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Tag protein_evolution [122 articles]

Recent papers classified by the tag protein_evolution.
  • An Improved General Amino Acid Replacement Matrix
    Mol Biol Evol, Vol. 25, No. 7. (1 July 2008), pp. 1307-1320.
    by Si Q Le, Olivier Gascuel
    posted to bioinformatics evolution methods molecular_evolution phylogenetics protein_evolution by stajich on 2008-06-14 07:08:00 as ** along with 2 people and 1 group friendpine dmp Berkeley Mycology
  • Evolution of a family of metazoan active-site-serine enzymes from penicillin-binding proteins: a novel facet of the bacterial legacy
    BMC Evolutionary Biology, Vol. 8, No. 1. (2008)
    by Nina Peitsaro, Zydrune Polianskyte, Jarno Tuimala, Isabella P Ares, Julius Liobikas, Oliver Speer, Dan Lindholm, James Thompson, Ove Eriksson
    posted to enzyme evolution metazoan protein_evolution by stajich on 2008-01-29 16:41:37 as ** along with 1 group Berkeley Mycology
  • A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast.
    Genome Res, Vol. 18, No. 1. (January 2008), pp. 137-147.
    by DR Scannell, KH Wolfe
    posted to duplication genome_evolution protein_evolution saccharomyces whole_genome yeast by stajich on 2008-03-10 17:52:44 as ** along with 3 people and 1 group djkt dandaman gjuggler Berkeley Mycology
  • Splicing and the Evolution of Proteins in Mammals
    PLoS Biology, Vol. 5, No. 2. (1 February 2007), e14.
    by Joanna L Parmley, Araxi O Urrutia, Lukasz Potrzebowski, Henrik Kaessmann, Laurence D Hurst
    posted to evolution intron phylogenetics protein protein_evolution alternative_splicing by stajich on 2007-06-27 05:34:01 as ** along with 7 people and 7 groups operon aalibes dpollard dchughes kehan jwestbrook gileswl biodiversity_conservation Bioinformatics EisenLab G4ID King_Lab GrassBase Genetics-of-Gambling
  • 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
  • Genome mosaicism and organismal lineages
    Trends in Genetics, Vol. 20, No. 5. (01 May 2004), pp. 254-260.
    by Olga Zhaxybayeva, Pascal Lapierre, Peter P Gogarten
    posted to protein_evolution by labedan on 2005-03-11 16:08:58 as ** along with 2 people operon fhsantanna
  • Simulating protein evolution in sequence and structure space.
    Curr Opin Struct Biol, Vol. 14, No. 2. (April 2004), pp. 202-207.
    by Y Xia, M Levitt
    posted to protein_evolution protein_folding by karbak on 2005-01-18 06:43:09 as ** along with 10 people and 4 groups betainverse korakot mdimmic rmj001 ana barry aalibes gbart analogAI insectopalo Philosophy_of_Information Blog_and_Wiki_Research structural_bioinformatics Bioinformatics
  • A universal trend of amino acid gain and loss in protein evolution
    Nature, Vol. aop, No. current. (19 January 2005)
    by King K Jordan, Fyodor A Kondrashov, Ivan A Adzhubei, Yuri I Wolf, Eugene V Koonin, Alexey S Kondrashov, Shamil Sunyaev
    posted to amino_acids evolution phylogeny protein_evolution by karbak on 2005-02-10 02:02:47 as *** along with 3 people gisle nagendranow michaelbarton
  • Transposition of hAT elements links transposable elements and V(D)J recombination
    Nature, Vol. 432, No. 7020. (23 December 2004), pp. 995-1001.
    by Liqin Zhou, Rupak Mitra, Peter W Atkinson, Alison B Hickman, Fred Dyda, Nancy L Craig
    posted to evolution immunology protein_evolution transpos by karbak on 2005-01-25 05:20:37 as ****
  • Protein structure: evolutionary bridges to new folds.
