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Tag protein_sequence [114 articles]

Recent papers classified by the tag protein_sequence.
  • Molecular dynamics study of time-correlated protein domain motions and molecular flexibility: cytochrome P450BM-3.
    Biophys. J., Vol. 73, No. 3. (1 September 1997), pp. 1147-1159.
    by GE Arnold, RL Ornstein
    posted to protein_sequence md_simulation distance_matrices correlated_motions by barry to the group Bioinformatics on 2007-07-26 02:46:16 as ** along with 1 group structural_bioinformatics
  • 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
  • Molecular evolution of FtsZ protein sequences encoded within the genomes of archaea, bacteria, and eukaryota.
    J Mol Evol, Vol. 58, No. 1. (January 2004), pp. 19-29.
    by S Vaughan, B Wickstead, K Gull, SG Addinall
    posted to cytoskeleton protein_evolution protein_sequence tubulin by barry to the group Bioinformatics on 2005-03-14 19:44:43 as ** along with 1 group structural_bioinformatics
  • Prediction of the occurrence of the ADP-binding [beta][alpha][beta]-fold in proteins, using an amino acid sequence fingerprint
    Journal of Molecular Biology, Vol. 187, No. 1. (5 January 1986), pp. 101-107.
    by Rik K Wierenga, Peter Terpstra, Wim G Hol
    posted to ctbp protein_sequence by barry to the group Bioinformatics on 2006-08-15 20:04:32 as ** along with 1 group structural_bioinformatics
  • Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces.
    Bioinformatics, Vol. 21, No. 12. (15 June 2005), pp. 2850-2855.
    by AS Aytuna, A Gursoy, O Keskin
    posted to bioinf_methods protein_protein protein_sequence protein_structure by barry to the group Bioinformatics on 2006-03-06 22:03:40 as ** along with 4 people and 1 group apaydin bicko j3xucite dyermd structural_bioinformatics
  • Multiple sequence alignment using partial order graphs.
    Bioinformatics, Vol. 18, No. 3. (March 2002), pp. 452-464.
    by C Lee, C Grasso, MF Sharlow
    posted to multiple_sequence_alignment protein_sequence sequence_comparison by ana to the group Bioinformatics on 2005-11-22 00:46:26 as *** along with 7 people and 2 groups treangen Neeperando Cortel AbnerCYH azazello wenhan gjuggler structural_bioinformatics MBLAB
  • Molecular dissection of the inhibitor binding pocket of mitotic kinesin Eg5 reveals mutants that confer resistance to antimitotic agents
    Journal Of Molecular Biology, Vol. 360, No. 2. (7 July 2006), pp. 360-376.
    by Sebastien Brier, David Lemaire, Salvatore Debonis, Eric Forest, Frank Kozielski
    posted to drug_design eg5 inhibitor_design kinesin molecular_motors monastrol protein_dynamics protein_sequence protein_structure by barry to the group Bioinformatics on 2006-07-24 19:02:13 as ***** along with 1 group 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
  • PhyloGenie: automated phylome generation and analysis.
    Nucleic Acids Res, Vol. 32, No. 17. (2004), pp. 5231-5238.
    by T Frickey, AN Lupas
    posted to comparative_genomics genome_evolution hgt orthology phylogeny protein_sequence sequence_comparison by ana to the group Bioinformatics on 2005-06-15 19:38:44 as *** along with 2 people and 1 group Garamonfok Patola structural_bioinformatics
  • Empirical and structural models for insertions and deletions in the divergent evolution of proteins.
    J Mol Biol, Vol. 229, No. 4. (20 February 1993), pp. 1065-1082.
    by SA Benner, MA Cohen, GH Gonnet
    posted to indels protein_sequence protein_structure by ana to the group Bioinformatics on 2005-11-17 21:55:38 as ***** along with 4 people and 3 groups gjuggler barry mattjb martainn structural_bioinformatics ComplexAdaptiveSystems DSTO-CAS
  • Amino acid preferences at protein binding sites
    FEBS Letters, Vol. 349, No. 1. (25 July 1994), pp. 125-130.
    by Hugo O Villar, Lawrence M Kauvar
    posted to protein_sequence protein_protein by barry to the group Bioinformatics on 2007-09-04 20:17:20 as * along with 1 group 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 2 people and 3 groups stevanspringer marcius structural_bioinformatics BioinfoCIPF SGU-CIPF
  • On the interactions of charged side chains with the alpha-helix backbone.
