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Tag protein [954 articles]

Recent papers classified by the tag protein.
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  • A Feature-Based Approach to Modeling Protein–DNA Interactions
    PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000154.
    by Eilon Sharon, Shai Lubliner, Eran Segal
    posted to dna interaction protein by zwang on 2008-08-30 03:58:06 as ** along with 5 people ptrobajo dakelley Stew emptyhb aalibes
  • High-throughput identification of Interacting Protein-Protein Binding Sites
    BMC Bioinformatics, Vol. 8 (27 June 2007), 223.
    by Jo-Lan Chung, Wei Wang, Philip E Bourne
    posted to binding interaction prediction protein site svm by zwang on 2007-08-27 08:57:42 as ***** along with 3 people and 1 group bicko grahamc Evangelia ParkinsonLab_at_MaRS
  • Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps
    PLoS Computational Biology, Vol. preprint, No. 2007. (1 September 2007), e214.eor.
    by Hailiang Huang, Bruno Jedynak, Joel S Bader
    posted to genome-wide interaction protein y2h yeast by zwang on 2007-10-22 05:10:19 as ** along with 1 person roys
  • Co-evolution and co-adaptation in protein networks
    FEBS Letters, Vol. In Press, Uncorrected Proof
    by David Juan, Florencio Pazos, Alfonso Valencia
    posted to co-evolution network protein by zwang on 2008-02-22 13:06:04 as **** along with 2 people and 1 group phoenixzxl smgomez GomezLab
  • Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System
    PLoS Biology, Vol. 6, No. 10. (1 October 2008), e255.
    by Daniel J Hogan, Daniel P Riordan, André P Gerber, Daniel Herschlag, Patrick O Brown
    posted to rna protein interaction binding by zwang on 2008-11-03 09:12:42 as *** along with 4 people and 1 group kieran101 reyez stajich djkt Berkeley Mycology
  • A Bayesian Estimator of Protein-Protein Association Probabilities
    Bioinformatics (22 May 2008), btn238.
    by JM Gilmore, DL Auberry, JL Sharp, AM White, KK Anderson, DS Daly
    posted to bayesian interaction prediction protein by zwang on 2008-06-03 04:01:29 as ** along with 2 people guhjy renatomilani
  • Single-molecule analysis of DNA-protein complexes using nanopores
    Nature Methods, Vol. 4, No. 4. (04 March 2007), pp. 315-317.
    by Breton Hornblower, Amy Coombs, Richard D Whitaker, Anatoly Kolomeisky, Stephen J Picone, Amit Meller, Mark Akeson
    posted to complex dna nanopore protein singlemolecule by zwang on 2007-04-04 15:02:49 as *
  • Genome-Wide Mapping of in Vivo Protein-DNA Interactions
    Science (31 May 2007), 1141319.
    by David S Johnson, Ali Mortazavi, Richard M Myers, Barbara Wold
    posted to genome interaction protein rna by zwang on 2007-06-09 08:08:23 as **** along with 19 people and 5 groups jo_davies aalibes balicea andersbj JeremyZucker aswin kengg giovanni cjeans ghattem epigenetics biomcgary george_g cabbagezs Jporci blobbybirdman caseybrown emptyhb dquest Bioinformatics microRNA Marcotte_Lab UH - Computational Biology Myxo group
  • The Modular Organization of Domain Structures: Insights into Protein–Protein Binding
    PLoS Computational Biology, Vol. 3, No. 12. (1 December 2007), e239.
    by Del, Pablo Carbonell
    posted to binding domain protein structure by zwang on 2007-12-08 08:54:46 as ** along with 9 people bicko chad_davis choonpeng grahamc cjeans niallhaslam biehl marti carlk
  • De Novo Computational Design of Retro-Aldol Enzymes
    Science, Vol. 319, No. 5868. (7 March 2008), pp. 1387-1391.
