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barry protein_design [61 articles]

最近 barry さんのライブラリに追加された論文の中から タグ protein_design. You can also see everyone's protein_design.
  • De Novo Computational Design of Retro-Aldol Enzymes
    Science, Vol. 319, No. 5868. (7 March 2008), pp. 1387-1391.
    by Lin Jiang, Eric A Althoff, Fernando R Clemente, Lindsey Doyle, Daniela Rothlisberger, Alexandre Zanghellini, Jasmine L Gallaher, Jamie L Betker, Fujie Tanaka, Carlos F Barbas, Donald Hilvert, Kendall N Houk, Barry L Stoddard, David Baker
    posted to protein_design protein_ligand structure_refinement by barry on 2008-03-20 00:05:53 as **** along with 12 people and 3 groups cambray joseph_x_zhou ucbcjbm aalibes jwm aprasad dgront zwang sobolevnrm davidlott msuarezdiez scienbox McCammon structural_bioinformatics baker-group
  • Supercharging Proteins Can Impart Unusual Resilience
    J. Am. Chem. Soc., Vol. 129, No. 33. (22 August 2007), pp. 10110-10112.
    by MS Lawrence, KJ Phillips, DR Liu
    posted to electrostatics journal_club protein_design protein_evolution protein_folding by barry on 2007-10-26 22:37:58 as read along with 2 people and 3 groups samjlord sobolevnrm structural_bioinformatics moernerlab baker-group
  • 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_design protein_dynamics protein_sequence protein_structure by barry on 2007-09-04 19:32:05 as ** along with 5 people and 2 groups ca3295 shuns jwm kevinchannon bethbromley structural_bioinformatics 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_design protein_evolution protein_protein protein_sequence protein_structure by barry on 2007-09-04 19:25:04 as ** along with 4 people and 2 groups phoenixzxl paolomarcatili grahamc cjeans structural_bioinformatics 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 fad protein_design protein_evolution protein_structure by barry on 2007-07-20 18:33:27 as *** along with 3 people and 2 groups Einat zwang mdimon structural_bioinformatics 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 protein_structure protein_fragments protein_design bioinf_methods by barry on 2007-02-07 21:30:06 as *** along with 3 people and 2 groups ana msierk krishnaJCSG structural_bioinformatics Bioinformatics
  • notes Principles determining the structure of [beta]-sheet barrels in proteins II. The observed structures
    Journal of Molecular Biology, Vol. 236, No. 5. (11 March 1994), pp. 1382-1400.
    by Alexey G Murzin, Arthur M Lesk, Cyrus Chothia
    posted to protein_structure protein_packing protein_design beta_sheet by barry on 2007-01-18 19:23:39 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Principles determining the structure of [beta]-sheet barrels in proteins I. A theoretical analysis
    Journal of Molecular Biology, Vol. 236, No. 5. (11 March 1994), pp. 1369-1381.
    by Alexey G Murzin, Arthur M Lesk, Cyrus Chothia
    posted to protein_structure protein_packing protein_design beta_sheet by barry on 2007-01-18 19:21:40 as *** along with 2 groups structural_bioinformatics Bioinformatics
  • Fluctuations in ion pairs and their stabilities in proteins.
    Proteins, Vol. 43, No. 4. (1 June 2001), pp. 433-454.
    by S Kumar, R Nussinov
    posted to ion_pairs protein_design protein_structure by barry on 2006-10-26 01:03:28 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Relationship between ion pair geometries and electrostatic strengths in proteins.
    Biophys J, Vol. 83, No. 3. (September 2002), pp. 1595-1612.
    by S Kumar, R Nussinov
    posted to ion_pairs protein_design protein_structure by barry on 2006-10-26 01:01:29 as ** along with 1 person and 2 groups bicko structural_bioinformatics Bioinformatics
  • Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge-based potentials, and clustering
    Proteins, Vol. 65, No. 2. (1 November 2006), pp. 463-479.
    by Jiang Zhu, Li Xie, Barry Honig
    posted to protein_design protein_fragments protein_structure by barry on 2006-10-10 01:34:49 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • The packing density in proteins: standard radii and volumes.
