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Tag protein_function [50 articles]

Recent papers classified by the tag protein_function.
  • Transitive functional annotation by shortest-path analysis of gene expression data.
    Proc Natl Acad Sci U S A, Vol. 99, No. 20. (1 October 2002), pp. 12783-12788.
    by X Zhou, MC Kao, WH Wong
    posted to protein_function by shivaram on 2005-10-10 20:46:11 as ** along with 2 people and 1 group cswinburne lfriedl kdl
  • Assessment of prediction accuracy of protein function from protein--protein interaction data.
    Yeast, Vol. 18, No. 6. (April 2001), pp. 523-531.
    by H Hishigaki, K Nakai, T Ono, A Tanigami, T Takagi
    posted to protein_function by shivaram on 2005-10-10 20:43:31 as ** along with 2 people jiny carlk
  • Global protein function prediction from protein-protein interaction networks.
    Nat Biotechnol, Vol. 21, No. 6. (June 2003), pp. 697-700.
    by A Vazquez, A Flammini, A Maritan, A Vespignani
    posted to protein_function by shivaram on 2005-10-10 20:44:38 as ** along with 8 people aprildh31 jiny eweaver gcalda grahamc iris_2001 maralena carlk
  • A combined algorithm for genome-wide prediction of protein function.
    Nature, Vol. 402, No. 6757. (4 November 1999), pp. 83-86.
    by EM Marcotte, M Pellegrini, MJ Thompson, TO Yeates, D Eisenberg
    posted to protein_function by shivaram on 2005-10-10 20:41:41 as ** along with 5 people and 1 group Robinder lfriedl ruvido cjeans carlk kdl
  • Whole-genome annotation by using evidence integration in functional-linkage networks.
    Proc Natl Acad Sci U S A, Vol. 101, No. 9. (2 March 2004), pp. 2888-2893.
    by U Karaoz, TM Murali, S Letovsky, Y Zheng, C Ding, CR Cantor, S Kasif
    posted to protein_function by shivaram on 2005-10-10 20:45:13 as ** along with 4 people and 1 group jiny lfriedl nedwards carlk kdl
  • Why are proteins marginally stable?
    Proteins: Structure, Function, and Genetics, Vol. 46, No. 1. (2002), pp. 105-109.
    by Darin M Taverna, Richard A Goldstein
    posted to stability sequence_space protein_function protein_evolution neutrality neutral_theory_of_evolution natural_selection marginal_stability lattice_protein foldability designability by scherrer on 2008-10-06 19:59:05 as read
  • Network-based prediction of protein function
    Mol Syst Biol, Vol. 3 (13 March 2007)
    by Roded Sharan, Igor Ulitsky, Ron Shamir
    posted to review protein_function predict network by pengchy on 2008-10-06 02:05:50 as ** along with 13 people and 1 group druvus jjray cmmorel wnpx julius mikaelhuss massivemayhem cjeans iris_2001 karfunkel mingzhi ellakat carlk SysbioMPI-TCells
  • Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information.
    Bioinformatics, Vol. 21, No. 13. (1 July 2005), pp. 2988-2993.
    by F Al-Shahrour, R Díaz-Uriarte, J Dopazo
    posted to bioinformatics classification protein_function by marcius on 2006-01-17 19:11:48 as ** along with 4 people and 2 groups eweaver rdiaz ealloza Garamonfok BioinfoCIPF SGU-CIPF
  • Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery.
    Drug Discov Today, Vol. 10, No. 21. (1 November 2005), pp. 1475-1482.
    by Y Ofran, M Punta, R Schneider, B Rost
    posted to bioinformatics protein_function review by marcius on 2006-01-13 23:55:53 as ** along with 3 people and 2 groups jwortman kuhn cjeans BioinfoCIPF SGU-CIPF
  • A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function.
    Bioinformatics, Vol. 19, No. 17. (22 November 2003), pp. 2199-2209.
    by VG Krishnan, DR Westhead
    posted to bioinformatics protein_function snp by marcius on 2006-04-30 01:11:59 as ** along with 5 people and 3 groups chrn eweaver caporaso rlhsiao rsantana biomedical-nlp BioinfoCIPF SGU-CIPF
  • Automated discovery of 3D motifs for protein function annotation
    Bioinformatics, Vol. 22, No. 6. (15 March 2006), pp. 723-730.
    by Benjamin J Polacco, Patricia C Babbitt
    posted to bioinformatics protein_function by marcius on 2006-04-04 00:31:57 as ** along with 2 people and 2 groups eweaver rabio BioinfoCIPF SGU-CIPF
  • Probabilistic annotation of protein sequences based on functional classifications.