    by Lin Jiang, Eric A Althoff, Fernando R Clemente, Lindsey Doyle, Daniela Rothlisberger, Alexandre Zanghellini, Jasmine L Gallaher, Jamie L Betker, Fujie Tanaka, Carlos F Barbas, Donald Hilvert, Kendall N Houk, Barry L Stoddard, David Baker
    posted to design prediction protein by zwang on 2008-03-07 03:02:39 as ** along with 13 people and 3 groups alexknight barry aalibes jwm aprasad dgront sobolevnrm davidlott msuarezdiez scienbox ucbcjbm joseph_x_zhou cambray structural_bioinformatics baker-group McCammon
  • Correlated evolution of interacting proteins: Looking behind the mirrortree
    Journal of Molecular Biology (09 October 2008)
    by M Kann, B Shoemaker, A Panchenko, T Przytycka
    posted to protein interaction co-evolution by zwang on 2008-12-30 06:07:02 as *** along with 3 people marti reyez paulschlesinger
  • The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics
    PLoS Computational Biology, Vol. 3, No. 4. (1 April 2007), e59.
    by Haiyuan Yu, Philip M Kim, Emmett Sprecher, Valery Trifonov, Mark Gerstein
    posted to dynamics network protein by zwang on 2007-04-28 12:38:55 as ** along with 5 people jiny jfr Takayuki hryk carlk
  • Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e178.
    by Ramon Aragues, Andrej Sali, Jaume Bonet, Marc A Marti-Renom, Baldo Oliva
    posted to hub interaction motif protein by zwang on 2007-11-02 08:03:44 as **** along with 1 person bicko
  • Molecular dynamics simulations of nucleic acid-protein complexes
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Mackerell, Lennart Nilsson
    posted to complex dna dynamics protein rna by zwang on 2008-02-27 02:28:21 as *** along with 3 people and 1 group ruvido sobolevnrm phoenixzxl baker-group
  • Structure-Templated Predictions of Novel Protein Interactions from Sequence Information
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e182.
    by Doron Betel, Kevin E Breitkreuz, Ruth Isserlin, Danielle Dewar-Darch, Mike Tyers, Christopher W Hogue
    posted to interaction prediction protein sequence structure by zwang on 2007-10-22 05:11:20 as **** along with 3 people agustinarce cjeans winterschlaefer
  • Community Proteomics of a Natural Microbial Biofilm
    Science, Vol. 308, No. 5730. (24 June 2005), pp. 1915-1920.
    by Rachna J Ram, Nathan C Verberkmoes, Michael P Thelen, Gene W Tyson, Brett J Baker, Robert C Blake, Manesh Shah, Robert L Hettich, Jillian F Banfield
    posted to protein by zwang on 2007-05-09 07:49:01 as * along with 5 people and 2 groups oamg jmeppley nitiniitk barberan BoranKartal Glimcher_Lab microbiology_nijmegen
  • Drug[mdash]target network
    Nat Biotech, Vol. 25, No. 10. (October 2007), pp. 1119-1126.
    by Muhammed A Yildirim, Kwang-Il Goh, Michael E Cusick, Albert-Laszlo Barabasi, Marc Vidal
    posted to interaction network protein by zwang on 2007-10-11 16:53:03 as ** along with 13 people and 1 group richardbickerton ramensky ptrobajo Yanno guhjy cannin jfr julius grahamc cjeans dejori mingzhi jerome_ucsf_slb libr
  • Predicting protein function from domain content
    Bioinformatics (30 June 2008), btn312.
    by Kristoffer Forslund, Erik L Sonnhammer
    posted to domain prediction protein by zwang on 2008-07-01 02:44:42 as *** along with 4 people saket druvus phoenixzxl reyez
  • Bayesian statistical analysis of protein side-chain rotamer preferences.