    Biophys Chem, Vol. 31, No. 1-2. (August 1988), pp. 29-34.
    by A Godzik, T Wesolowski
    posted to interaction_hierarchy protein_sequence protein_structure sequence_comparison by ana to the group Bioinformatics on 2005-08-29 21:43:25 as * along with 1 person and 1 group pansapiens structural_bioinformatics
  • Fast embedding methods for clustering tens of thousands of sequences.
    Computational biology and chemistry, Vol. 32, No. 4. (August 2008), pp. 282-286.
    by G Blackshields, M Larkin, IM Wallace, A Wilm, DG Higgins
    posted to bioinf_methods clustering protein_sequence by barry to the group Bioinformatics on 2008-08-23 20:27:35 as **** along with 1 group structural_bioinformatics
  • A phylogenomic approach to microbial evolution.
    Nucleic Acids Res, Vol. 29, No. 2. (15 January 2001), pp. 545-552.
    by T Sicheritz-Pontén, SG Andersson
    posted to comparative_genomics genome_evolution hgt orthology phylogeny protein_sequence sequence_comparison by ana to the group Bioinformatics on 2005-06-16 19:33:02 as * along with 2 people and 1 group LeightonP greger_halltorp structural_bioinformatics
  • How does a protein fold?
    Nature, Vol. 369, No. 6477. (19 May 1994), pp. 248-251.
    by A Sali, E Shakhnovich, M Karplus
    posted to fold_space protein_evolution protein_folding protein_sequence protein_structure structural_bioinformatics by barry to the group Bioinformatics on 2005-03-16 03:16:39 as ***** along with 2 people and 1 group ucbcjbm evaf structural_bioinformatics
  • FtsZ, a prokaryotic homolog of tubulin?
    Cell, Vol. 80, No. 3. (10 February 1995), pp. 367-370.
    by HP Erickson
    posted to cytoskeleton protein_evolution protein_sequence tubulin by barry to the group Bioinformatics on 2005-03-16 02:51:10 as ** along with 1 group structural_bioinformatics
  • Hidden Markov models for detecting remote protein homologies.
    Bioinformatics, Vol. 14, No. 10. (1998), pp. 846-856.
    by K Karplus, C Barrett, R Hughey
    posted to hmm protein_sequence sequence_alignment sequence_comparison by ana to the group Bioinformatics on 2006-12-07 22:44:11 as *** along with 6 people and 1 group treangen j3xucite dgront rabio saunders granujilla structural_bioinformatics
  • Optimal classification of protein sequences and selection of representative sets from multiple alignments: application to homologous families and lessons for structural genomics.
    Protein Eng, Vol. 14, No. 4. (April 2001), pp. 209-217.
    by AC May
    posted to bioinf_methods protein_sequence sequence_comparison by barry to the group Bioinformatics on 2006-05-04 17:16:42 as **** along with 1 group structural_bioinformatics
  • Comparison of sequence profiles. Strategies for structural predictions using sequence information.
    Protein Sci, Vol. 9, No. 2. (February 2000), pp. 232-241.
    by L Rychlewski, L Jaroszewski, W Li, A Godzik
    posted to protein_sequence sequence_alignment sequence_comparison structure_prediction by ana to the group Bioinformatics on 2005-03-05 01:36:38 as ***** along with 3 people and 1 group j3xucite aalibes dgront structural_bioinformatics
  • An Accurate, Sensitive, and Scalable Method to Identify Functional Sites in Protein Structures
    Journal of Molecular Biology, Vol. 326, No. 1. (07 February 2003), pp. 255-261.
    by Hui Yao, David M Kristensen, Ivana Mihalek, Mathew E Sowa, Chad Shaw, Marek Kimmel, Lydia Kavraki, Olivier Lichtarge
    posted to protein_protein protein_sequence protein_structure structural_bioinformatics by barry to the group Bioinformatics on 2005-04-14 19:37:04 as ***** along with 1 person and 1 group BragilMassoud 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
  • 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 1 person and 1 group tny structural_bioinformatics
  • An aspartate residue in yeast alcohol dehydrogenase I determines the specificity for coenzyme
    BIOCHEMISTRY, Vol. 30, No. 26. (1991), pp. 6397-6401.
    by F Fan, JA Lorenzen, BV Plapp
    posted to ctbp nadp protein_sequence by barry to the group Bioinformatics on 2006-08-15 20:06:56 as * along with 1 group structural_bioinformatics
  • 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
  • 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
  • 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 14 people and 4 groups stevanspringer pansapiens imouthesmp dayjm Einat marcius i41m nirfriedman cmm RowanBarrett ramensky Vaquero Ema bpcusack structural_bioinformatics FAB-lab BioinfoCIPF SGU-CIPF
  • Derivation of rules for comparative protein modeling from a database of protein structure alignments.
