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Tag domain [334 articles]

Recent papers classified by the tag domain.
  • Functional evaluation of domain-domain interactions and human protein interaction networks
    Bioinformatics, Vol. 23, No. 7. (1 April 2007), pp. 859-865.
    by Andreas Schlicker, Carola Huthmacher, Fidel Ramirez, Thomas Lengauer, Mario Albrecht
    posted to domain interaction network protein by zwang on 2007-04-29 05:10:56 as *** along with 1 person carlk
  • Predicting protein function from domain content
    Bioinformatics (30 June 2008), btn312.
    by Kristoffer Forslund, Erik L Sonnhammer
    posted to protein prediction domain by zwang on 2008-07-01 02:44:42 as *** along with 2 people reyez phoenixzxl
  • Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins
    PLoS Comput Biol, Vol. 4, No. 5. (16 May 2008), e1000063.
    by Nan Song, Jacob M Joseph, George B Davis, Dannie Durand
    posted to protein domain by zwang on 2008-06-27 04:08:47 as **** along with 2 people Ema tmmurali
  • Specific binding of a Pop6/Pop7 heterodimer to the P3 stem of the yeast RNase MRP and RNase P RNAs
    RNA (23 August 2007), rna.654407.
    by Anna Perederina, Olga Esakova, Hasan Koc, Mark E Schmitt, Andrey S Krasilnikov
    posted to binding domain rna rnasep site yeast by zwang on 2007-09-02 07:31:22 as *****
  • Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution
    BMC Evolutionary Biology, Vol. 7 (16 May 2007), 78.
    by Chrstian Rausch, Ilka Hoof, Tilmann Weber, Wolfgang Wohlleben, Daniel H Huson
    posted to domain evolution phylogeny by zwang on 2007-06-14 02:21:21 as **
  • Evolution of Function in the “Two Dinucleotide Binding Domains” Flavoproteins
    PLoS Computational Biology, Vol. 3, No. 7. (1 July 2007), e121.
    by Sunil Ojha, Elaine C Meng, Patricia C Babbitt
    posted to binding domain evolution interaction protein site by zwang on 2007-08-29 02:31:54 as *** along with 3 people and 2 groups barry Einat mdimon structural_bioinformatics Bioinformatics
  • 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 13 people higueruelo carlk Yanno jyuh aalibes bicko jfr chad_davis cjeans iris_2001 lpfernandes groepl Evangelia
  • Detecting the Coevolution in and among Protein Domains
    PLoS Computational Biology, Vol. preprint, No. 2007. (1 September 2007), e211.eor.
    by Chen-Hsiang Yeang, David Haussler
    posted to co-evolution domain protein by zwang on 2007-09-22 08:05:24 as ***
  • 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 2007-11-03 03:07:56 as **** along with 1 person cjeans
  • 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 protein interface evolution domain by zwang on 2008-05-09 02:40:12 as **** along with 3 people marck choonpeng cmzmasek
  • An intramolecular FRET system monitors fingers subdomain opening in Klentaq1
    Protein Sci, Vol. 17, No. 3. (1 March 2008), pp. 401-408.
    by William J Allen, Paul J Rothwell, Gabriel Waksman
    posted to domain fret invivo subunit by zwang on 2008-02-22 12:42:25 as ***
  • Reuse of structural domain-domain interactions in protein networks
    BMC Bioinformatics, Vol. 8 (18 July 2007), 259.
    by Benjamin Schuster-Bockler, Alex Bateman
    posted to domain interaction network protein structure by zwang on 2007-08-15 03:32:04 as ** along with 3 people carlk saket chad_davis
  • 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 carlk bicko chad_davis choonpeng grahamc cjeans niallhaslam biehl marti
  • Domain-enhanced analysis of microarray data using GO annotations
    Bioinformatics, Vol. 23, No. 10. (15 May 2007), pp. 1225-1234.
    by Jiajun Liu, Jacqueline M Hughes-Oliver, Alan J Menius
    posted to annotation domain microarray by zwang on 2007-05-29 02:25:26 as ** along with 2 people jyuh jfr
  • The Leucine-Rich Repeat Domain of Internalin B Folds along a Polarized N-Terminal Pathway
    Structure, Vol. 16, No. 5. (7 May 2008), pp. 705-714.