    Protein Sci, Vol. 6, No. 8. (August 1997), pp. 1661-1681.
    by RL Dunbrack, FE Cohen
    posted to bayesian protein by zwang on 2008-08-29 07:02:40 as ** along with 12 people and 2 groups karbak nknii j3xucite dgront blackbart kazemi rsantana hmk LamBras mijam jwm phoenixzxl MuraLab TCR_Signaling
  • Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast
    Mol Syst Biol, Vol. 3 (5 June 2007)
    by Ronish Gupta, Bart Kus, Christopher Fladd, James Wasmuth, Raffi Tonikian, Sachdev Sidhu, Nevan J Krogan, John Parkinson, Daniela Rotin
    posted to interaction microarray protein yeast by zwang on 2007-06-06 01:20:33 as **
  • Structure-based activity prediction for an enzyme of unknown function
    Nature (01 July 2007)
    by Johannes C Hermann, Ricardo Marti-Arbona, Alexander A Fedorov, Elena Fedorov, Steven C Almo, Brian K Shoichet, Frank M Raushel
    posted to function prediction protein structure by zwang on 2007-08-18 08:45:55 as *** along with 9 people operon tny ucbcjbm aheilbut tjimenez daevans pkolb kimicc ivke
  • Probabilistic prediction and ranking of human protein-protein interactions
    BMC Bioinformatics, Vol. 8 (05 July 2007), 239.
    by Michelle S Scott, Geoffrey J Barton
    posted to interaction prediction protein by zwang on 2007-07-13 17:19:17 as **** along with 4 people and 1 group cerca wnpx grahamc mingzhi ParkinsonLab_at_MaRS
  • An in Vivo Map of the Yeast Protein Interactome
    Science, Vol. 320, No. 5882. (13 June 2008), pp. 1465-1470.
    by Kirill Tarassov, Vincent Messier, Christian R Landry, Stevo Radinovic, Mercedes M Molina, Igor Shames, Yelena Malitskaya, Jackie Vogel, Howard Bussey, Stephen W Michnick
    posted to genome interaction protein yeast by zwang on 2008-06-27 03:58:03 as ** along with 5 people carlk thomaskelder Petersarkies renatomilani balicea
  • Analysis on multi-domain cooperation for predicting protein-protein interactions
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Rui S Wang, Yong Wang, Ling Y Wu, Xiang S Zhang, Luonan Chen
    posted to co-evolution domain interaction prediction protein by zwang on 2007-10-22 01:55:10 as *** along with 2 people guhjy phoenixzxl
  • Predicting Protein Function with Hierarchical Phylogenetic Profiles: The Gene3D Phylo-Tuner Method Applied to Eukaryotic Genomes
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e237.
    by Juan A Ranea, Corin Yeats, Alastair Grant, Christine A Orengo
    posted to eukaryota genome hierarchical phylogeny prediction protein by zwang on 2007-12-10 04:43:48 as *** along with 5 people and 1 group marti eckart_bindewald skhadar asddd hpaces Orengo Group functional genomics watchlist
  • False occurrences of functional motifs in protein sequences highlight evolutionary constraints
    BMC Bioinformatics, Vol. 8 (01 March 2007), 68.
    by Allegra Via, Pier F Gherardini, Enrico Ferraro, Gabriele Ausiello, Gianpaolo S Tomba, Manuela Helmer-Citterich
    posted to evolution motif protein by zwang on 2007-03-19 12:56:19 as ** along with 1 person rabio
  • Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network.
    Bioinformatics (1 June 2007)
    by Zheng Guo, Yongjin Li, Xue Gong, Chen Yao, Wencai Ma, Dong Wang, Yanhui Li, Jing Zhu, Min Zhang, Da Yang, Jing Wang
    posted to interaction network protein by zwang on 2007-09-17 09:41:41 as ** along with 1 person and 1 group grahamc ParkinsonLab_at_MaRS
  • Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks
    Mol Syst Biol, Vol. 3 (17 April 2007)
    by Igor Ulitsky, Ron Shamir
    posted to interaction network protein yeast by zwang on 2007-04-17 17:30:27 as **** along with 2 people nicoleq carlk
  • A Maximum Likelihood Method for Detecting Directional Evolution in Protein Sequences and its Application to Influenza A Virus.
