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Group: Bioinformatics - with tag protein_sequence [92 articles]

グループ Bioinformatics のメンバーが最近追加した論文の一覧 with tag protein_sequence
  • 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
  • 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
  • Localization of protein-binding sites within families of proteins.
    Protein Sci, Vol. 14, No. 9. (September 2005), pp. 2350-2360.
    by D Korkin, FP Davis, A Sali
    posted to protein_structure protein_sequence protein_protein by barry to the group Bioinformatics on 2007-09-14 01:51:37 as ** along with 5 people and 3 groups wilbur tjimenez bicko chad_davis marcius structural_bioinformatics BioinfoCIPF SGU-CIPF
  • 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
  • Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces.
    Proc Natl Acad Sci U S A, Vol. 100, No. 10. (13 May 2003), pp. 5772-5777.
    by B Ma, T Elkayam, H Wolfson, R Nussinov
    posted to protein_structure protein_sequence protein_protein hot_spots by barry to the group Bioinformatics on 2007-09-04 19:49:40 as ** along with 8 people and 1 group mdimmic bicko lyongu nickolay choonpeng cjeans carlescorbi ladab structural_bioinformatics
  • Computational Design of a Single Amino Acid Sequence that Can Switch between Two Distinct Protein Folds.
    J Am Chem Soc, Vol. 128, No. 4. (1 February 2006), pp. 1154-1161.
    by XI Ambroggio, B Kuhlman
    posted to protein_structure protein_sequence protein_dynamics protein_design by barry to the group Bioinformatics on 2007-09-04 19:32:05 as ** along with 5 people and 1 group ca3295 shuns jwm kevinchannon bethbromley 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
  • 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
  • Structural Evolution of the Protein Kinase-Like Superfamily.
    PLoS Comput Biol, Vol. 1, No. 5. (21 October 2005)
    by Eric D D Scheeff, Philip E E Bourne
    posted to protein_structure protein_sequence phylogenetics jcsg by ana to the group Bioinformatics on 2007-06-02 03:59:29 as **** along with 3 people and 1 group renatomilani BragilMassoud anwazo 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 McCammon structural_bioinformatics biomedical-nlp
  • Multivariate Analysis of Conserved Sequence-Structure Relationships in Kinesins: Coupling of the Active Site and a Tubulin-binding Sub-domain
    Journal of Molecular Biology, Vol. 368, No. 5. (18 May 2007), pp. 1231-1248.
    by Barry J Grant, Andrew J Mccammon, Leo S Caves, Robert A Cross
    posted to torsion_angles swi-swii structural_bioinformatics sca r protein_structure protein_sequence protein_dynamics pca p-loop ntpases molecular_motors mine kinesin domain_motions correlated_motions core_structure clustering bioinf_methods by barry to the group Bioinformatics on 2007-04-27 17:41:06 as read along with 3 people and 1 group choonpeng cactus insectopalo 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
  • 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 4 people and 1 group granujilla saunders dgront rabio 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
  • A comparison of profile hidden Markov model procedures for remote homology detection.
    Nucleic Acids Res, Vol. 30, No. 19. (1 October 2002), pp. 4321-4328.
    by M Madera, J Gough
    posted to hmm protein_sequence sequence_comparison by ana to the group Bioinformatics on 2006-11-27 23:37:23 as read along with 1 group 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
  • 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
  • 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
  • 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
  • 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
  • Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved.
    Structure, Vol. 13, No. 4. (April 2005), pp. 565-577.
    by W Zheng, BR Brooks, S Doniach, D Thirumalai
    posted to nma protein_dynamics protein_sequence protein_structure by barry to the group Bioinformatics on 2006-08-15 19:16:49 as * along with 1 group structural_bioinformatics
  • 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
  • Annotation transfer for genomics: measuring functional divergence in multi-domain proteins.
    Genome Res, Vol. 11, No. 10. (October 2001), pp. 1632-1640.
    by H Hegyi, M Gerstein
    posted to multi-domain protein_sequence protein_structure sequence_comparison structure_comparison by ana to the group Bioinformatics on 2006-06-21 22:21:00 as ***** along with 1 person and 1 group tny 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
  • Analysis of insertions/deletions in protein structures.
