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Group: Bioinformatics - with tag protein_evolution [74 articles]

Recent papers posted by members of the Bioinformatics group with tag protein_evolution
  • 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 1 person and 1 group sunhwan structural_bioinformatics
  • Optimization of specificity in a cellular protein interaction network by negative selection.
    Nature, Vol. 426, No. 6967. (11 December 2003), pp. 676-680.
    by A Zarrinpar, SH Park, WA Lim
    posted to protein_structure protein_sequence protein_protein protein_evolution protein_design by barry to the group Bioinformatics on 2007-09-04 19:25:04 as ** along with 3 people and 1 group paolomarcatili grahamc cjeans structural_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 6 people and 1 group sim82 tjimenez jjray chad_davis tny Minty structural_bioinformatics
  • 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 protein_structure protein_evolution protein_design fad by barry to the group Bioinformatics on 2007-07-20 18:33:27 as *** along with 3 people and 1 group Einat zwang mdimon structural_bioinformatics
  • Proteins of the same fold and unrelated sequences have similar amino acid composition.
    Proteins (24 March 2006)
    by Yanay Ofran, Hanah Margalit
    posted to protein_structure protein_sequence protein_evolution by barry to the group Bioinformatics on 2007-02-09 04:56:15 as ** along with 2 people and 1 group Einat msierk 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
  • 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
  • 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
  • Early Protein Evolution: Building Domains from Ligand-binding Polypeptide Segments
    Journal of Molecular Biology, Vol. 363, No. 2. (20 October 2006), pp. 460-468.
    by Lutz Riechmann, Greg Winter
    posted to protein_evolution protein_folding protein_fragments by barry to the group Bioinformatics on 2006-09-29 19:10:15 as ** along with 1 person and 1 group cjeans structural_bioinformatics
  • The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by F Pearl, A Todd, I Sillitoe, M Dibley, O Redfern, T Lewis, C Bennett, R Marsden, A Grant, D Lee, A Akpor, M Maibaum, A Harrison, T Dallman, G Reeves, I Diboun, S Addou, S Lise, C Johnston, A Sillero, J Thornton, C Orengo
    posted to cath protein_evolution protein_structure by barry to the group Bioinformatics on 2006-07-07 19:59:52 as ** along with 3 people and 1 group tjimenez chrn alexg structural_bioinformatics
  • 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
  • Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes
    BMC Genomics, Vol. 7 (2006), pp. 18-18.
    by Dale N Richardson, Mark P Simmons, Anireddy S Reddy
    posted to kinesin molecular_motors phylogeny protein_evolution protein_sequence by barry to the group Bioinformatics on 2006-06-12 19:39:17 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 7 people and 1 group chad_davis marti pansapiens bicko sriram_s cjeans sobolevnrm structural_bioinformatics
  • Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins
    Science, Vol. 312, No. 5770. (7 April 2006), pp. 111-114.
    by Daniel M Weinreich, Nigel F Delaney, Mark A Depristo, Daniel L Hartl
    posted to protein_design protein_evolution protein_sequence by barry to the group Bioinformatics on 2006-04-07 20:25:19 as ***** along with 13 people and 4 groups stevanspringer pansapiens imouthesmp dayjm Einat marcius i41m nirfriedman cmm RowanBarrett ramensky Vaquero Ema structural_bioinformatics FAB-lab BioinfoCIPF SGU-CIPF
  • Ran's C-terminal, basic patch, and nucleotide exchange mechanisms in light of a canonical structure for Rab, Rho, Ras, and Ran GTPases.