    Molecular biology and evolution (29 May 2008)
    by Sergei L L Kosakovsky Pond, Art F Y F Poon, Andrew J J Leigh Brown, Simon D W D Frost
    posted to evolution protein sequence by zwang on 2008-06-27 03:55:48 as ** along with 3 people and 1 group pradiptaray stajich phoenixzxl Berkeley Mycology
  • Insights into Protein–DNA Interactions through Structure Network Analysis
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000170.
    by R Sathyapriya, MS Vijayabaskar, Saraswathi Vishveshwara
    posted to structure protein interaction dna by zwang on 2008-09-06 04:04:30 as ** along with 7 people and 1 group Zephyrus Ema emptyhb aalibes AbnerCYH Totobox hmk Roswell Cancer Crosstalk
  • Imaging mass spectrometry of proteins and peptides: 3D volume reconstruction
    Nature Methods, Vol. 5, No. 1., pp. 101-108.
    by Malin Andersson, Reid M Groseclose, Ariel Y Deutch, Richard M Caprioli
    posted to massspectrometry peptide protein protocol by zwang on 2007-12-30 15:28:43 as **** along with 1 person guhjy
  • Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners
    PLoS Computational Biology, Vol. 3, No. 4. (1 April 2007), e43.
    by Benjamin A Shoemaker, Anna R Panchenko
    posted to domain interaction prediction protein by zwang on 2007-04-28 12:23:05 as *** along with 17 people zdai Robinder giovenko Yanno guhjy aalibes bicko jfr chad_davis cjeans iris_2001 lpfernandes groepl carlk Evangelia higueruelo phoenixzxl
  • The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication
    Proceedings of the National Academy of Sciences (16 January 2008), 0707293105.
    by Aviva Presser, Michael B Elowitz, Manolis Kellis, Roy Kishony
    posted to dynamics evolution interaction network protein yeast by zwang on 2008-01-24 13:09:27 as *** along with 4 people pradiptaray cjeans roys phoenixzxl
  • A synthetic gene network for tuning protein degradation in Saccharomyces cerevisiae
    Mol Syst Biol, Vol. 3 (31 July 2007)
    by Chris Grilly, Jesse Stricker, Wyming L Pang, Matthew R Bennett, Jeff Hasty
    posted to interaction network protein synthetic yeast by zwang on 2007-08-01 07:24:07 as *** along with 3 people kfm9876 austin balicea
  • A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis
    Proceedings of the National Academy of Sciences, Vol. 104, No. 40. (2 October 2007), pp. 15711-15716.
    by Amit Ghosh, Saraswathi Vishveshwara
    posted to network protein rna simulation structure by zwang on 2007-11-01 07:34:35 as ** along with 3 people and 1 group cactus sobolevnrm phoenixzxl baker-group
  • The selection of acceptable protein mutations
    PNAS (31 May 2007), 0703737104.
    by Rajkumar Sasidharan, Cyrus Chothia
    posted to evolution protein selection by zwang on 2007-06-04 07:15:05 as *** along with 2 people aalibes gpalidwor
  • Large-scale chemical dissection of mitochondrial function.
    Nat Biotechnol (24 February 2008)
    by Bridget K K Wagner, Toshimori Kitami, Tamara J J Gilbert, David Peck, Arvind Ramanathan, Stuart L L Schreiber, Todd R R Golub, Vamsi K K Mootha
    posted to function protein by zwang on 2008-03-19 14:25:22 as ** along with 3 people dullhunk guhjy giovanni
  • Message-Passing Algorithms for the Prediction of Protein Domain Interactions from Protein-Protein Interaction Data
    Bioinformatics (17 July 2008), btn366.
    by Mudassar Iqbal, Alex A Freitas, Colin G Johnson, Massimo Vergassola
    posted to protein interaction domain algorithm by zwang on 2008-09-06 02:54:38 as **** along with 5 people grahamc afon reyez iris_2001 phoenixzxl
  • I-TASSER server for protein 3D structure prediction
    BMC Bioinformatics, Vol. 9 (23 January 2008), 40.
    by Yang Zhang
    posted to prediction protein structure by zwang on 2008-02-24 13:43:46 as ** along with 4 people chad_davis mkurc rabio mclarenv
  • An in vitro microfluidic approach to generating protein-interaction networks
    Nature Methods, Vol. 6, No. 1. (21 December 2008), pp. 71-74.
