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Tag protein [951 articles]

Recent papers classified by the tag protein.
  • NMR structures of two designed proteins with high sequence identity but different fold and function
    Proceedings of the National Academy of Sciences, Vol. 105, No. 38. (2008), pp. 14412-14417.
    by Yanan He, Yihong Chen, Patrick Alexander, Philip N Bryan, John Orban
    posted to structure protein nmr function folding by zwang on 2008-10-09 08:58:11 as ** along with 4 people wilbur markchen reyez kentsis
  • Classifying RNA-Binding Proteins Based on Electrostatic Properties
    PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000146.
    by Shula Shazman, Yael Mandel-Gutfreund
    posted to binding protein rna by zwang on 2008-08-30 04:00:30 as ** along with 1 person Ema
  • 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 marti eckart_bindewald skhadar asddd hpaces
  • Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen
    Science (10 January 2008), 1152725.
    by Abraham L Brass, Derek M Dykxhoorn, Yair Benita, Nan Yan, Alan Engelman, Ramnik J Xavier, Judy Lieberman, Stephen J Elledge
    posted to genome hiv hostspecialization immunity protein by zwang on 2008-02-22 12:53:05 as ** along with 5 people tmmurali gokhan davidlott renatomilani kieran101
  • Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding
    PNAS, Vol. 104, No. 3. (16 January 2007), pp. 808-813.
    by Tom Young, Robert Abel, Byungchan Kim, Bruce J Berne, Richard A Friesner
    posted to molecularrecognition motif protein by zwang on 2007-04-16 13:42:41 as ** along with 3 people LamBras daevans jwagoner
  • Multiple Routes and Structural Heterogeneity in Protein Folding
    Annual Review of Biophysics, Vol. 37, No. 1. (2008), pp. 489-510.
    by Jayant B Udgaonkar
    posted to folding protein structure by zwang on 2008-05-08 09:59:05 as **
  • Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy
    PNAS, Vol. 104, No. 27. (3 July 2007), pp. 11257-11262.
    by Paul Schanda, Vincent Forge, Bernhard Brutscher
    posted to folding nmr protein structure by zwang on 2007-08-15 04:12:29 as ** along with 1 person rph
  • The sensitive side of protein-DNA interactions
    Nature Methods, Vol. 4, No. 4., pp. 298-299.
    by Allison Doerr
    posted to dna interaction protein by zwang on 2007-04-04 11:11:10 as **
  • Structural insights into the evolutionary paths of oxylipin biosynthetic enzymes
    Nature (20 August 2008)
    by Dong-Sun Lee, Pierre Nioche, Mats Hamberg, CS Raman
    posted to structure protein evolution by zwang on 2008-10-16 13:54:36 as **
  • Structural basis for the selectivity of the external thioesterase of the surfactin synthetase
    Nature, Vol. 454, No. 7206., pp. 907-911.
    by Alexander Koglin, Frank Löhr, Frank Bernhard, Vladimir V Rogov, Dominique P Frueh, Eric R Strieter, Mohammad R Mofid, Peter Güntert, Gerhard Wagner, Christopher T Walsh, Mohamed A Marahiel, Volker Dötsch
    posted to protein structure by zwang on 2008-08-15 01:51:57 as **
  • Transcriptional regulation of protein complexes within and across species
    PNAS, Vol. 104, No. 4. (23 January 2007), pp. 1283-1288.
    by Kai Tan, Tomer Shlomi, Hoda Feizi, Trey Ideker, Roded Sharan
    posted to complex protein specy transcription by zwang on 2007-04-16 13:12:52 as ** along with 5 people and 2 groups kaarsinogen icases nickluscombe dylan77 carlk EBI-regulation TNT
  • 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
  • A statistical approach using network structure in the prediction of protein characteristics
    Bioinformatics (28 June 2007), btm342.
    by Pao-Yang Chen, Charlotte M Deane, Gesine Reinert
    posted to network prediction protein statistical structure by zwang on 2007-08-15 03:41:38 as * along with 5 people and 1 group grahamc iris_2001 cabbagezs cdeane Pao-Yang ParkinsonLab_at_MaRS
  • Co-evolving residues in membrane proteins
    Bioinformatics, Vol. 23, No. 24. (15 December 2007), pp. 3312-3319.
    by Angelika Fuchs, Antonio J Martin-Galiano, Matan Kalman, Sarel Fleishman, Nir Ben-Tal, Dmitrij Frishman
    posted to co-evolution membrane protein residue by zwang on 2007-12-10 03:52:09 as *** along with 6 people and 2 groups operon breden cjeans blasco_morozzo phoenixzxl Lombardo_7 SFUAntibodyResearch signal-duplication
  • 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
  • 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
  • A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds
    PLoS Computational Biology, Vol. 3, No. 7. (1 July 2007), e139.
    by Konstantin B Zeldovich, Peiqiu Chen, Boris E Shakhnovich, Eugene I Shakhnovich
    posted to evolution folding gene modeling protein specy by zwang on 2007-08-28 07:39:34 as ** along with 6 people and 1 group BioNica grahamc cjeans Jporci farhat biinins ParkinsonLab_at_MaRS
  • Protein subcellular relocalization: a new perspective on the origin of novel genes
    Trends in Ecology & Evolution, Vol. 22, No. 7. (July 2007), pp. 338-344.
    by Ashley S Byun-Mckay, R Geeta
    posted to gene localization protein by zwang on 2007-08-18 08:58:16 as *** along with 2 people cjeans Jporci
  • Predicting transcription factor specificity with all-atom models.