    Curr Biol, Vol. 17, No. 2. (23 January 2007)
    by TO Yeates
    posted to protein_families protein_evolution by jwm on 2007-02-07 18:03:03 as ** along with 2 groups Radiation_Damage Stressosome
  • A Single Determinant Dominates the Rate of Yeast Protein Evolution.
    Mol Biol Evol (19 October 2005)
    by D Allan A Drummond, Alpan Raval, Claus O O Wilke
    posted to bio113paper expression kaks protein_evolution yeast by penka to the group Nie on 2006-02-08 07:23:19 as ***** along with 3 people bjorns jpoyatos bicko
  • The proteins of linked genes evolve at similar rates.
    Nature, Vol. 407, No. 6806. (19 October 2000), pp. 900-903.
    by EJ Williams, LD Hurst
    posted to bio113paper protein_evolution by penka to the group Nie on 2006-02-08 07:26:06 as ** along with 3 people and 1 group stevanspringer bjorns bpcusack FAB-lab
  • Highly goes slowly
    J. Cell Biol., Vol. 171, No. 1. (10 October 2005), 10.
    by William A Wells
    posted to bio113paper protein_evolution by penka to the group Nie on 2006-02-15 09:25:50 as ****
  • 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 bio113paper protein_evolution by penka to the group Nie on 2006-02-22 06:40:50 as ** along with 14 people and 4 groups rklancer stevanspringer bjorns imouthesmp aprasad dayjm Einat marcius xwbcn balabu malcook balicea RamuAnandakrishnan wilbur structural_bioinformatics FAB-lab BioinfoCIPF SGU-CIPF
  • Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences.
    Proc Natl Acad Sci U S A, Vol. 102, No. 38. (20 September 2005), pp. 13526-13531.
    by Y Xing, C Lee
    posted to bio113paper protein_evolution splicing by penka to the group Nie on 2006-02-22 06:37:09 as **** along with 3 people and 2 groups aprasad radek bsmagic Bioinformatics bioinplant
  • Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets.
    BMC Evol Biol, Vol. 3 (2 October 2003)
    by JD Bloom, C Adami
    posted to bio113paper protein_evolution by penka to the group Nie on 2006-02-22 03:19:49 as ** along with 4 people diamantis bjorns balajis rsantana
  • Protein Evolution in the Context of <i>Drosophila</i> Development
    Journal of Molecular Evolution, Vol. 60, No. 6. (June 2005), pp. 774-785.
    by Jerel C Davis, Onn Brandman, Dmitri A Petrov
    posted to bio113paper_q drosophila expression protein_evolution by penka to the group Nie on 2006-02-22 03:38:45 as ** along with 1 person imouthesmp
  • Converging on a general model of protein evolution.
    Trends Biotechnol, Vol. 23, No. 10. (October 2005), pp. 485-487.
    by JT Herbeck, DP Wall
    posted to bio113paper protein_evolution by penka to the group Nie on 2006-02-22 03:46:19 as *** along with 2 people bjorns i41m
  • Size of the protein-coding genome and rate of molecular evolution.
    J Hum Genet, Vol. 50, No. 5. (2005), pp. 217-229.
    by ZA Rajic, GM Jankovic, A Vidovic, NM Milic, D Skoric, M Pavlovic, V Lazarevic
    posted to bio113paper protein_evolution by penka to the group Nie on 2006-02-22 04:27:59 as ** along with 1 person aprasad
  • Highly expressed genes in yeast evolve slowly.
