Dietmann, Takeaki Uno, Philipp Pagel, Koji Tsuda posted to protein_interaction network clustering by hryk on 2009-09-30 09:11:32 as along with 5 people carlk eesruiz imina grahamc mhamada
	A simple method for displaying the hydropathic character of a protein. [My Copy] Journal of molecular biology, Vol. 157, No. 1. (5 May 1982), pp. 105-132. by J. Kyte, R. F. Doolittle posted to hydrophobicity protein-structure by hryk on 2009-07-10 15:57:42 as along with 8 people barmak7282 thaliana chad_davis dgront medic0747 ashaytan Ema bicko
	Prediction of protein antigenic determinants from amino acid sequences [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 78, No. 6. (June 1981), pp. 3824-3828. by T. P. Hopp, K. R. Woods posted to hydrophobicity protein-structure by hryk on 2009-07-10 15:49:45 as along with 1 person ashaytan
	MAFFT version 5: improvement in accuracy of multiple sequence alignment. [My Copy] Nucleic acids research, Vol. 33, No. 2. (2005), pp. 511-518. by K. Katoh, K. Kuma, H. Toh, T. Miyata posted to alignment bioinformatics by hryk on 2009-06-30 01:38:20 as along with 8 people and 1 group BioNica druvus treangen CharlesM caporaso rabio timflutre urgi biomedical-nlp
	Rose: generating sequence families. [My Copy] Bioinformatics (Oxford, England), Vol. 14, No. 2. (1 March 1998), pp. 157-163. by J. Stoye, D. Evers, F. Meyer posted to bioinformatics model phylogenetic by hryk on 2009-06-29 22:47:54 as along with 3 people and 1 group djkt gjuggler adijr iSEEM
	MUSCLE: a multiple sequence alignment method with reduced time and space complexity [My Copy] BMC Bioinformatics, Vol. 5, No. 1. (19 August 2004), 113. by Robert Edgar posted to alignment bioinformatics by hryk on 2009-06-29 22:21:03 as along with 29 people and 5 groups rneches gwallau OscarLopez ivanffcc Helenita Joaquin kmma13 khlevy Pal tomjad mgomes BioNica natstreet Md_2007 sebk wallacei knaseanka chrn jwm balajis gbart caporaso sriram_s cdallett sanchezbuelna timflutre gisle urgi Ema LabDros References for 3DSim paper Radiation_Damage Stressosome biomedical-nlp
	RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models [My Copy] Bioinformatics, Vol. 22, No. 21. (1 November 2006), pp. 2688-2690. by Alexandros Stamatakis posted to bioinformatics maximum-likelifood phylogenetic by hryk on 2009-06-29 19:55:05 as along with 7 people operon jpsullivan anisbet aprasad druvus johanviklund dmp
	Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees [My Copy] Science, Vol. 324, No. 5934. (19 June 2009), pp. 1561-1564. by Kevin Liu, Sindhu Raghavan, Serita Nelesen, C. Randal Linder, Tandy Warnow posted to alignment bioinformatics phylogenetic-tree by hryk on 2009-06-26 13:54:38 as along with 26 people and 4 groups gjuggler parnell kinestetika robertrentzsch xianjun gdb jbhiatt stajich operon biomcgary kieran101 zwang michaelbarton vingron tatman303 lizbiogen pkonings ppgardne dokky aprasad timflutre inquil TRHvidsten djkt fenghezi phoenixzxl Orengo Group Journal Picks Mycology Journal picks iSEEM
	DisProt: the Database of Disordered Proteins. [My Copy] Nucleic acids research, Vol. 35, No. Database issue. (January 2007), pp. D786-D793. by Megan Sickmeier, Justin A. Hamilton, Tanguy LeGall, et al.Vladimir Vacic, Marc S. Cortese, Agnes Tantos, Beata Szabo, Peter Tompa, Jake Chen, Vladimir N. Uversky, Zoran Obradovic, A. Keith Dunker posted to disorder protein-structure by hryk on 2009-06-26 12:56:38 as along with 2 people pablocarb robfsouza