    by Naomi Courtemanche, Doug Barrick
    posted to protein domain by zwang on 2008-06-26 04:08:33 as **
  • 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 6 people carlk saket dchughes michC neils grahamc
  • 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 1 person phoenixzxl
  • 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 pradiptaray balicea skhadar sobolevnrm niallhaslam hpaces mingzhi Ema phoenixzxl penpen926 friendpine baker-group
  • PDZ Domain Binding Selectivity Is Optimized Across the Mouse Proteome
    Science, Vol. 317, No. 5836. (20 July 2007), pp. 364-369.
    by Michael A Stiffler, Jiunn R Chen, Viara P Grantcharova, Ying Lei, Daniel Fuchs, John E Allen, Lioudmila A Zaslavskaia, Gavin Macbeath
    posted to binding domain genome interaction proteome by zwang on 2007-07-23 07:12:01 as **** along with 1 person carlk
  • Evolutionary Genomics: Transdomain Gene Transfers
    Current Biology, Vol. 17, No. 21. (6 November 2007), pp. R935-R936.
    by Seth R Bordenstein
    posted to domain evolution genome by zwang on 2007-11-16 06:44:29 as ** along with 3 people skhadar mblwhoi hpaces
  • Structure of the Chloroplast Ribosome: Novel Domains for Translation Regulation
    PLoS Biology, Vol. 5, No. 8. (1 August 2007), e209.
    by Andrea L Manuell, Joel Quispe, Stephen P Mayfield
    posted to domain regulation structure translation by zwang on 2007-08-15 06:29:51 as *
  • Prediction of structures of multidomain proteins from structures of the individual domains.
    Protein Sci (22 December 2006)
    by Andrew M M Wollacott, Alexandre Zanghellini, Paul Murphy, David Baker
    posted to domain prediction protein structure by zwang on 2007-04-16 13:37:00 as ** along with 4 people wouterboomsma choonpeng IrinaMoreira rph
  • Interaction of signal-recognition particle 54 GTPase domain and signal-recognition particle RNA in the free signal-recognition particle
    Proceedings of the National Academy of Sciences, Vol. 104, No. 38. (18 September 2007), pp. 14911-14916.
    by Tobias Hainzl, Shenghua Huang, Elisabeth A Sauer-Eriksson
    posted to domain interaction rna by zwang on 2007-11-01 02:11:19 as **
  • Modeling the Evolution of Protein Domain Architectures Using Maximum Parsimony
    Journal of Molecular Biology, Vol. 366, No. 1. (9 February 2007), pp. 307-315.
    by Jessica H Fong, Lewis Y Geer, Anna R Panchenko, Stephen H Bryant
    posted to domain evolution mp protein by zwang on 2007-03-19 12:52:24 as * along with 5 people and 3 groups icases marcius tny choonpeng redelings BioinfoCIPF SGU-CIPF TNT
  • Structural insights into the interaction of the evolutionarily conserved ZPR1 domain tandem with eukaryotic EF1A, receptors, and SMN complexes
    Proceedings of the National Academy of Sciences, Vol. 104, No. 35. (28 August 2007), pp. 13930-13935.
    by Ashwini K Mishra, Laxman Gangwani, Roger J Davis, David G Lambright
    posted to complex domain eukaryota evolution interaction structure by zwang on 2007-11-01 02:01:47 as ***
  • Photonic Generation of Ultrawideband Signals
    Lightwave Technology, Journal of, Vol. 25, No. 11. (2007), pp. 3219-3235.
    by Jianping Yao, Fei Zeng, Qing Wang
    posted to domain frequency generate optical range signals techniques ultrawideband uwb by ze on 2008-02-29 17:57:30 as read
  • The Domain Theory for Requirements Engineering
    IEEE Trans. Softw. Eng., Vol. 24, No. 3. (March 1998), pp. 174-196.
    by Alistair Sutcliffe, Neil Maiden
    posted to domain requirements theory by yijunyu on 2006-12-30 13:13:40 as **
  • A MADS domain gene involved in the transition to flowering in Arabidopsis.
