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Group: Bioinformatics - with tag protein_structure [353 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_structure
  • Crystal structure of an extensively simplified variant of bovine pancreatic trypsin inhibitor in which over one-third of the residues are alanines.
    Proceedings of the National Academy of Sciences of the United States of America (30 September 2008)
    by Mohammad Monirul M Islam, Shihori Sohya, Keiichi Noguchi, Masafumi Yohda, Yutaka Kuroda
    posted to protein_structure protein_design bpti by barry to the group Bioinformatics on 2008-10-05 19:12:36 as ** along with 2 groups structural_bioinformatics McCammon
  • The structure of protein evolution and the evolution of protein structure
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Richard A Goldstein
    posted to review protein_structure protein_evolution fold_space by barry to the group Bioinformatics on 2008-10-02 19:46:30 as ** along with 3 people and 2 groups bpb zwang cmzmasek structural_bioinformatics McCammon
  • 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 6 people and 1 group chad_davis zwang druvus reyez mdstobbe jameswasmuth structural_bioinformatics
  • From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes
    Proteins: Structure, Function, and Bioinformatics, Vol. 68, No. 3. (2007), pp. 646-661.
    by Allison P Heath, Lydia E Kavraki, Cecilia Clementi
    posted to protein_structure coarse_grain by barry to the group Bioinformatics on 2008-09-26 18:14:38 as *** along with 2 people and 2 groups aqeel mijam structural_bioinformatics McCammon
  • 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
  • Mapping the Nucleotide and Isoform-Dependent Structural and Dynamical Features of Ras Proteins
    Structure, Vol. 16, No. 6. (11 June 2008), pp. 885-896.
    by Alemayehu A Gorfe, Barry J Grant, Andrew J Mccammon
    posted to md_simulation mine ntpases pca protein_dynamics protein_structure ras by barry to the group Bioinformatics on 2008-06-10 22:34:01 as read along with 1 group structural_bioinformatics
  • Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation
    Current Opinion in Structural Biology, Vol. 17, No. 6. (December 2007), pp. 633-640.
    by Ivet Bahar, Chakra Chennubhotla, Dror Tobi
    posted to allosteric protein_dynamics protein_structure review by barry to the group Bioinformatics on 2007-12-04 22:56:25 as ** along with 8 people and 3 groups aqeel ruvido cactus sobolevnrm jennifermbui higueruelo LamBras jmccammon structural_bioinformatics baker-group McCammon
  • Signal Propagation in Proteins and Relation to Equilibrium Fluctuations
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e172.
    by Chakra Chennubhotla, Ivet Bahar
    posted to allosteric correlated_motions nma protein_dynamics protein_structure time_series_analysis by barry to the group Bioinformatics on 2007-09-22 23:29:36 as ***** along with 1 group structural_bioinformatics
  • Molecular basis for specificity in the druggable kinome: sequence-based analysis
    Bioinformatics, Vol. 23, No. 5. (March 2007), pp. 563-572.
    by Chen, Jianping, Zhang, Xi
    posted to protein_structure kinases hbond dehydron by barry to the group Bioinformatics on 2007-09-14 19:21:35 as ** along with 1 group 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 4 people and 3 groups tjimenez bicko marcius wilbur structural_bioinformatics BioinfoCIPF SGU-CIPF
  • How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues.
    Biophys J, Vol. 88, No. 3. (March 2005), pp. 1552-1559.
    by T Haliloglu, O Keskin, B Ma, R Nussinov
    posted to protein_structure protein_protein nma by barry to the group Bioinformatics on 2007-09-13 18:55:42 as ** along with 4 people and 1 group baaden aqeel eweaver choonpeng structural_bioinformatics
  • Dehydron: a structurally encoded signal for protein interaction.
    Biophys J, Vol. 85, No. 3. (September 2003), pp. 1914-1928.
    by A Fernández, R Scott
    posted to protein_structure protein_protein protein_packing hbond dehydron by barry to the group Bioinformatics on 2007-09-13 18:45:52 as ** along with 2 people and 1 group BragilMassoud Evangelia structural_bioinformatics
  • Insufficiently dehydrated hydrogen bonds as determinants of protein interactions.