    BMC Bioinformatics, Vol. 6 (2005)
    by ED Levy, CA Ouzounis, WR Gilks, B Audit
    posted to algorithms bioinformatics protein_function statistics by marcius on 2006-09-07 17:17:23 as ** along with 2 people and 2 groups sgoetz shung BioinfoCIPF SGU-CIPF
  • Why highly expressed proteins evolve slowly.
    Proc Natl Acad Sci U S A (21 September 2005)
    by D Allan A Drummond, Jesse D D Bloom, Christoph Adami, Claus O O Wilke, Frances H H Arnold
    posted to evolution pleiotropy protein_function by marcius on 2005-10-21 02:44:11 as **** along with 14 people and 5 groups rklancer stevanspringer bjorns imouthesmp aprasad dayjm Einat xwbcn penka balabu malcook balicea RamuAnandakrishnan wilbur structural_bioinformatics Nie FAB-lab BioinfoCIPF SGU-CIPF
  • Bayesian search of functionally divergent protein subgroups and their function specific residues
    Bioinformatics, Vol. 22, No. 20. (15 October 2006), pp. 2466-2474.
    by Marttinen, Pekka, Corander, Jukka, Toronen, Petri, Holm, Liisa
    posted to algorithms bioinformatics protein_function by marcius on 2006-10-20 13:21:03 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design.
    Nucleic Acids Res, Vol. 33, No. 18. (2005), pp. 5861-5867.
    by Gong Cheng, Bin Qian, Ram Samudrala, David Baker
    posted to biophysics evolution protein_function protein_structure by marcius on 2005-11-02 09:14:59 as ** along with 6 people and 3 groups bicko Einat alexg nickolay sriram_s ladab structural_bioinformatics BioinfoCIPF SGU-CIPF
  • The prediction of protein function at CASP6.
    Proteins (26 September 2005)
    by Simonetta Soro, Anna Tramontano
    posted to casp protein_function by marcius on 2005-10-22 08:55:56 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology.
    Proteins, Vol. 58, No. 4. (1 March 2005), pp. 855-865.
    by JV Ponomarenko, PE Bourne, IN Shindyalov
    posted to bioinformatics evolution protein_function protein_structure by marcius on 2006-09-07 17:24:49 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Automatic annotation of protein function
    Current Opinion in Structural Biology, Vol. 15, No. 3. (June 2005), pp. 267-274.
    by Alfonso Valencia
    posted to bioinformatics protein_function review by marcius on 2005-10-22 09:02:45 as *** along with 6 people and 2 groups sgoetz tjimenez dimka kuhn eweaver bootsy BioinfoCIPF SGU-CIPF
  • PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.
    BMC Bioinformatics, Vol. 7, No. 1. (6 February 2006)
    by Marcin von Grotthuss, Dariusz Plewczynski, Krzysztof Ginalski, Leszek Rychlewski, Eugene I Shakhnovich
    posted to bioinformatics databases protein_function protein_structure by marcius on 2006-02-27 20:16:54 as ** along with 2 people and 3 groups caporaso sim82 biomedical-nlp BioinfoCIPF SGU-CIPF
  • Designed divergent evolution of enzyme function
    Nature (22 February 2006)
    by Yasuo Yoshikuni, Thomas E Ferrin, Jay D Keasling
    posted to bioinformatics evolution protein_function by marcius on 2006-04-20 21:51:55 as ** along with 3 people and 2 groups lingchong tny dbikard BioinfoCIPF SGU-CIPF
  • Revisiting the prediction of protein function at CASP6
    FEBS Journal, Vol. 273, No. 13. (July 2006), pp. 2977-2983.
    by Pellegrini-Calace, Marialuisa, Soro, Simonetta, Tramontano, Anna
    posted to casp protein_function by marcius on 2006-08-31 17:02:04 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • The C-type lectin fold as an evolutionary solution for massive sequence variation
    Nature Structural & Molecular Biology, Vol. 12, No. 10. (18 September 2005), pp. 886-892.