	Prediction of disordered regions in proteins from position specific score matrices. [My Copy] Proteins, Vol. 53 Suppl 6 (2003), pp. 573-578. by D. T. Jones, J. J. Ward posted to disorder protein-structure by hryk on 2009-06-26 12:55:13 as along with 2 people pablocarb chad_davis
	Statistical analysis of protein kinase specificity determinants. [My Copy] FEBS letters, Vol. 430, No. 1-2. (23 June 1998), pp. 45-50. by A. Kreegipuu, N. Blom, S. Brunak, J. Järv posted to phosphorylation protein structure by hryk on 2009-06-25 14:39:16 as
	Use of an oriented peptide library to determine the optimal substrates of protein kinases. [My Copy] Curr Biol, Vol. 4, No. 11. (1 November 1994), pp. 973-982. by Z. Songyang, S. Blechner, N. Hoagland, M. F. Hoekstra, H. Piwnica-Worms, L. C. Cantley posted to phosphorylation protein structure by hryk on 2009-06-25 14:37:26 as along with 1 person mloewer
	Assessment of disorder predictions in CASP7. [My Copy] Proteins, Vol. 69 Suppl 8 (6 August 2007), pp. 129-136. by Lorenza Bordoli, Florian Kiefer, Torsten Schwede posted to protein- by hryk on 2009-06-21 20:21:33 as
	Power and Centrality: A Family of Measures [My Copy] The American Journal of Sociology, Vol. 92, No. 5. (March 1987), pp. 1170-1182. by Phillip Bonacich posted to algorithm network by hryk on 2009-06-15 17:43:12 as along with 7 people and 2 groups rumi_ghosh krisl nkorf ddahlem bigbossman merazzle hannu Semantic-Social-Networks ThinkTank
	Correlated Mutation Analysis on the Catalytic Domains of Serine/Threonine Protein Kinases [My Copy] PLoS ONE, Vol. 4, No. 6. (15 June 2009), e5913. by Feng Xu, Pan Du, Hongbo Shen, et al.Hairong Hu, Qi Wu, Jun Xie, Long Yu posted to no-tag by hryk on 2009-06-15 16:27:40 as along with 3 people qluo sobolevnrm dimka
	Proteome-wide Prediction of Signal Flow Direction in Protein Interaction Networks Based on Interacting Domains [My Copy] Mol Cell Proteomics, Vol. 8, No. 9. (1 September 2009), pp. 2063-2070. by Wei Liu, Dong Li, Jian Wang, Hongwei Xie, Yunping Zhu, Fuchu He posted to interaction ppi by hryk on 2009-06-08 18:29:46 as along with 1 person brianb
	SpaK/SpaR Two-component System Characterized by a Structure-driven Domain-fusion Method and <italic>in Vitro</italic> Phosphorylation Studies [My Copy] PLoS Comput Biol, Vol. 5, No. 6. (5 June 2009), e1000401. by Anu Chakicherla, Ecale, Martha L. Dang, Virginia Rodriguez, Norman J. Hansen, Adam Zemla posted to domain_fusion phosphorylation protein structure by hryk on 2009-06-08 15:49:41 as
	Prediction of Protein Binding Regions in Disordered Proteins [My Copy] PLoS Comput Biol, Vol. 5, No. 5. (1 May 2009), e1000376. by Bálint Mészáros, István Simon, Zsuzsanna Dosztányi posted to protein structure by hryk on 2009-06-08 15:21:15 as along with 3 people and 1 group kiekyon CorinYeats niallhaslam Orengo Group Journal Picks
	Structural Bioinformatics-Based Prediction of Exceptional Selectivity of p38 MAP Kinase Inhibitor PH-797804. [My Copy] Biochemistry (4 June 2009) by Li Xing, Huey S. Shieh, Shaun R. Selness, et al.Rajesh V. Devraj, John K. Walker, Balekudru Devadas, Heidi R. Hope, Robert P. Compton, John F. Schindler, Jeffrey L. Hirsch, Alan G. Benson, Ravi G. Kurumbail, Roderick A. Stegeman, Jennifer M. Williams, Richard M. Broadus, Zara Walden, Joseph B. Monahan posted to phosphorylation protein structure by hryk on 2009-06-08 08:55:31 as
	The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value. [My Copy] Comput Appl Biosci, Vol. 12, No. 6. (December 1996), pp. 525-529. by R. W. Hooft, C. Sander, M. Scharf, G. Vriend posted to no-tag by hryk on 2009-06-08 07:22:51 as