    Plant J, Vol. 24, No. 5. (December 2000), pp. 591-599.
    by R Borner, G Kampmann, J Chandler, R Gleissner, E Wisman, K Apel, S Melzer
    posted to a arabidopsis domain flowering gene in involved mads the to transition by xixibio on 2006-04-19 13:43:18 as ** along with 1 person Happybene
  • The PANTHER database of protein families, subfamilies, functions and pathways.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by H Mi, B Lazareva-Ulitsky, R Loo, A Kejariwal, J Vandergriff, S Rabkin, N Guo, A Muruganujan, O Doremieux, MJ Campbell, H Kitano, PD Thomas
    posted to database domain family pathways protein subfamily by xico on 2005-12-24 16:17:33 as *** along with 3 people and 2 groups AlexanderPico Cortel yas T_lab WetBiology
  • Statistical analysis of domains in interacting protein pairs
    Bioinformatics, Vol. 21, No. 7. (01 April 2005), pp. 993-1001.
    by MW Nye, Berzuini Carlo, R Gilks, Babu M Madan, A Teichmann
    posted to domain interaction protein statistics by wnpx on 2007-03-17 11:38:37 as ** along with 5 people and 1 group lfriedl chad_davis neils iris_2001 phoenixzxl kdl
  • Empirical estimates of adaptation: the chance of two noriegas is closer to p/2 than p<sup>2</sup>
    (2000), pp. 180-186.
    by Kenneth W Church
    posted to adaptation domain language modelling by vlachmore on 2007-10-24 14:25:02 as read
  • Structure-function relationships in human Class III alcohol dehydrogenase (formaldehyde dehydrogenase)
    Chemico-Biological Interactions, Vol. 143-144 (1 February 2003), pp. 195-200.
    by Paresh C Sanghani, Howard Robinson, Riccardo Bennett-Lovsey, Thomas D Hurley, WF Bosron
    posted to structure domain active by unglee on 2008-04-29 05:13:49 as **
  • Automatic classification of protein structure by using Gauss integrals.
    Proc Natl Acad Sci U S A, Vol. 100, No. 1. (7 January 2003), pp. 119-124.
    by P Rogen, B Fain
    posted to domain prediction protein by tny on 2005-12-06 03:41:44 as ** along with 3 people and 2 groups ana barry dimka structural_bioinformatics Bioinformatics
  • notes Protein similarity from knot theory: geometric convolution and line weavings.
    J Comput Biol, Vol. 12, No. 6. (g 2005), pp. 609-637.
    by MA Erdmann
    posted to domain prediction protein by tny on 2005-12-06 03:39:04 as **
  • Multi-domain Proteins in the Three Kingdoms of Life: Orphan Domains and Other Unassigned Regions
    Journal of Molecular Biology, Vol. 348, No. 1. (22 April 2005), pp. 231-243.
    by Diana Ekman, Asa K Bjorklund, Johannes Frey-Skott, Arne Elofsson
    posted to domain protein by tny on 2005-12-06 03:24:01 as read along with 2 people and 2 groups ana choonpeng structural_bioinformatics Bioinformatics
  • DIAL: a web-based server for the automatic identification of structural domains in proteins.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by G Pugalenthi, G Archunan, R Sowdhamini
    posted to database_issue domain domain_swapping by tny on 2006-02-04 06:59:01 as **
  • Domain combinations in archaeal, eubacterial and eukaryotic proteomes.
    J Mol Biol, Vol. 310, No. 2. (6 July 2001), pp. 311-325.
    by G Apic, J Gough, SA Teichmann
    posted to domain domain_combination evolution protein by tny on 2005-11-27 08:56:27 as read along with 3 people Schmidtc eweaver cjeans
  • notes WW Domains Provide a Platform for the Assembly of Multiprotein Networks
    Mol. Cell. Biol., Vol. 25, No. 16. (15 August 2005), pp. 7092-7106.
    by Robert J Ingham, Karen Colwill, Caley Howard, Sabine Dettwiler, Caesar S Lim, Joanna Yu, Kadija Hersi, Judith Raaijmakers, Gerald Gish, Geraldine Mbamalu, Lorne Taylor, Benny Yeung, Galina Vassilovski, Manish Amin, Fu Chen, Liudmila Matskova, Gosta Winberg, Ingemar Ernberg, Rune Linding, Paul O'Donnell, Andrei Starostine, Walter Keller, Pavel Metalnikov, Chris Stark, Tony Pawson
    posted to domain experiment protein ww by tny on 2005-12-05 08:00:32 as **
  • Proteomic, Functional, and Domain-Based Analysis of In Vivo 14-3-3 Binding Proteins Involved in Cytoskeletal Regulation and Cellular Organization
    Current Biology, Vol. 14, No. 16. (24 August 2004), pp. 1436-1450.
    by Jing Jin, Donelson F Smith, Chris Stark, Clark D Wells, James P Fawcett, Sarang Kulkarni, Pavel Metalnikov, Paul O'Donnell, Paul Taylor, Lorne Taylor
    posted to 14-3-3 domain experiment protein by tny on 2005-12-05 07:59:41 as ** along with 1 person winterschlaefer
  • Multi-subunit acetyl-CoA carboxylases.