    J Mol Biol, Vol. 224, No. 2. (20 March 1992), pp. 461-471.
    by S Pascarella, P Argos
    posted to indels protein_sequence protein_structure by ana to the group Bioinformatics on 2006-05-18 00:50:31 as ***** along with 1 group structural_bioinformatics
  • Prediction of protein three-dimensional structures in insertion and deletion regions: a procedure for searching data bases of representative protein fragments using geometric scoring criteria.
    J Mol Biol, Vol. 253, No. 1. (13 October 1995), pp. 114-131.
    by T Fechteler, U Dengler, D Schomburg
    posted to indels protein_sequence protein_structure structure_prediction by ana to the group Bioinformatics on 2006-05-18 00:49:35 as *** along with 2 people and 3 groups GermanErlenkamp marcius structural_bioinformatics BioinfoCIPF SGU-CIPF
  • 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 3 people and 1 group granujilla barry analogAI 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • Clustering of low-energy conformations near the native structures of small proteins.
    Proc Natl Acad Sci U S A, Vol. 95, No. 19. (15 September 1998), pp. 11158-11162.
    by D Shortle, KT Simons, D Baker
    posted to protein_design protein_dynamics protein_folding protein_sequence protein_structure by barry to the group Bioinformatics on 2006-03-22 20:15:18 as *** along with 3 people and 4 groups thaliana dgront joergkurtwegner structural_bioinformatics Molecular-Modelling Drug-Design Cheminformatics
  • 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
  • Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships.
    Bioinformatics, Vol. 21, No. 16. (15 August 2005), pp. 3360-3368.
    by J Espadaler, O Romero-Isart, RM Jackson, B Oliva
    posted to protein_protein protein_sequence protein_structure sequence_comparison structure_comparison by barry to the group Bioinformatics on 2006-03-06 22:20:06 as ** along with 2 people and 1 group bicko baldo 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
  • Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins.
    J Mol Biol, Vol. 307, No. 5. (13 April 2001), pp. 1487-1502.
    by R Landgraf, I Xenarios, D Eisenberg
    posted to protein_design protein_protein protein_sequence protein_structure residue_annotation by barry to the group Bioinformatics on 2006-03-02 22:37:16 as ** along with 6 people and 1 group pansapiens sriram_s cjeans mingzhi Pao-Yang marti 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 raylim ealloza structural_bioinformatics BioinfoCIPF
  • A tutorial of recent developments in the seeding of local alignment.
    J Bioinform Comput Biol, Vol. 2, No. 4. (December 2004), pp. 819-842.
    by DG Brown, M Li, B Ma
    posted to bioinf_methods protein_sequence sequence_comparison by barry to the group Bioinformatics on 2006-01-25 03:04:09 as * along with 1 person and 1 group nedwards structural_bioinformatics
  • 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
  • Analysis and prediction of functional sub-types from protein sequence alignments
    Journal of Molecular Biology, Vol. 303, No. 1. (13 October 2000), pp. 61-76.
    by Sridhar S Hannenhalli, Robert B Russell
    posted to protein_sequence sequence_comparison by barry to the group Bioinformatics on 2005-12-13 13:27:13 as ** along with 1 person and 1 group marti structural_bioinformatics
  • Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases
    PNAS, Vol. 100, No. 8. (15 April 2003), pp. 4463-4468.
    by Lewyn Li, Eugene I Shakhnovich, Leonid A Mirny
    posted to kinases protein_sequence protein_structure by barry to the group Bioinformatics on 2005-12-13 13:25:02 as ** along with 2 people and 1 group Einat ankur_iitg 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
  • 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 5 people and 2 groups Cortel AbnerCYH azazello wenhan gjuggler structural_bioinformatics MBLAB
  • 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
  • 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
  • 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 3 people and 3 groups barry mattjb martainn structural_bioinformatics ComplexAdaptiveSystems DSTO-CAS
  • Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity.
    Proteins, Vol. 37, No. 3. (15 November 1999), pp. 379-387.
    by N Blomberg, RR Gabdoulline, M Nilges, RC Wade
    posted to electrostatics protein_design protein_sequence protein_structure by barry to the group Bioinformatics on 2005-10-10 09:29:59 as ***** along with 1 group structural_bioinformatics
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