    Genome Res, Vol. 13, No. 4. (April 2003), pp. 673-692.
    by AF Neuwald, N Kannan, A Poleksic, N Hata, JS Liu
    posted to allosteric bioinf_methods contacts core_residues g_proteins ntpases p-loop protein_design protein_dynamics protein_evolution protein_sequence protein_structure by barry to the group Bioinformatics on 2006-01-07 03:57:13 as ***** along with 1 group structural_bioinformatics
  • Intrinsically Disordered Loops Inserted into the Structural Domains of Human Proteins
    Journal of Molecular Biology, Vol. 355, No. 4. (27 January 2006), pp. 845-857.
    by Satoshi Fukuchi, Keiichi Homma, Yoshiaki Minezaki, Ken Nishikawa
    posted to disorder protein_dynamics protein_evolution protein_sequence protein_structure by barry to the group Bioinformatics on 2006-01-02 19:14:30 as *** along with 3 people and 1 group chad_davis tny sotaro structural_bioinformatics
  • 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 function_prediction gene_duplication hgt orthology phylogenomics protein_evolution protein_function protein_sequence by ana to the group Bioinformatics on 2005-11-22 19:15:19 as ** along with 7 people and 3 groups kentsis eoghanharr Einat dlr marcius sriram_s bootsy structural_bioinformatics BioinfoCIPF SGU-CIPF
  • Highways of gene sharing in prokaryotes
    PNAS, Vol. 102, No. 40. (4 October 2005), pp. 14332-14337.
    by Robert G Beiko, Timothy J Harlow, Mark A Ragan
    posted to hgt phylogeny protein_evolution protein_sequence by ana to the group Bioinformatics on 2005-11-22 00:44:19 as ***** along with 3 people and 1 group AaronDarling treangen Minty structural_bioinformatics
  • Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.
    Nature, Vol. 399, No. 6734. (27 May 1999), pp. 323-329.
    by KE Nelson, RA Clayton, SR Gill, ML Gwinn, RJ Dodson, DH Haft, EK Hickey, JD Peterson, WC Nelson, KA Ketchum, L McDonald, TR Utterback, JA Malek, KD Linher, MM Garrett, AM Stewart, MD Cotton, MS Pratt, CA Phillips, D Richardson, J Heidelberg, GG Sutton, RD Fleischmann, JA Eisen, O White, SL Salzberg, HO Smith, JC Venter, CM Fraser
    posted to hgt protein_evolution by ana to the group Bioinformatics on 2005-11-19 21:39:08 as read along with 2 people and 1 group jmeppley karfunkel structural_bioinformatics
  • Convergent evolution: the need to be explicit.
    Trends Biochem Sci, Vol. 19, No. 1. (January 1994), pp. 15-18.
    by RF Doolittle
    posted to protein_evolution by ana to the group Bioinformatics on 2005-11-19 21:36:51 as read along with 1 person and 1 group barry structural_bioinformatics
  • The multiplicity of domains in proteins.
    Annu Rev Biochem, Vol. 64 (1995), pp. 287-314.
    by RF Doolittle
    posted to protein_evolution by ana to the group Bioinformatics on 2005-11-19 21:35:02 as read along with 2 people and 1 group barry dlr structural_bioinformatics
  • Distinguishing homologous from analogous proteins.
    Syst Zool, Vol. 19, No. 2. (June 1970), pp. 99-113.
    by WM Fitch
    posted to protein_evolution by ana to the group Bioinformatics on 2005-11-19 21:32:52 as read along with 1 person and 1 group barry structural_bioinformatics
  • Evolution of the protein repertoire.
    Science, Vol. 300, No. 5626. (13 June 2003), pp. 1701-1703.
    by C Chothia, J Gough, C Vogel, SA Teichmann
    posted to protein_evolution by ana to the group Bioinformatics on 2005-11-19 21:30:23 as read along with 3 people and 1 group karbak barry tny structural_bioinformatics
  • Prediction of functional specificity determinants from protein sequences using log-likelihood ratios
    Bioinformatics (8 August 2005)
    by J Pei, W Cai, LN Kinch, NV Grishin
    posted to classification function_prediction protein_evolution protein_function by ana to the group Bioinformatics on 2005-11-09 18:56:06 as *** along with 2 people and 1 group barry Einat 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
  • The cobweb of life revealed by genome-scale estimates of horizontal gene transfer.