	F²Dock: Fast Fourier Protein-Protein Docking [My Copy] IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 99, No. 1. (5555) by Chandrajit L. Bajaj, Rezaul Chowdhury, Vinay Siddahanavalli posted to protein software structure by hryk on 2009-06-05 13:55:39 as
	Structural modes of stabilization of permissive phosphorylation sites in protein kinases: distinct strategies in Ser/Thr and Tyr kinases. [My Copy] Journal of molecular biology, Vol. 339, No. 5. (18 June 2004), pp. 1025-1039. by A. Krupa, G. Preethi, N. Srinivasan posted to phosphorylation review structure by hryk on 2009-06-05 10:35:53 as
	Structural instability in an autophosphorylating kinase switch [My Copy] Mathematical Biosciences, Vol. 219, No. 2. (June 2009), pp. 92-96. by Michael Grinfeld, Steven D. Webb posted to phosphorylation structure by hryk on 2009-06-05 10:33:41 as
	Tyrosine phosphorylation in plant cell signaling. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 18. (3 September 2002), pp. 11567-11569. by S. Luan posted to ebi phosphorylation by hryk on 2009-06-02 10:54:36 as
	Kinomer v. 1.0: a database of systematically classified eukaryotic protein kinases [My Copy] Nucl. Acids Res., Vol. 37, No. suppl_1. (1 January 2009), pp. D244-250. by David M. A. Martin, Diego Miranda-Saavedra, Geoffrey J. Barton posted to ebi phosphorylation by hryk on 2009-06-02 07:48:07 as along with 3 people lptolik guhjy renatomilani
	Kinase-specific prediction of protein phosphorylation sites. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 527 (2009) by M. L. Miller, N. Blom posted to ebi must phosphorylation by hryk on 2009-06-02 07:34:11 as along with 2 people niallhaslam kgutwin
	Phosphotyrosine-binding domains in signal transduction. [My Copy] Nature reviews. Molecular cell biology, Vol. 3, No. 3. (March 2002), pp. 177-186. by M. B. Yaffe posted to ebi phosphorylation review by hryk on 2009-06-02 07:28:48 as
	Global and site-specific quantitative phosphoproteomics: principles and applications. [My Copy] Annual review of pharmacology and toxicology, Vol. 49 (3 October 2009), pp. 199-221. by Boris Macek, Matthias Mann, Jesper V. Olsen posted to ebi phosphorylation by hryk on 2009-06-02 07:24:17 as along with 1 person guhjy
	A helix scaffold for the assembly of active protein kinases [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 38. (2008), pp. 14377-14382. by Alexandr P. Kornev, Susan S. Taylor, Ten posted to ebi phosphorylation by hryk on 2009-06-02 07:22:29 as along with 1 person renatomilani
	A curated compendium of phosphorylation motifs [My Copy] Nature Biotechnology, Vol. 25, No. 3., pp. 285-286. by Ramars Amanchy, Balamurugan Periaswamy, Suresh Mathivanan, Raghunath Reddy, Sudhir G. Tattikota, Akhilesh Pandey posted to ebi phosphorylation by hryk on 2009-06-02 07:22:17 as along with 5 people coela neils cjeans alwinpremanand Evangelia
	Linking the kinome and phosphorylome--a comprehensive review of approaches to find kinase targets. [My Copy] Molecular bioSystems, Vol. 4, No. 9. (September 2008), pp. 920-933. by Richelle Sopko, Brenda J. Andrews posted to ebi phosphorylation review by hryk on 2009-06-02 07:21:34 as along with 3 people nzm oelemento guhjy
	Large-scale identification and evolution indexing of tyrosine phosphorylation sites from murine brain. [My Copy] Journal of proteome research, Vol. 7, No. 1. (January 2008), pp. 311-318. by B. A. Ballif, G. R. Carey, S. R. Sunyaev, S. P. Gygi posted to ebi phosphorylation by hryk on 2009-06-02 07:20:43 as
	[A motif-based scanning approach for prediction of protein phosphorylation] [My Copy] Sheng wu gong cheng xue bao = Chinese journal of biotechnology, Vol. 20, No. 4. (July 2004), pp. 623-626. by Y. Tang, L. Q. Zhang, F. C. He posted to ebi phosphorylation by hryk on 2009-06-02 07:20:29 as