    Nucleic acids research (1 October 2008)
    by Sahand Jamal J Rahi, Peter Virnau, Leonid A A Mirny, Mehran Kardar
    posted to structure protein prediction interaction dna by zwang on 2008-11-04 09:08:12 as ***** along with 4 people reyez maximilianh lptolik aalibes
  • 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
  • Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)
    Nature Biotechnology, Vol. 26, No. 3. (07 March 2008), pp. 305-312.
    by Eric W Deutsch, Catherine A Ball, Jules J Berman, Steven G Bova, Alvis Brazma, Roger E Bumgarner, David Campbell, Helen C Causton, Jeffrey H Christiansen, Fabrice Daian, Delphine Dauga, Duncan R Davidson, Gregory Gimenez, Young A Goo, Sean Grimmond, Thorsten Henrich, Bernhard G Herrmann, Michael H Johnson, Martin Korb, Jason C Mills, Asa J Oudes, Helen E Parkinson, Laura E Pascal, Nicolas Pollet, John Quackenbush, Mirana Ramialison, Martin Ringwald, David Salgado, Susanna-Assunta Sansone, Gavin Sherlock, Christian J Stoeckert, Jason Swedlow, Ronald C Taylor, Laura Walashek, Anthony Warford, David G Wilkinson, Yi Zhou, Leonard I Zon, Alvin Y Liu, Lawrence D True
    posted to immunohistochemistry protein rna by zwang on 2008-03-19 14:26:07 as ** along with 4 people and 1 group katerinakal guhjy psique jfr parkinson's disease references
  • 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 ***
  • The structure of protein evolution and the evolution of protein structure
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Richard A Goldstein
    posted to evolution protein structure by zwang on 2008-03-11 01:11:59 as *** along with 3 people and 3 groups barry bpb cmzmasek structural_bioinformatics McCammon Bioinformatics
  • 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
  • Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins
    BMC Bioinformatics, Vol. 8 (05 May 2007), 147.
    by Qiwen Dong, Xiaolong Wang, Lei Lin, Yi Guan
    posted to binding interface prediction profile protein residue by zwang on 2007-05-06 09:28:10 as **** along with 2 people bicko marti
  • Evolution of protein domain promiscuity in eukaryotes
    Genome Res. (29 January 2008), gr.6943508.
    by Malay K Basu, Liran Carmel, Igor B Rogozin, Eugene V Koonin
    posted to domain eukaryota evolution protein by zwang on 2008-03-03 04:15:14 as **** along with 7 people saket cmzmasek michC neils grahamc carlk dchughes
  • A yeast two-hybrid smart-pool-array system for protein-interaction mapping
    Nat Meth, Vol. 4, No. 5. (May 2007), pp. 405-407.
    by Fulai Jin, Larisa Avramova, Jing Huang, Tony Hazbun
    posted to interaction protein y2h yeast by zwang on 2007-04-27 12:15:28 as *** along with 2 people guhjy Dualsystems
  • Thermodynamics of Neutral Protein Evolution
    Genetics, Vol. 175, No. 1. (1 January 2007), pp. 255-266.
    by Jesse D Bloom, Alpan Raval, Claus O Wilke
    posted to dynamics evolution protein by zwang on 2007-04-16 13:30:53 as ** along with 1 person BioNica
  • 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
  • The Protein Folding Problem
    Annual Review of Biophysics, Vol. 37, No. 1. (2008), pp. 289-316.
    by Ken A Dill, Banu S Ozkan, Scott M Shell, Thomas R Weikl
    posted to folding protein by zwang on 2008-05-08 09:53:48 as ** along with 1 person dsekaran
  • Using viral species specificity to define a critical protein/RNA interaction surface
    Genes Dev., Vol. 15, No. 10. (15 May 2001), pp. 1194-1205.
    by Glen A Coburn, Heather L Wiegand, Yibin Kang, Dona N Ho, Millie M Georgiadis, Bryan R Cullen
    posted to interaction interface protein rna surface virus by zwang on 2007-10-12 08:53:11 as ****
  • Design of protein function leaps by directed domain interface evolution
    Proceedings of the National Academy of Sciences (29 April 2008), 0801097105.
    by Jin Huang, Akiko Koide, Koki Makabe, Shohei Koide
    posted to domain evolution interface protein by zwang on 2008-05-09 02:40:12 as **** along with 5 people GeeSharpMinor cmzmasek choonpeng marck phoenixzxl
  • 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
  • Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis
    Bioinformatics, Vol. 24, No. 18. (15 September 2008), pp. 2002-2009.