    Genetics, Vol. 158, No. 2. (June 2001), pp. 927-931.
    by C Pál, B Papp, LD Hurst
    posted to bio113paper expression protein_evolution yeast by penka to the group Nie on 2006-02-24 10:06:09 as ** along with 4 people bjorns lewbin balicea skumagai
  • Correlated Evolution of Synonymous and Nonsynonymous Sites in Drosophila
    Journal of Molecular Evolution, Vol. 59, No. 6. (December 2004), pp. 771-779.
    by Marais, Gabriel, Domazet-Loso, Tomislav, Tautz, Diethard, Charlesworth, Brian
    posted to bio113paper_q drosophila expression kaks melanogaster protein_evolution by penka to the group Nie on 2006-02-22 03:41:20 as ** along with 1 person bjorns
  • A periodic pattern of mRNA secondary structure created by the genetic code
    Nucl. Acids Res., Vol. 34, No. 8. (8 May 2006), pp. 2428-2437.
    by Svetlana A Shabalina, Aleksey Y Ogurtsov, Nikolay A Spiridonov
    posted to protein_evolution read_next by penka to the group Nie on 2006-06-04 07:29:58 as ** along with 2 people eckart_bindewald raylim
  • What determines the rate of sequence evolution?
    Curr Biol, Vol. 10, No. 11. (1 June 2000)
    by JF Brookfield
    posted to bio113paper protein_evolution by penka to the group Nie on 2006-02-08 07:38:30 as **
  • Essential Genes Are More Evolutionarily Conserved Than Are Nonessential Genes in Bacteria
    Genome Res., Vol. 12, No. 6. (1 June 2002), pp. 962-968.
    by King I Jordan, Igor B Rogozin, Yuri I Wolf, Eugene V Koonin
    posted to bio113paper protein_evolution by penka to the group Nie on 2006-02-22 08:42:31 as **** along with 4 people bjorns BarrosH ankur_iitg tfogal
  • Determinants of Adaptive Evolution at the Molecular Level: the Extended Complexity Hypothesis
    Molecular Biology and Evolution, Vol. 22, No. 2., 200.
    by Stephane Aris-Brosou
    posted to bio113paper protein_evolution theory by penka to the group Nie on 2006-02-22 08:59:18 as **** along with 1 person hdopazo
  • An analysis of determinants of amino acids substitution rates in bacterial proteins.
    Mol Biol Evol, Vol. 21, No. 1. (January 2004), pp. 108-116.
    by EP Rocha, A Danchin
    posted to bacteria bio113paper protein_evolution by penka to the group Nie on 2006-02-22 08:43:21 as **** along with 4 people bjorns tny jpoyatos skumagai
  • Intrinsically unstructured proteins and their functions
    Nature Reviews Molecular Cell Biology, Vol. 6, No. 3. (01 March 2005), pp. 197-208.
    by Jane J Dyson, Peter E Wright
    posted to positive_selection protein_evolution read_next by penka to the group Nie on 2006-06-04 03:11:53 as ***** along with 2 people chad_davis cactus
  • Protein Superfamily Evolution and the Last Universal Common Ancestor (LUCA)
    Journal of Molecular Evolution
    by Juan AG Ranea, Antonio Sillero, Janet M Thornton, Christine A Orengo
    posted to superfamily protein_evolution luca by cmura to the group MuraLab on 2008-10-31 13:43:18 as *** along with 6 people and 2 groups ucbcjbm ana barry tny grottenolm jwm structural_bioinformatics Bioinformatics
  • Convergent Evolution of Enzyme Active Sites Is not a Rare Phenomenon
    Journal of Molecular Biology, Vol. 372, No. 3. (21 September 2007), pp. 817-845.
    by Pier F Gherardini, Mark N Wass, Manuela Helmer-Citterich, Michael J Sternberg
    posted to protein_structure protein_evolution convergent_evolution by barry to the group Bioinformatics on 2007-08-31 19:04:36 as * along with 8 people and 1 group ucbcjbm tjimenez jjray chad_davis tny shung Minty sim82 structural_bioinformatics
  • Point Mutations in Protein Globular Domains: Contributions from Function, Stability and Misfolding
    Journal of Molecular Biology, Vol. 363, No. 2. (20 October 2006), pp. 422-432.