    Protein Sci, Vol. 3, No. 9. (September 1994), pp. 1582-1596.
    by A Sali, JP Overington
    posted to comparative_modeling protein_sequence protein_structure structure_prediction by ana to the group Bioinformatics on 2006-04-07 21:00:38 as read along with 2 people and 3 groups bicko marcius 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 4 people and 1 group laurabailey Einat tny leemary4 structural_bioinformatics
  • Divergent Evolution Within Protein Superfolds Inferred from Profile-based Phylogenetics
    Journal of Molecular Biology, Vol. 354, No. 3. (2 December 2005), pp. 722-737.
    by Douglas L Theobald, Deborah S Wuttke
    posted to protein_structure protein_sequence phylogenetics jcsg by ana to the group Bioinformatics on 2007-06-02 03:54:22 as **** along with 3 people and 3 groups barry dlr caporaso structural_bioinformatics biomedical-nlp McCammon
  • Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme
    Proteins: Structure, Function, and Genetics, Vol. 30, No. 2. (1998), pp. 144-154.
    by Steven Hayward, Herman JC Berendsen
    posted to domain_motions protein_dynamics protein_sequence by barry to the group Bioinformatics on 2006-08-15 19:31:25 as ** along with 1 person and 1 group nigham structural_bioinformatics
  • Protein sequence entropy is closely related to packing density and hydrophobicity
    Protein Engineering, Design and Selection, Vol. 18, No. 2. (February 2005), pp. 59-64.
    by H Liao, W Yeh, D Chiang, R Jernigan, B Lustig
    posted to packing_density protein_sequence protein_structure by ana to the group Bioinformatics on 2006-03-10 06:01:02 as **** along with 1 person and 1 group operon 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
  • Identification of functionally conserved residues with the use of entropy-variability plots.
    Proteins, Vol. 52, No. 4. (1 September 2003), pp. 544-552.
    by L Oliveira, PB Paiva, AC Paiva, G Vriend
    posted to bioinformatics protein_design protein_sequence sequence_comparison by barry to the group Bioinformatics on 2005-08-01 22:41:32 as ** along with 1 group structural_bioinformatics
  • Codon bias and base composition are poor indicators of horizontally transferred genes.
    Mol Biol Evol, Vol. 18, No. 3. (March 2001), pp. 404-412.
    by LB Koski, RA Morton, GB Golding
    posted to base_composition codon_bias comparative_genomics hgt phylogeny protein_sequence sequence_comparison by ana to the group Bioinformatics on 2005-06-15 19:44:51 as ** along with 3 people and 1 group operon jmeppley karfunkel structural_bioinformatics
  • Solving the protein sequence metric problem.
    Proc Natl Acad Sci U S A, Vol. 102, No. 18. (3 May 2005), pp. 6395-6400.
    by WR Atchley, J Zhao, AD Fernandes, T Drüke
    posted to protein_sequence scoring_matrix sequence_comparison by ana to the group Bioinformatics on 2005-05-11 18:49:56 as ** along with 2 people and 1 group barry friendpine 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
  • Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.
    J Mol Biol, Vol. 300, No. 4. (21 July 2000), pp. 1005-1016.
    by O Emanuelsson, H Nielsen, S Brunak, G von Heijne
    posted to protein_sequence sequence_comparison subcellular_localization by ana to the group Bioinformatics on 2005-06-16 19:31:13 as *** along with 4 people and 1 group nlapalu raiyar bpcusack mloewer structural_bioinformatics
  • Local Function Conservation in Sequence and Structure Space
    PLoS Comput Biol, Vol. 4, No. 7. (4 July 2008), e1000105.