    by Stephen A Mcmahon, Jason L Miller, Jeffrey A Lawton, Donald E Kerkow, Asher Hodes, Marc A Marti-Renom, Sergei Doulatov, Eswar Narayanan, Andrej Sali, Jeff F Miller, Partho Ghosh
    posted to computational_biology evolution immunology protein_function protein_structure by marcius on 2005-10-21 09:26:57 as read along with 2 people and 4 groups stevanspringer ana structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • Inferring functional information from domain co-evolution
    Bioinformatics, Vol. 22, No. 1. (1 January 2006), pp. 40-49.
    by Yohan Kim, Mehmet Koyuturk, Umut Topkara, Ananth Grama, Shankar Subramaniam
    posted to bioinformatics evolution protein_function by marcius on 2006-01-12 19:07:33 as ** along with 1 person and 2 groups eweaver BioinfoCIPF SGU-CIPF
  • PRODISTIN Web Site: a tool for the functional classification of proteins from interaction networks
    Bioinformatics, Vol. 22, No. 2. (15 January 2006), pp. 248-250.
    by Anais Baudot, David Martin, Alain Guenoche, Bernard Jacq, Christine Brun
    posted to bioinformatics genome protein_function protein_interactions by marcius on 2006-02-02 05:50:04 as ** along with 2 people and 2 groups eweaver maralena BioinfoCIPF SGU-CIPF
  • Protein function prediction via graph kernels.
    Bioinformatics, Vol. 21, No. suppl_1. (1 June 2005)
    by Karsten MM Borgwardt, Cheng, Stefan Schönauer, Sv NV Vishwanathan, Alex JJ Smola, Hans-Peter P Kriegel
    posted to bioinformatics classification clustering protein_function by marcius on 2006-02-17 20:36:39 as ** along with 8 people and 4 groups MarcoAlvarez tmmurali okarsligil vavi lfriedl eweaver kt wnpx kdl Bioinformatics BioinfoCIPF SGU-CIPF
  • Probing the beta2 adrenoceptor binding site with catechol reveals differences in binding and activation by agonists and partial agonists.
    J Biol Chem, Vol. 280, No. 23. (10 June 2005), pp. 22165-22171.
    by G Swaminath, X Deupi, TW Lee, W Zhu, FS Thian, TS Kobilka, B Kobilka
    posted to biology biophysics protein_function by marcius on 2005-10-22 21:55:55 as * along with 1 person and 3 groups xdeupi BioinfoCIPF LabCompMed SGU-CIPF
  • Moonlighting proteins
    Trends in Biochemical Sciences, Vol. 24, No. 1. (1 January 1999), pp. 8-11.
    by Constance J Jeffery
    posted to pleiotropy protein_function by marcius on 2005-10-21 02:42:03 as *** along with 3 people and 3 groups stevanspringer tny benlin FAB-lab BioinfoCIPF SGU-CIPF
  • Protein Molecular Function Prediction by Bayesian Phylogenomics.
    PLoS Comput Biol, Vol. 1, No. 5. (7 October 2005)
    by Barbara E E Engelhardt, Michael I I Jordan, Kathryn E E Muratore, Steven E E Brenner
    posted to bioinformatics prediction protein_function by marcius on 2006-09-07 17:43:33 as ** along with 7 people and 4 groups kentsis ana eoghanharr Einat dlr sriram_s bootsy structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • Introduction to informatics approaches in structural genomics: modeling and representation of function from macromolecular structure.
    Pac Symp Biocomput (2005), pp. 319-321.
    by PC Babbitt, PE Bourne, SD Mooney
    posted to protein_function structural_genomics by marcius on 2006-09-07 17:24:03 as ** along with 1 person and 2 groups penka BioinfoCIPF SGU-CIPF
  • Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models.
    PLoS Comput Biol, Vol. 1, No. 3. (19 August 2005)
    by Lei Xie, Philip E E Bourne
    posted to protein_function structural_genomics by marcius on 2006-09-07 17:23:24 as ** along with 2 people and 3 groups bicko caporaso biomedical-nlp BioinfoCIPF SGU-CIPF
  • Systemic determinants of gene evolution and function
    Molecular Systems Biology, Vol. 1, No. 1. (13 September 2005), pp. msb4100029-E1-msb4100029-E2.
    by Eugene V Koonin
    posted to evolution protein_function systems_biology by marcius on 2005-10-22 04:22:41 as **** along with 4 people and 3 groups ataheri Schmidtc bluto niallhaslam plant-development BioinfoCIPF SGU-CIPF
  • Evolution of protein structures and functions.