    by IE Sanchez, J Tejero, C Gomez-Moreno, M Medina, L Serrano
    posted to protein_evolution protein_sequence protein_structure by barry to the group Bioinformatics on 2006-09-29 22:48:42 as ** along with 2 people and 1 group chad_davis cat_worth structural_bioinformatics
  • Protein Differentiation: Emergence of Novel Proteins during Evolution
    Angewandte Chemie International Edition in English, Vol. 20, No. 2. (22 December 2003), pp. 143-151.
    by Georg E Schulz
    posted to protein_evolution protein_structure by ana to the group Bioinformatics on 2005-05-03 03:38:34 as **** along with 1 group structural_bioinformatics
  • Scoring residue conservation.
    Proteins, Vol. 48, No. 2. (1 August 2002), pp. 227-241.
    by WS Valdar
    posted to protein_evolution protein_sequence residue_annotation review by barry to the group Bioinformatics on 2006-05-03 23:58:00 as read along with 6 people and 1 group pansapiens bicko sriram_s cjeans sobolevnrm marti structural_bioinformatics
  • Understanding protein folding via free-energy surfaces from theory and experiment.
    Trends Biochem Sci, Vol. 25, No. 7. (July 2000), pp. 331-339.
    by AR Dinner, A Sali, LJ Smith, CM Dobson, M Karplus
    posted to protein_evolution protein_folding protein_structure by ana to the group Bioinformatics on 2005-05-03 03:49:29 as ***** along with 1 person and 1 group rabio 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
  • Evolution of protein structures and functions
    Current Opinion in Structural Biology, Vol. 12, No. 3. (01 June 2002), pp. 400-408.
    by Lisa N Kinch, Nick V Grishin
    posted to protein_evolution protein_structure structure_comparison by ana to the group Bioinformatics on 2005-06-06 19:09:49 as read along with 1 person and 1 group barry structural_bioinformatics
  • The evolutionary capacity of protein structures
    (2004), pp. 290-297.
    by Leonid Meyerguz, David Kempe, Jon Kleinberg, Ron Elber
    posted to protein_evolution protein_structure by ana to the group Bioinformatics on 2005-05-25 19:02:32 as ** along with 1 person and 1 group apaydin structural_bioinformatics
  • A class of eukaryotic GTPase with a punctate distribution suggesting multiple functional replacements of translation elongation factor 1alpha.
    Proc Natl Acad Sci U S A, Vol. 101, No. 43. (26 October 2004), pp. 15380-15385.
    by PJ Keeling, Y Inagaki
    posted to evolution hgt protein_evolution taxonomy by ana to the group Bioinformatics on 2005-10-29 18:56:22 as *** along with 1 person and 2 groups vwchan structural_bioinformatics beta
  • Structural Diversity of Domain Superfamilies in the CATH Database.
    J Mol Biol (2 June 2006)
    by Gabrielle A A Reeves, Timothy J J Dallman, Oliver C C Redfern, Adrian Akpor, Christine A A Orengo
    posted to cath protein_design protein_evolution protein_protein protein_structure by barry to the group Bioinformatics on 2006-07-07 19:57:04 as **** along with 2 people and 4 groups marcius sobolevnrm structural_bioinformatics BioinfoCIPF SGU-CIPF baker-group
  • Understanding hierarchical protein evolution from first principles.
    J Mol Biol, Vol. 312, No. 1. (7 September 2001), pp. 289-307.
    by NV Dokholyan, EI Shakhnovich
    posted to protein_evolution protein_structure structure_classification by ana to the group Bioinformatics on 2005-03-03 19:56:39 as *** along with 3 people and 1 group mdimmic barry pansapiens structural_bioinformatics
  • The Relationship Between Domain Duplication and Recombination
    Journal of Molecular Biology, Vol. 346, No. 1. (11 February 2005), pp. 355-365.