    Proc Natl Acad Sci U S A, Vol. 100, No. 1. (7 January 2003), pp. 113-118.
    by A Fernández, HA Scheraga
    posted to protein_structure protein_protein protein_packing hbond dehydron by barry to the group Bioinformatics on 2007-09-13 18:45:36 as **** along with 1 person and 1 group BragilMassoud structural_bioinformatics
  • On the precision of calculated solvent-accessible surface areas
    Acta Crystallographica Section D Biological Crystallography
    by Novotny
    posted to solvent sas protein_structure by barry to the group Bioinformatics on 2007-09-08 00:50:42 as ** along with 1 group structural_bioinformatics
  • Detecting similarities among distant homologous proteins by comparison of domain flexibilities
    Protein Engineering, Design and Selection (30 June 2007), gzm021.
    by Alessandro Pandini, Giancarlo Mauri, Annalisa Bordogna, Laura Bonati
    posted to protein_structure protein_dynamics by barry to the group Bioinformatics on 2007-09-05 01:57:38 as * along with 2 people and 1 group aqeel edvin structural_bioinformatics
  • Evolutionary Conservation of Protein Backbone Flexibility
    Journal of Molecular Evolution, Vol. 63, No. 4. (14 October 2006), pp. 448-457.
    by Sandra Maguid, Sebastián Fernández-Alberti, Gustavo Parisi, Julián Echave
    posted to protein_structure protein_dynamics nma by barry to the group Bioinformatics on 2007-09-05 01:48:20 as ** along with 4 people and 1 group gisle jlh64 edvin tny 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 shuns jwm kevinchannon bethbromley ca3295 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 4 people and 1 group grahamc cjeans paolomarcatili phoenixzxl 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 8 people and 1 group ucbcjbm tjimenez jjray chad_davis tny shung Minty sim82 structural_bioinformatics
  • Comparison of side chain interactions performed by structurally equivalent residues in homologous protein structures
    Comput. Appl. Biosci., Vol. 11, No. 6. (1 December 1995), pp. 577-581.
    by Domenico Bordo
    posted to protein_structure hbond by barry to the group Bioinformatics on 2007-08-27 20:00:38 as * along with 1 group structural_bioinformatics
  • Characterization of Protein Conformational States by Normal-Mode Frequencies
    J. Am. Chem. Soc. (23 August 2007)
    by BA Hall, SL Kaye, A Pang, R Perera, PC Biggin
    posted to protein_structure pca nma md_simulation clustering by barry to the group Bioinformatics on 2007-08-27 19:15:41 as **** along with 5 people and 2 groups ubcg08l aqeel choonpeng sobolevnrm LamBras structural_bioinformatics baker-group
  • How Well Can We Understand Large-Scale Protein Motions Using Normal Modes of Elastic Network Models?
    Biophys J (4 May 2007)
    by Lei Yang, Guang Song, Robert L L Jernigan
    posted to protein_structure protein_dynamics nma correlated_motions by barry to the group Bioinformatics on 2007-08-13 19:53:33 as ** along with 3 people and 1 group aqeel choonpeng willpitt structural_bioinformatics
  • Protein Flexibility and Mobility in Structure-Based Drug Design
    pp. 455-476.
    by Aqeel Ahmed
    posted to review protein_structure protein_ligand protein_dynamics drug_design docking by barry to the group Bioinformatics on 2007-08-13 19:47:46 as * along with 1 group structural_bioinformatics
  • Phylogeny of protein-folding trajectories reveals a unique pathway to native structure.