    Curr Opin Struct Biol, Vol. 12, No. 3. (June 2002), pp. 400-408.
    by LN Kinch, NV Grishin
    posted to homology_analogy protein_evolution protein_function protein_structure sequence_structure structure_function by ana to the group Bioinformatics on 2005-04-26 05:12:27 as read along with 5 people and 6 groups korakot karbak matzke barry joergkurtwegner Philosophy_of_Information Blog_and_Wiki_Research structural_bioinformatics Molecular-Modelling Drug-Design Cheminformatics
  • Evolution of protein fold in the presence of functional constraints
    Current Opinion in Structural Biology, Vol. 16, No. 3. (June 2006), pp. 399-408.
    by Antonina Andreeva, Alexey G Murzin
    posted to structure_classification protein_structure protein_function protein_evolution by ana to the group Bioinformatics on 2007-01-24 03:21:02 as *** along with 4 people and 1 group barry Einat tny cjeans structural_bioinformatics
  • Comparing functional annotation analyses with Catmap.
    BMC Bioinformatics, Vol. 5, No. 1. (9 December 2004)
    by T Breslin, P Edén, M Krogh
    posted to gene_ontology protein_function protein_sequence by ana to the group Bioinformatics on 2006-01-25 19:05:39 as *** along with 2 people and 2 groups ealloza raylim structural_bioinformatics BioinfoCIPF
  • Conformational diversity and protein evolution--a 60-year-old hypothesis revisited.
    Trends Biochem Sci, Vol. 28, No. 7. (July 2003), pp. 361-368.
    by LC James, DS Tawfik
    posted to protein_structure protein_function protein_evolution protein_dynamics by ana to the group Bioinformatics on 2007-01-24 03:21:40 as **** along with 1 person and 1 group barry structural_bioinformatics
  • Protein families and their evolution-a structural perspective.
    Annu Rev Biochem, Vol. 74 (2005), pp. 867-900.
    by CA Orengo, JM Thornton
    posted to protein_evolution protein_function protein_structure by ana to the group Bioinformatics on 2005-09-01 23:12:18 as *** along with 13 people and 5 groups barry tjimenez jwm chad_davis Einat Schmidtc marcius sriram_s ezotenko redelings medic0747 nigham sim82 structural_bioinformatics Radiation_Damage Stressosome BioinfoCIPF SGU-CIPF
  • 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 protein_structure protein_function by barry to the group Bioinformatics on 2008-09-26 21:48:09 as ** along with 9 people and 1 group i000 pengchy raik chad_davis zwang druvus reyez mdstobbe jameswasmuth structural_bioinformatics
  • On evolutionary conservation of thermodynamic coupling in proteins.
    J Biol Chem, Vol. 279, No. 18. (30 April 2004), pp. 19046-19050.
    by AA Fodor, RW Aldrich
    posted to correlated_mutations protein_evolution protein_folding protein_function protein_structure statistical_coupling_analysis by ana to the group Bioinformatics on 2005-09-27 22:12:45 as *** along with 7 people and 1 group barry gbart cjeans tale friendpine ca3295 Lombardo_7 structural_bioinformatics
  • Finding local structural similarities among families of unrelated protein structures: a generic non-linear alignment algorithm.
    Proteins, Vol. 34, No. 3. (15 February 1999), pp. 341-355.
    by JV Lehtonen, K Denessiouk, AC May, MS Johnson
    posted to local_structure_similarity protein_evolution protein_function by ana to the group Bioinformatics on 2005-05-03 03:45:04 as ** along with 1 group structural_bioinformatics
  • Fragnostic: walking through protein structure space.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by I Friedberg, A Godzik
    posted to protein_function protein_structure protein_universe structure_classification structure_comparison by ana to the group Bioinformatics on 2005-08-29 20:57:23 as read along with 7 people and 3 groups barry pansapiens aalibes Einat marcius alexg eweaver structural_bioinformatics BioinfoCIPF SGU-CIPF
  • Backbone and side chain dynamics of mutant calmodulin-Peptide complexes.