    PLoS Biol, Vol. 3, No. 10. (October 2005)
    by F Ge, LS Wang, J Kim
    posted to evolution hgt protein_evolution taxonomy tree_of_life by ana to the group Bioinformatics on 2005-10-29 18:51:34 as *** along with 2 people and 1 group jmeppley AaronDarling structural_bioinformatics
  • Structure of bacterial tubulin BtubA/B: evidence for horizontal gene transfer.
    Proc Natl Acad Sci U S A, Vol. 102, No. 26. (28 June 2005), pp. 9170-9175.
    by D Schlieper, MA Oliva, JM Andreu, J Löwe
    posted to cytoskeleton protein_evolution tubulin by barry to the group Bioinformatics on 2005-10-26 00:01:46 as *** along with 1 person and 1 group karfunkel structural_bioinformatics
  • Electrotactins: a class of adhesion proteins with conserved electrostatic and structural motifs.
    Protein Eng, Vol. 11, No. 6. (June 1998), pp. 415-420.
    by SA Botti, CE Felder, JL Sussman, I Silman
    posted to bioinf_methods electrostatics protein_evolution protein_structure by barry to the group Bioinformatics on 2005-10-10 09:22:28 as *** along with 1 group structural_bioinformatics
  • Conservation of electrostatic properties within enzyme families and superfamilies.
    Biochemistry, Vol. 42, No. 12. (1 April 2003), pp. 3464-3473.
    by DR Livesay, P Jambeck, A Rojnuckarin, S Subramaniam
    posted to electrostatics protein_design protein_evolution protein_structure by barry to the group Bioinformatics on 2005-10-09 01:28:18 as read along with 1 person and 1 group Einat structural_bioinformatics
  • Structural Features can be Unconserved in Proteins with Similar Folds : An Analysis of Side-chain to Side-chain Contacts Secondary Structure and Accessibility
    Journal of Molecular Biology, Vol. 244, No. 3. (1 December 1994), pp. 332-350.
    by Robert B Russell, Geoffrey J Barton
    posted to contact_prediction protein_evolution protein_structure structure_comparison by ana to the group Bioinformatics on 2005-10-05 22:30:59 as **** along with 1 person and 1 group rabio structural_bioinformatics
  • 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 protein_evolution protein_sequence protein_structure by ana to the group Bioinformatics on 2005-10-05 19:51:48 as *** along with 1 person and 3 groups marcius structural_bioinformatics BioinfoCIPF SGU-CIPF
  • 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
  • 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 6 people and 1 group ca3295 friendpine barry gbart cjeans tale 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 5 people and 1 group dgront gbart cjeans jlh64 mingzhi structural_bioinformatics
  • Evolutionary information for specifying a protein fold
    Nature, Vol. 437, No. 7058., pp. 512-518.
    by Michael Socolich, Steve W Lockless, William P Russ, Heather Lee, Kevin H Gardner, Rama Ranganathan
    posted to correlated_mutations protein_evolution protein_sequence protein_structure statistical_coupling_analysis by ana to the group Bioinformatics on 2005-09-22 23:02:40 as read along with 14 people and 4 groups barry lna bpb Einat balajis marcius gbart analogAI nirfriedman caporaso massivemayhem mingzhi bethbromley ca3295 structural_bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF
  • Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding.
    Protein Sci, Vol. 3, No. 5. (May 1994), pp. 769-778.
    by D Fischer, H Wolfson, SL Lin, R Nussinov
    posted to bioinf_methods protein_design protein_evolution protein_structure structural_bioinformatics structure_comparison by barry to the group Bioinformatics on 2005-09-19 22:03:37 as ***** along with 4 people and 1 group aalibes shadowman tjimenez chrys structural_bioinformatics
  • In silico Discovery of Enzyme-Substrate Specificity-determining Residue Clusters
    Journal of Molecular Biology, Vol. 352, No. 5. (7 October 2005), pp. 1105-1117.
    by Gong-Xin Yu, Byung-Hoon Park, Praveen Chandramohan, Rajesh Munavalli, Al Geist, Nagiza F Samatova
    posted to bioinf_methods correlated_mutations protein_design protein_evolution protein_sequence sequence_comparison by barry to the group Bioinformatics on 2005-09-15 18:06:44 as **** along with 1 person and 1 group cjeans structural_bioinformatics
  • Detection of hydrogen-bond signature patterns in protein families.