    by Christine Vogel, Sarah A Teichmann, Jose Pereira-Leal
    posted to gene_duplication genome_evolution power-law protein_evolution protein_interaction protein_universe selection stochastic_process by ana to the group Bioinformatics on 2005-06-27 18:10:37 as * along with 5 people and 3 groups marcius tny cjeans martainn mdimon structural_bioinformatics BioinfoCIPF SGU-CIPF
  • notes Tracing evolutionary pressure
    Bioinformatics, Vol. 24, No. 7. (1 April 2008), pp. 908-915.
    by Kai Ye, Gert Vriend, Adriaan P Ijzerman
    posted to bioinf_methods phylogeny protein_evolution protein_sequence residue_annotation by barry to the group Bioinformatics on 2008-04-11 19:13:22 as *** along with 2 people and 1 group sunhwan gulkur structural_bioinformatics
  • 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
  • Tubulin and FtsZ form a distinct family of GTPases.
    Nat Struct Biol, Vol. 5, No. 6. (June 1998), pp. 451-458.
    by E Nogales, KH Downing, LA Amos, J Löwe
    posted to cytoskeleton ntpases protein_evolution tubulin by barry to the group Bioinformatics on 2005-03-16 03:06:12 as **** along with 1 group structural_bioinformatics
  • Expanding protein universe and its origin from the biological Big Bang.
    Proc Natl Acad Sci U S A, Vol. 99, No. 22. (29 October 2002), pp. 14132-14136.
    by NV Dokholyan, B Shakhnovich, EI Shakhnovich
    posted to protein_evolution protein_universe by ana to the group Bioinformatics on 2005-03-03 19:48:01 as *** along with 2 people and 1 group barry lulab structural_bioinformatics
  • Influence of conservation on calculations of amino acid covariance in multiple sequence alignments.
    Proteins, Vol. 56, No. 2. (1 August 2004), pp. 211-221.
    by AA Fodor, RW Aldrich
    posted to correlated_mutations multiple_sequence_alignment protein_evolution protein_sequence protein_structure statistical_coupling_analysis by ana to the group Bioinformatics on 2005-09-27 22:05:54 as *** along with 6 people and 1 group gbart cjeans jlh64 mingzhi dgront Lombardo_7 structural_bioinformatics
  • Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap.
    Proc Natl Acad Sci U S A, Vol. 97, No. 7. (28 March 2000), pp. 3288-3291.
    by KR Wollenberg, WR Atchley
    posted to bioinf_methods protein_evolution protein_sequence sequence_comparison by barry to the group Bioinformatics on 2005-08-01 22:45:50 as *** along with 2 people and 1 group druvus friendpine structural_bioinformatics
  • Small Libraries of Protein Fragments Model Native Protein Structures Accurately
    Journal of Molecular Biology, Vol. 323, No. 2. (18 October 2002), pp. 297-307.
    by Rachel Kolodny, Patrice Koehl, Leonidas Guibas, Michael Levitt
    posted to comparative_model protein_design protein_evolution protein_structure structural_bioinformatics structure_comparison by barry to the group Bioinformatics on 2005-09-07 17:59:27 as ***** along with 1 group structural_bioinformatics
  • Evolution and similarity evaluation of protein structures in contact map space.
    Proteins, Vol. 59, No. 2. (1 May 2005), pp. 196-204.
    by N Gupta, N Mangal, S Biswas
    posted to contact_maps protein_evolution protein_structure structure_prediction by ana to the group Bioinformatics on 2005-04-20 23:53:24 as ** along with 1 person and 1 group vavi structural_bioinformatics
  • 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
  • Cytoskeletal proteins: the evolution of cell division.
    Curr Biol, Vol. 8, No. 10. (7 May 1998)
    by DM Faguy, WF Doolittle
    posted to cytoskeleton protein_evolution protein_sequence tubulin by barry to the group Bioinformatics on 2005-03-16 02:51:40 as **** along with 1 group structural_bioinformatics
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