    Biochemistry, Vol. 44, No. 38. (27 September 2005), pp. 12627-12639.
    by TI Igumenova, AL Lee, AJ Wand
    posted to protein_dynamics protein_function protein_structure structure_comparison by ana to the group Bioinformatics on 2005-10-09 04:05:20 as ** along with 1 person and 1 group lna structural_bioinformatics
  • The properties of protein family space depend on experimental design
    Bioinformatics, Vol. 21, No. 11. (1 June 2005), pp. 2618-2622.
    by Victor Kunin, Sarah A Teichmann, Martijn A Huynen, Christos A Ouzounis
    posted to power-law protein_evolution protein_function protein_universe by ana to the group Bioinformatics on 2005-06-15 20:20:37 as ** along with 2 people and 1 group barry cjeans structural_bioinformatics
  • Data mining the protein data bank: residue interactions.
    Proteins, Vol. 49, No. 4. (1 December 2002), pp. 510-528.
    by TJ Oldfield
    posted to active_site algorithms data_mining protein_function protein_structure structure_comparison structure_superposition by ana to the group Bioinformatics on 2006-01-31 18:26:40 as read along with 2 people and 1 group blackbart rabio structural_bioinformatics
  • FSSA: a novel method for identifying functional signatures from structural alignments.
    Bioinformatics (28 April 2005)
    by Kai Wang, Ram Samudrala
    posted to function_prediction protein_function protein_structure structure_comparison by ana to the group Bioinformatics on 2005-06-16 19:29:55 as * along with 2 people and 1 group barry Einat structural_bioinformatics
  • Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function.
    J Mol Biol, Vol. 291, No. 1. (6 August 1999), pp. 177-196.
    by LA Mirny, EI Shakhnovich
    posted to protein_evolution protein_folding protein_function protein_structure sequence_comparison structure_comparison by ana to the group Bioinformatics on 2005-09-28 01:09:51 as ***** along with 3 people and 3 groups barry Einat marcius structural_bioinformatics BioinfoCIPF SGU-CIPF
  • Defining functional distances over Gene Ontology
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Angela D Pozo, Florencio Pazos, Alfonso Valencia
    posted to clustering gene_ontology protein_function by barry to the group Bioinformatics on 2008-03-20 01:06:15 as ** along with 6 people and 1 group tny grahamc sobolevnrm barriot carlk guhjy baker-group
  • The Protein Feature Ontology: A Tool for the Unification of Protein Feature Annotations.
    Bioinformatics (Oxford, England) (20 October 2008)
    by Gabrielle A A Reeves, Karen Eilbeck, Michele Magrane, Claire O'Donovan, Luisa Montecchi-Palazzi, Midori A A Harris, Sandra Orchard, Rafael C C Jimenez, Andreas Prlic, Tim J P J Hubbard, Henning Hermjakob, Janet M M Thornton
    posted to proteomics protein_function protein_features ontologies by grahamc on 2008-10-27 15:33:57 as ** along with 7 people and 2 groups zimbo1 barriot guhjy chad_davis Zephyrus i000 dullhunk Roswell Cancer Crosstalk MuraLab
  • Protein informatics towards function identification
    Current Opinion in Structural Biology, Vol. 13, No. 3. (June 2003), pp. 396-400.
    by Kengo Kinoshita, Haruki Nakamura
    posted to protein_function by chrn on 2005-08-05 14:18:05 as **
  • Pervasive and Persistent Redundancy among Duplicated Genes in Yeast
    PLoS Genet, Vol. 4, No. 7. (4 July 2008), e1000113.
    by Jedediah E Dean, Jerel C Davis, Ronald W Davis, Dmitri A Petrov
    posted to yeast subfunctionalization protein_function growth_rate genome_duplication gene_redundant gene_duplication evolution_rate convergent_evolution by biomcgary on 2008-11-12 22:48:26 as ** along with 3 people djkt bpcusack caseybrown
  • Functional protein divergence in the evolution of Homo sapiens
    Genome Biology, Vol. 9 (15 February 2008), R33.
    by Nuria Lopez-Bigas, Subhajyoti De, Sarah A Teichmann
    posted to evolution evolution_rate gene_duplication human protein_function sequence_divergence by biomcgary on 2008-02-15 16:00:14 as ** along with 4 people aalibes djkt grahamc zhanglab
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