    by Nils Weinhold, Oliver Sander, Francisco S Domingues, Thomas Lengauer, Ingolf Sommer
    posted to protein_structure protein_sequence function_prediction by barry to the group Bioinformatics on 2008-09-08 17:53:09 as read along with 2 people and 2 groups cabbagesofdoom Ema structural_bioinformatics McCammon
  • Comparative Protein Modelling by Satisfaction of Spatial Restraints
    Journal of Molecular Biology, Vol. 234, No. 3. (5 December 1993), pp. 779-815.
    by Andrej Sali, Tom L Blundell
    posted to comparative_modeling protein_sequence protein_structure structure_prediction by ana to the group Bioinformatics on 2006-04-07 00:50:57 as **** along with 1 group structural_bioinformatics
  • Functional Specificity Lies within the Properties and Evolutionary Changes of Amino Acids
    Journal of Molecular Biology, Vol. 373, No. 3. (26 October 2007), pp. 801-810.
    by Saikat Chakrabarti, Stephen H Bryant, Anna R Panchenko
    posted to clustering protein_sequence subfamily by barry to the group Bioinformatics on 2007-10-31 21:58:01 as ** along with 3 people and 1 group Einat biehl mingzhi structural_bioinformatics
  • Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments.
    J Mol Biol, Vol. 341, No. 2. (6 August 2004), pp. 617-631.
    by MS Chang, SA Benner
    posted to indels protein_sequence by ana to the group Bioinformatics on 2006-05-18 00:48:43 as ***** along with 1 group structural_bioinformatics
  • A "Holistic" Kinesin Phylogeny Reveals New Kinesin Families and Predicts Protein Functions.
    Mol Biol Cell (15 February 2006)
    by Bill Wickstead, Keith Gull
    posted to kinesin molecular_motors phylogeny protein_sequence by barry to the group Bioinformatics on 2006-11-29 00:42:26 as ** along with 1 person and 1 group kristophe structural_bioinformatics
  • Improving the quality of twilight-zone alignments.
    Protein Sci, Vol. 9, No. 8. (August 2000), pp. 1487-1496.
    by L Jaroszewski, L Rychlewski, A Godzik
    posted to protein_sequence sequence_alignment sequence_comparison by ana to the group Bioinformatics on 2005-03-05 01:37:15 as ***** along with 1 person and 1 group barry structural_bioinformatics
  • Predicting conformational switches in proteins
    Protein Science, Vol. 8, No. 9. (1999), pp. 1752-1764.
    by M Young, K Kirshenbaum, KA Dill, S Highsmith
    posted to bioinf_methods protein_dynamics protein_sequence by barry to the group Bioinformatics on 2005-09-28 01:06:18 as * along with 1 group structural_bioinformatics
  • SATCHMO: sequence alignment and tree construction using hidden Markov models
    Bioinformatics, Vol. 19, No. 11. (22 July 2003), pp. 1404-1411.
    by Robert C Edgar, Kimmen Sjolander
    posted to algorithms multiple_sequence_alignment protein_sequence by ana to the group Bioinformatics on 2006-09-08 07:28:56 as *** along with 1 person and 1 group cdallett structural_bioinformatics
  • Contact-based sequence alignment
    Nucl. Acids Res., Vol. 32, No. 8. (30 April 2004), pp. 2464-2473.
    by Jens Kleinjung, John Romein, Kuang Lin, Jaap Heringa
    posted to contact_prediction protein_sequence protein_structure sequence_alignment by ana to the group Bioinformatics on 2005-11-21 23:08:02 as ***** along with 1 person and 1 group rabio structural_bioinformatics
  • Inter-residue distances derived from fold contact propensities correlate with evolutionary substitution costs.
    BMC Bioinformatics, Vol. 5 (18 October 2004)
    by G Williams, P Doherty
    posted to interaction_hierarchy protein_sequence protein_structure sequence_comparison by ana to the group Bioinformatics on 2005-08-29 21:41:54 as **** along with 1 group structural_bioinformatics
  • Gaps in structurally similar proteins: towards improvement of multiple sequence alignment.
    Proteins, Vol. 54, No. 1. (1 January 2004), pp. 71-87.
    by JO Wrabl, NV Grishin
    posted to indels protein_sequence protein_structure by ana to the group Bioinformatics on 2006-05-18 00:49:03 as **** along with 4 people and 1 group j3xucite barry analogAI granujilla structural_bioinformatics
  • 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
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