    Bioinformatics, Vol. 19, No. 1. (January 2003), pp. 167-168.
    by T Prasad, MN Prathima, N Chandra
    posted to hydrogen-bond protein_evolution protein_stability protein_structure structure_comparison web_server by ana to the group Bioinformatics on 2005-09-07 20:01:20 as read along with 1 group 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
  • Small libraries of protein fragments model native protein structures accurately.
    J Mol Biol, Vol. 323, No. 2. (18 October 2002), pp. 297-307.
    by R Kolodny, P Koehl, L Guibas, M Levitt
    posted to comparative_modeling protein_design protein_evolution protein_structure structure_comparison structure_fragments by ana to the group Bioinformatics on 2005-09-07 17:58:32 as ** along with 3 people and 1 group barry eckart_bindewald j3xucite 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 sim82 nigham barry tjimenez jwm chad_davis Einat Schmidtc marcius sriram_s ezotenko redelings medic0747 structural_bioinformatics Radiation_Damage Stressosome BioinfoCIPF SGU-CIPF
  • How old is your fold?
    Bioinformatics, Vol. 21 Suppl 1 (1 June 2005)
    by HF Winstanley, S Abeln, CM Deane
    posted to protein_evolution protein_sequence protein_structure by ana to the group Bioinformatics on 2005-08-12 21:03:50 as ** along with 2 people and 1 group pansapiens cdeane structural_bioinformatics
  • Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis.
    Mol Biol Evol, Vol. 17, No. 1. (January 2000), pp. 164-178.
    by WR Atchley, KR Wollenberg, WM Fitch, W Terhalle, AW Dress
    posted to bioinf_methods protein_evolution protein_sequence sequence_comparison by barry to the group Bioinformatics on 2005-08-01 22:49:52 as **** along with 1 person and 1 group friendpine 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 1 person and 1 group friendpine 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
  • 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 p-loop protein_evolution protein_sequence protein_structure by barry to the group Bioinformatics on 2005-06-24 23:37:49 as read along with 3 people and 1 group Einat tny leemary4 structural_bioinformatics
  • Evolutionary lines of cysteine peptidases.
    Biol Chem, Vol. 382, No. 5. (May 2001), pp. 727-733.
    by AJ Barrett, ND Rawlings
    posted to molecular_mimicry protein_evolution protein_sequence protein_structure virulence_factor by ana to the group Bioinformatics on 2005-06-20 19:06:44 as **** along with 1 group 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
  • In search of the limits of evolution
    Nature Genetics, Vol. 37, No. 1. (January 2005), pp. 9-10.
    by Fyodor A Kondrashov
    posted to directed_evolution neofunctionalization protein_evolution protein_function protein_moonlighting by ana to the group Bioinformatics on 2005-06-06 21:14:46 as *** along with 1 person and 1 group LeightonP structural_bioinformatics
  • The 'evolvability' of promiscuous protein functions
    Nature Genetics, Vol. 37, No. 1. (January 2005), pp. 73-76.
    by Amir Aharoni, Leonid Gaidukov, Olga Khershonsky, Stephen M Gould, Cintia Roodveldt, Dan S Tawfik
    posted to directed_evolution neofunctionalization protein_evolution protein_function protein_moonlighting by ana to the group Bioinformatics on 2005-06-06 21:12:37 as **** along with 1 person and 1 group LeightonP structural_bioinformatics
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