    Proc Natl Acad Sci U S A, Vol. 101, No. 51. (21 December 2004), pp. 17658-17663.
    by M Ota, M Ikeguchi, A Kidera
    posted to protein_structure protein_folding md_simulation contacts clustering by barry to the group Bioinformatics on 2007-08-10 18:38:42 as ** along with 1 group structural_bioinformatics
  • Unfolding Pathways of Goat [alpha]-Lactalbumin as Revealed in Multiple Alignment of Molecular Dynamics Trajectories
    Journal of Molecular Biology, Vol. 371, No. 5. (31 August 2007), pp. 1354-1364.
    by Tomotaka Oroguchi, Mitsunori Ikeguchi, Motonori Ota, Kunihiro Kuwajima, Akinori Kidera
    posted to protein_structure protein_folding md_simulation contacts clustering by barry to the group Bioinformatics on 2007-08-10 18:36:13 as ** along with 1 person and 1 group choonpeng structural_bioinformatics
  • Predicting Absolute Ligand Binding Free Energies to a Simple Model Site
    Journal of Molecular Biology, Vol. 371, No. 4. (24 August 2007), pp. 1118-1134.
    by David L Mobley, Alan P Graves, John D Chodera, Andrea C Mcreynolds, Brian K Shoichet, Ken A Dill
    posted to protein_structure protein_ligand docking by barry to the group Bioinformatics on 2007-08-06 18:14:06 as ** along with 4 people and 2 groups insilico daevans superpyrin dmobley structural_bioinformatics Computer Aided Drug Design
  • Structure of Human Eg5 in Complex with a New Monastrol-based Inhibitor Bound in the R Configuration
    J. Biol. Chem., Vol. 282, No. 13. (30 March 2007), pp. 9740-9747.
    by Isabel Garcia-Saez, Salvatore Debonis, Roman Lopez, Fernando Trucco, Bernard Rousseau, Pierre Thuery, Frank Kozielski
    posted to protein_structure monastrol molecular_motors kinesin by barry to the group Bioinformatics on 2007-07-27 02:03:03 as ** along with 1 group 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
  • A new method for estimating the importance of hydrophobic groups in the binding site of a protein.
    J Med Chem, Vol. 48, No. 4. (24 February 2005), pp. 1069-1078.
    by MD Kelly, RL Mancera
    posted to protein_structure protein_ligand hydrophobic docking bioinf_methods by barry to the group Bioinformatics on 2007-07-19 18:29:38 as ** along with 3 people and 1 group nickolay blackbart ladab structural_bioinformatics
  • Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    Acta Crystallographica Section D: Biological Crystallography, Vol. 60, No. 1. (01 December 2004), pp. 2256-2268.
    by Krissinel, , Henrick,
    posted to structure_comparison protein_structure graph bioinf_methods by barry to the group Bioinformatics on 2007-07-13 19:39:15 as read along with 3 people and 3 groups jwm analogAI robert structural_bioinformatics Radiation_Damage Stressosome
  • Geometric criteria of hydrogen bonds in proteins and identification of "bifurcated" hydrogen bonds.
    Protein Eng, Vol. 15, No. 5. (May 2002), pp. 359-363.
    by IY Torshin, IT Weber, RW Harrison
    posted to protein_structure hbond by barry to the group Bioinformatics on 2007-06-21 22:57:54 as * along with 2 people and 2 groups medic0747 sobolevnrm structural_bioinformatics baker-group
  • Hydrogen bonding in globular proteins
    Progress in Biophysics and Molecular Biology, Vol. 44, No. 2. (1984), pp. 97-179.
    by EN Baker, RE Hubbard
    posted to review protein_structure hbond by barry to the group Bioinformatics on 2007-06-21 22:53:50 as read 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 BragilMassoud anwazo renatomilani 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
  • SISYPHUS--structural alignments for proteins with non-trivial relationships.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by A Andreeva, A Prlić, TJ Hubbard, AG Murzin
    posted to structure_comparison structure_classification protein_structure by ana to the group Bioinformatics on 2007-05-29 23:18:59 as ***** along with 4 people and 1 group barry dgront massivemayhem martainn structural_bioinformatics
  • Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins.