    by Doron Gerber, Sebastian J Maerkl, Stephen R Quake
    posted to protein network interaction by zwang on 2009-01-05 08:52:21 as ** along with 1 person and 1 group skoch3 Koch_Lab
  • Structure-Templated Predictions of Novel Protein Interactions from Sequence Information
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e182.
    by Doron Betel, Kevin E Breitkreuz, Ruth Isserlin, Danielle Dewar-Darch, Mike Tyers, Christopher W Hogue
    posted to interaction prediction protein sequence structure by zwang on 2007-11-02 08:05:43 as *** along with 2 people bicko dquest
  • Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms
    Proceedings of the National Academy of Sciences, Vol. 105, No. 32. (2008), pp. 11182-11187.
    by Kei-Ichi Okazaki, Shoji Takada
    posted to binding protein structure by zwang on 2008-08-14 07:25:41 as * along with 3 people and 2 groups raik ruvido barry structural_bioinformatics McCammon
  • A Specificity Map for the PDZ Domain Family
    PLoS Biology, Vol. 6, No. 9. (1 September 2008), e239.
    by Raffi Tonikian, Yingnan Zhang, Stephen L Sazinsky, Bridget Currell, Jung-Hua Yeh, Boris Reva, Heike A Held, Brent A Appleton, Marie Evangelista, Yan Wu, Xiaofeng Xin, Andrew C Chan, Somasekar Seshagiri, Laurence A Lasky, Chris Sander, Charles Boone, Gary D Bader, Sachdev S Sidhu
    posted to protein interaction domain by zwang on 2008-10-20 05:11:28 as **** along with 5 people and 3 groups balicea grahamc markchen cabbagesofdoom barry structural_bioinformatics McCammon Bioinformatics
  • Molecular Basis for Evolving Modularity in the Yeast Protein Interaction Network
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e226.
    by Ariel Fernández
    posted to evolution interaction network protein yeast by zwang on 2007-12-10 04:36:22 as **** along with 5 people pradiptaray tomhebbron niallhaslam Ema phoenixzxl
  • High-throughput fluorescent-based optimization of eukaryotic membrane protein overexpression and purification in Saccharomyces cerevisiae
    PNAS, Vol. 104, No. 35. (28 August 2007), pp. 13936-13941.
    by Simon Newstead, Hyun Kim, Gunnar von Heijne, So Iwata, David Drew
    posted to eukaryota fluorescent protein purification yeast by zwang on 2007-08-29 04:48:42 as *** along with 1 person happy_manatee
  • Yeast surface display for protein engineering and characterization
    Current Opinion in Structural Biology, Vol. 17, No. 4. (August 2007), pp. 467-473.
    by Annie S Gai, Dane K Wittrup
    posted to interaction protein yeast ysd by zwang on 2007-09-30 11:33:01 as ***
  • Predicting PDZ domain–peptide interactions from primary sequences
    Nature Biotechnology, Vol. 26, No. 9. (17 August 2008), pp. 1041-1045.
    by Jiunn R Chen, Bryan H Chang, John E Allen, Michael A Stiffler, Gavin Macbeath
    posted to protein prediction interaction domain by zwang on 2008-09-10 07:31:56 as **** along with 5 people Evangelia yzlab phoenixzxl guhjy cabbagesofdoom
  • Identification of Protein Domains by Shotgun Proteolysis
    Journal of Molecular Biology, Vol. In Press, Corrected Proof
    by Daniel Christ, Greg Winter
    posted to structure protein domain by zwang on 2008-09-16 14:28:20 as ** along with 1 person tny
  • Detection of protein catalytic residues at high precision using local network properties
    BMC Bioinformatics, Vol. 9 (04 December 2008), 517.
    by Patrick, Michael Lappe
    posted to residue protein network by zwang on 2009-01-06 05:14:27 as **
  • Selected reaction monitoring for quantitative proteomics: a tutorial
    Mol Syst Biol, Vol. 4 (14 October 2008)
    by Vinzenz Lange, Paola Picotti, Bruno Domon, Ruedi Aebersold
    posted to protein massspectrometry by zwang on 2008-10-16 09:46:18 as *** along with 2 people pengchy roys
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