    Prog Lipid Res, Vol. 41, No. 5. (September 2002), pp. 407-435.
    by JE Cronan, GL Waldrop
    posted to acc domain enzyme multifunctional_enzyme subunit by tny on 2006-12-06 11:39:08 as **
  • Crosstalk between the catalytic and regulatory domains allows bidirectional regulation of Src.
    Nat Struct Biol, Vol. 7, No. 4. (April 2000), pp. 281-286.
    by S Gonfloni, A Weijland, J Kretzschmar, G Superti-Furga
    posted to domain example by tny on 2006-06-15 14:01:04 as **
  • From protein domains to drug candidates-natural products as guiding principles in the design and synthesis of compound libraries.
    Angew Chem Int Ed Engl, Vol. 41, No. 16. (16 August 2002), pp. 2879-2890.
    by R Breinbauer, IR Vetter, H Waldmann
    posted to compound domain drug by tny on 2006-12-06 11:26:18 as ** along with 1 person jerome_ucsf_slb
  • Evolutionary history and higher order classification of AAA+ ATPases
    Journal of Structural Biology, Vol. 146, No. 1-2. (April 2004), pp. 11-31.
    by Lakshminarayan M Iyer, Detlef D Leipe, Eugene V Koonin, L Aravind
    posted to domain evolution p-loop by tny on 2006-05-07 05:59:41 as ** along with 1 person leemary4
  • Classification and evolution of P-loop GTPases and related ATPases.
    J Mol Biol, Vol. 317, No. 1. (15 March 2002), pp. 41-72.
    by DD Leipe, YI Wolf, EV Koonin, L Aravind
    posted to domain evolution p-loop by tny on 2006-05-07 05:59:40 as ** along with 3 people and 2 groups barry Einat leemary4 structural_bioinformatics Bioinformatics
  • Diversification of Catalytic Activities and Ligand Interactions in the Protein Fold Shared by the Sugar Isomerases, eIF2B, DeoR Transcription Factors, Acyl-CoA Transferases and Methenyltetrahydrofolate Synthetase
    Journal of Molecular Biology, Vol. 356, No. 3. (24 February 2006), pp. 823-842.
    by Vivek Anantharaman, L Aravind
    posted to catalytic domain evolution by tny on 2006-05-07 05:59:28 as **
  • Evolution and Classification of P-loop Kinases and Related Proteins
    Journal of Molecular Biology, Vol. 333, No. 4. (31 October 2003), pp. 781-815.
    by Detlef D Leipe, Eugene V Koonin, L Aravind
    posted to domain evolution p-loop by tny on 2006-05-07 05:59:21 as **
  • Evidence that human genes of modular proteins have retained significantly more ancestral introns than their fly or worm orthologues
    FEBS Letters, Vol. 565, No. 1-3. (7 May 2004), pp. 127-132.
    by Laszlo Banyai, Laszlo Patthy
    posted to domain exon intron protein by tny on 2005-12-08 00:12:41 as ** along with 1 person and 1 group penka Nie
  • Partitioning Protein Structures into Domains: Why Is it so Difficult?
    Journal of Molecular Biology, Vol. 361, No. 3. (18 August 2006), pp. 562-590.
    by Timothy A Holland, Stella Veretnik, Ilya N Shindyalov, Philip E Bourne
    posted to benchmark domain classification by tny on 2006-08-05 09:23:03 as ** along with 2 people and 2 groups chad_davis marcius BioinfoCIPF SGU-CIPF
  • Modular Enzyme Design: Regulation by Mutually Exclusive Protein Folding
    Journal of Molecular Biology, Vol. 357, No. 4. (7 April 2006), pp. 1058-1062.
    by Jeung-Hoi Ha, James S Butler, Diana M Mitrea, Stewart N Loh
    posted to domain enzyme example by tny on 2006-06-06 10:20:20 as **
  • Comparative Genomics and Protein Domain Graph Analyses Link Ubiquitination and RNA Metabolism
    Journal of Molecular Biology, Vol. 357, No. 1. (17 March 2006), pp. 9-17.
    by Ignasi J Lucas, Vicente Arnau, Ignacio Marin
    posted to comparative domain metabolism by tny on 2006-06-06 10:20:02 as **
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