    Proc Natl Acad Sci U S A (9 May 2007)
    by Vincent J J Hilser, E Brad B Thompson
    posted to protein_structure protein_protein protein_dynamics disorder allosteric by barry to the group Bioinformatics on 2007-05-25 01:36:39 as **** along with 5 people and 2 groups apaydin choonpeng cursonivel1 cactus allmensch structural_bioinformatics cursonivel1
  • Mechanism of the receptor-catalyzed activation of heterotrimeric G proteins
    Nature Structural & Molecular Biology, Vol. 13, No. 9. (06 August 2006), pp. 772-777.
    by William M Oldham, Ned Van Eps, Anita M Preininger, Wayne L Hubbell, Heidi E Hamm
    posted to protein_structure p-loop g_proteins by barry to the group Bioinformatics on 2007-05-18 03:01:32 as ** along with 2 people and 2 groups gcaltabiano cen4ik structural_bioinformatics LabCompMed
  • Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs.
    Protein Sci, Vol. 14, No. 5. (May 2005), pp. 1253-1265.
    by K Ikeda, K Tomii, T Yokomizo, D Mitomo, K Maruyama, S Suzuki, J Higo
    posted to protein_structure protein_fragments pca by barry to the group Bioinformatics on 2007-05-03 21:50:25 as ** along with 1 person and 1 group lsdc1 structural_bioinformatics
  • 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
  • AAA+ superfamily ATPases: common structure-diverse function
    Genes to Cells, Vol. 6, No. 7. (2001), pp. 575-597.
    by Teru Ogura, Anthony J Wilkinson
    posted to review protein_structure dynein aaa by barry to the group Bioinformatics on 2007-04-13 23:27:10 as ** along with 1 group structural_bioinformatics
  • 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 protein_structure function_evolution by ana to the group Bioinformatics on 2007-03-29 19:26:06 as *** along with 5 people and 1 group ucbcjbm barry tny grottenolm jwm structural_bioinformatics
  • Less is more: towards an optimal universal description of protein folds.
    Bioinformatics, Vol. 21 Suppl 2 (1 September 2005)
    by JD Szustakowski, S Kasif, Z Weng
    posted to structure_comparison structure_classification protein_structure fold_space by ana to the group Bioinformatics on 2007-03-28 04:20:00 as *** along with 3 people and 1 group barry msierk krishnaJCSG 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
  • Residue depth: a novel parameter for the analysis of protein structure and stability.
    Structure, Vol. 7, No. 7. (15 July 1999), pp. 723-732.
    by S Chakravarty, R Varadarajan
    posted to protein_structure bioinf_methods by barry to the group Bioinformatics on 2007-02-06 19:34:03 as ** along with 1 group structural_bioinformatics
  • Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure.
    Bioinformatics, Vol. 18, No. 10. (October 2002), pp. 1365-1373.
    by BJ McConkey, V Sobolev, M Edelman
    posted to protein_structure bioinf_methods by barry to the group Bioinformatics on 2007-02-06 19:32:08 as ** along with 3 people and 1 group bicko j3xucite siebertm structural_bioinformatics
  • Atom depth in protein structure and function.
    Trends Biochem Sci, Vol. 28, No. 11. (November 2003), pp. 593-597.
    by A Pintar, O Carugo, S Pongor
    posted to protein_structure protein_packing core_structure by barry to the group Bioinformatics on 2007-02-06 19:23:55 as ** along with 1 person and 1 group lna structural_bioinformatics
  • Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling
    Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 2. (2006), pp. 347-361.
    by Kim Sharp, John J Skinner
    posted to protein_structure protein_dynamics md_simulation bioinf_methods allosteric by barry to the group Bioinformatics on 2007-01-30 20:09:59 as **** along with 3 people and 2 groups lna choonpeng sobolevnrm structural_bioinformatics baker-group
  • Travel depth, a new shape descriptor for macromolecules: application to ligand binding.
    J Mol Biol, Vol. 362, No. 3. (22 September 2006), pp. 441-458.
    by RG Coleman, KA Sharp
    posted to protein_structure bioinf_methods by barry to the group Bioinformatics on 2007-01-30 20:08:02 as ** along with 1 person and 1 group nickolay 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
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