	Protein phosphorylation in signaling – 50 years and counting [My Copy] Trends in Biochemical Sciences, Vol. 30, No. 6. (June 2005), pp. 286-290. by Tony Pawson, John D. Scott posted to ebi phosphorylation review by hryk on 2009-06-02 07:20:08 as along with 2 people saradtc guhjy
	A lock on phosphotyrosine signaling. [My Copy] ACS chemical biology, Vol. 2, No. 7. (20 July 2007), pp. 454-456. by K. E. Muratore, P. A. Cole posted to ebi phosphorylation by hryk on 2009-06-02 07:19:41 as
	PepCyber:P~PEP: a database of human protein protein interactions mediated by phosphoprotein-binding domains. [My Copy] Nucleic acids research, Vol. 36, No. Database issue. (January 2008) by W. Gong, D. Zhou, Y. Ren, et al.Y. Wang, Z. Zuo, Y. Shen, F. Xiao, Q. Zhu, A. Hong, X. Zhou, X. Gao, T. Li posted to database ebi phosphorylation by hryk on 2009-06-02 07:19:16 as along with 2 people renatomilani guhjy
	Mechanisms of specificity in protein phosphorylation [My Copy] Nature Reviews Molecular Cell Biology, Vol. 8, No. 7. (01 July 2007), pp. 530-541. by Jeffrey A. Ubersax, James E. Ferrell Jr posted to ebi phosphorylation review by hryk on 2009-06-02 07:18:59 as along with 6 people and 2 groups kokphinchooi coela guhjy dchughes Evangelia oelemento G4ID Genetics-of-Gambling
	Immunoreceptor tyrosine-based inhibition motifs: a quest in the past and future [My Copy] Immunological Reviews, Vol. 224, No. 1. (August 2008), pp. 11-43. by Daeron, Marc, Jaeger, et al. Sebastien, Du Pasquier, Louis, Vivier, Eric posted to phosphorylation review by hryk on 2009-06-02 07:18:41 as
	Large-scale phosphorylation analysis of mouse liver. [My Copy] Proc Natl Acad Sci U S A, Vol. 104, No. 5. (30 January 2007), pp. 1488-1493. by J. Villén, S. A. Beausoleil, S. A. Gerber, S. P. Gygi posted to ebi phosphorylation by hryk on 2009-06-02 07:18:25 as along with 2 people renatomilani guhjy
	PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database [My Copy] Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i14-20. by Chia-Ying Yang, Chao-Hui Chang, Ya-Ling Yu, et al.Tsu-Chun E. Lin, Sheng-An Lee, Chueh-Chuan Yen, Jinn-Moon Yang, Jin-Mei Lai, Yi-Ren Hong, Tzu-Ling Tseng, Kun-Mao Chao, Chi-Ying F. Huang posted to database phosphorylation by hryk on 2009-06-02 07:18:08 as along with 5 people guhjy Yanno renatomilani neils brianb

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phosphorylation	47
ebi	35
network	35
protein-structure	33
protein_asa_set	13
metabolic	12
essential	11
structure	11
bioinformatics	8
review	8
ppi	7
pathway	6
protein	6
software	6
yeast	6
ecoli	5
prediction	5
tool	5
evolution	4
visualize	4
algorithm	3
alignment	3
cluster	3
database	3
gene	3
model	3
protein_structures	3
topology	3
accessible_surface_area	2
analysis	2
bacillus	2
disorder	2
game	2
graph	2
hydrophobicity	2
interaction	2
maximum-likelifood	2
molecular_dynamics	2
phylogenetic	2
programming	2
protein_structure	2
signaling	2
3d	1
atom_depth	1
atoms	1
betweeness	1
casp	1
clustering	1
construction	1
cytokine	1
domain	1
domain_fusion	1
dpx	1
egfr	1
genetic_interaction	1
gnutella	1
grid	1
hiv	1
il-1	1
imaging	1
informatics	1
inheritance	1
language	1
ligand_binding	1
mashup	1
method	1
multiple-knockout	1
must	1
nmr	1
phylogenetic-tree	1
protein-	1
protein_interaction	1
protein_surface	1
regulatory	1
robustness	1
saccharomyces	1
salmonella_typhi	1
solvent_accessible_surface	1
synthetic	1
transcript	1
transposon_insertion	1
virus	1
webservice	1

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