    by Majid Masso, Iosif I Vaisman
    posted to svm structure stability protein prediction by zwang on 2008-10-09 08:57:06 as ** along with 2 people kluck afon
  • Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences
    Nucl. Acids Res. (4 April 2008), gkn159.
    by Yanzhi Guo, Lezheng Yu, Zhining Wen, Menglong Li
    posted to interaction prediction protein svm by zwang on 2008-06-16 03:51:12 as **** along with 4 people guhjy marck phoenixzxl tmmurali
  • Dissecting protein structure and function using directed evolution
    Nat Meth, Vol. 4, No. 12. (December 2007), pp. 995-997.
    by Courtney M Yuen, David R Liu
    posted to evolution function protein structure by zwang on 2007-12-10 05:04:21 as *** along with 1 person cjeans
  • Cavities and Atomic Packing in Protein Structures and Interfaces
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000188.
    by Shrihari Sonavane, Pinak Chakrabarti
    posted to structure protein interface by zwang on 2008-10-07 11:17:40 as **** along with 1 person raik
  • The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins
    Proceedings of the National Academy of Sciences, Vol. 105, No. 34. (2008), pp. 12259-12264.
    by David A Beck, Darwin O Alonso, Daigo Inoyama, Valerie Daggett
    posted to cooccurrence protein by zwang on 2008-08-27 14:32:56 as ** along with 2 people paulschlesinger phoenixzxl
  • 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
  • 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
  • A simple selection strategy for evolving highly efficient enzymes.
    Nat Biotechnol, Vol. 25, No. 10. (October 2007), pp. 1145-1147.
    by M Neuenschwander, M Butz, C Heintz, P Kast, D Hilvert
    posted to evolution protein by zwang on 2007-10-11 17:00:55 as ** along with 2 people cjeans Jporci
  • Structure-Guided Comparative Analysis of Proteins: Principles, Tools, and Applications for Predicting Function
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000151.
    by Raja Mazumder, Sona Vasudevan
    posted to structure protein prediction function by zwang on 2008-10-07 11:19:53 as ** along with 9 people and 2 groups i000 pengchy raik chad_davis druvus reyez mdstobbe barry jameswasmuth structural_bioinformatics Bioinformatics
  • Fluorogen-activating single-chain antibodies for imaging cell surface proteins
    Nature Biotechnology, Vol. 26, No. 2. (23 December 2007), pp. 235-240.
    by Christopher Szent-Gyorgyi, Brigitte A Schmidt, Yehuda Creeger, Gregory W Fisher, Kelly L Zakel, Sally Adler, James AJ Fitzpatrick, Carol A Woolford, Qi Yan, Kalin V Vasilev, Peter B Berget, Marcel P Bruchez, Jonathan W Jarvik, Alan Waggoner
    posted to antibody fluorescent protein surface by zwang on 2008-02-19 13:02:24 as ** along with 2 people and 1 group samjlord ohara moernerlab
  • Ensemble Non-negative Matrix Factorization Methods for Clustering Protein-Protein Interactions
    Bioinformatics (12 June 2008), btn286.
    by Derek Greene, Gerard Cagney, Nevan Krogan, Padraig Cunningham
    posted to clustering interaction protein by zwang on 2008-06-27 03:43:26 as ** along with 2 people chad_davis grahamc
  • A generative, probabilistic model of local protein structure
    Proceedings of the National Academy of Sciences, Vol. 105, No. 26. (1 July 2008), pp. 8932-8937.
    by Wouter Boomsma, Kanti V Mardia, Charles C Taylor, Jesper Ferkinghoff-Borg, Anders Krogh, Thomas Hamelryck
    posted to modeling protein structure by zwang on 2008-07-02 11:49:14 as * along with 5 people j3xucite bertelsen biehl apaydin mijam
  • Detecting Coevolution in and among Protein Domains
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e211.
    by Chen-Hsiang Yeang, David Haussler
    posted to co-evolution domain prediction protein by zwang on 2007-12-10 04:24:46 as ***** along with 11 people and 1 group balicea skhadar sobolevnrm niallhaslam hpaces mingzhi Ema phoenixzxl penpen926 friendpine pradiptaray baker-group
  • The biological impact of mass-spectrometry-based proteomics
    Nature, Vol. 450, No. 7172. (13 December 2007), pp. 991-1000.
    by Benjamin F Cravatt, Gabriel M Simon, Yates
    posted to proteomics protein massspectrometry by zwang on 2007-12-13 05:28:53 as **** along with 5 people guhjy becarmson Jporci phoenixzxl Yanno
  • 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
  • Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size
    Mol Syst Biol, Vol. 4 (2008)
    by Jingshan Zhang, Sergei Maslov, Eugene I Shakhnovich
    posted to expression interaction protein by zwang on 2008-08-07 02:49:43 as ** along with 3 people grahamc Ema biehl
  • Conformational entropy in molecular recognition by proteins
    Nature, Vol. 448, No. 7151., pp. 325-329.
    by Kendra K Frederick, Michael S Marlow, Kathleen G Valentine, Joshua A Wand
    posted to molecularrecognition protein by zwang on 2007-08-18 15:47:14 as * along with 5 people cactus Jporci jlh64 dmobley psique
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