    J Mol Biol, Vol. 290, No. 1. (2 July 1999), pp. 253-266.
    by J Tsai, R Taylor, C Chothia, M Gerstein
    posted to core_structure protein_design protein_packing protein_structure by barry on 2006-09-29 19:28:21 as ** along with 5 people and 3 groups sobolevnrm ana bicko blackbart medic0747 baker-group structural_bioinformatics Bioinformatics
  • notes Volume changes in protein evolution.
    J Mol Biol, Vol. 236, No. 4. (4 March 1994), pp. 1067-1078.
    by M Gerstein, EL Sonnhammer, C Chothia
    posted to protein_design protein_sequence protein_structure residue_effect by barry on 2006-09-29 19:27:20 as ** along with 2 people and 2 groups ana kuhn structural_bioinformatics Bioinformatics
  • Principles that determine the structure of proteins.
    Annu Rev Biochem, Vol. 53 (1984), pp. 537-572.
    by C Chothia
    posted to protein_design protein_folding protein_structure by barry on 2006-09-29 19:25:47 as **** along with 2 people and 2 groups ana nigham structural_bioinformatics Bioinformatics
  • Local complexity of amino acid interactions in a protein core.
    Proc Natl Acad Sci U S A, Vol. 101, No. 1. (6 January 2004), pp. 111-116.
    by RK Jain, R Ranganathan
    posted to core_residues core_structure correlated_mutations protein_design protein_structure by barry on 2006-09-29 19:24:22 as ** along with 5 people and 4 groups ana lna marcius gbart choonpeng structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • The role of geometric complementarity in secondary structure packing: A systematic docking study
    Protein Sci, Vol. 12, No. 8. (1 August 2003), pp. 1646-1651.
    by Sulin Jiang, Andrei Tovchigrechko, Ilya A Vakser
    posted to docking helix_helix protein_design protein_structure by barry on 2006-09-29 19:22:38 as ** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • notes How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins
    Journal of Molecular Biology, Vol. 136, No. 3. (25 January 1980), pp. 225-230.
    by Arthur M Lesk, Cyrus Chothia
    posted to core_residues core_structure protein_design protein_evolution protein_sequence protein_structure sequence_comparison structure_comparison by barry on 2006-09-29 19:18:54 as ** along with 2 people and 4 groups ana marcius structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • Helix to helix packing in proteins
    Journal of Molecular Biology, Vol. 145, No. 1. (5 January 1981), pp. 215-250.
    by Cyrus Chothia, Michael Levitt, Douglas Richardson
    posted to helix_helix protein_design protein_structure by barry on 2006-09-29 19:15:32 as ** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • 'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments
    Bioinformatics, Vol. 22, No. 2. (15 January 2006), pp. 129-133.
    by Jean-Christophe Gelly, Alexandre G de Brevern, Serge Hazout
    posted to protein_design protein_fragments protein_structure by barry on 2006-09-29 19:13:14 as ** along with 6 people and 4 groups ana dimka ttjoseph marcius nickolay choonpeng structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • Protein flexibility acclimatizes photosynthetic energy conversion to the ambient temperature
    Nature, Vol. 442, No. 7104. (23 July 2006), pp. 827-830.
    by Oksana Shlyk-Kerner, Ilan Samish, David Kaftan, Neta Holland, Maruthi PS Sai, Hadar Kless, Avigdor Scherz
    posted to domain_motions protein_design protein_dynamics protein_structure by barry on 2006-08-16 21:45:51 as ***** along with 2 groups structural_bioinformatics Bioinformatics
  • notes 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 on 2006-07-07 19:57:04 as **** along with 2 people and 5 groups marcius sobolevnrm structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF baker-group
  • Composites of local structure propensities: evidence for local encoding of long-range structure
    Protein Science: a Publication Of The Protein Society, Vol. 11, No. 1. (January 2002), pp. 18-26.
    by David Shortle
    posted to protein_design protein_structure by barry on 2006-04-10 19:44:48 as ***** along with 1 person and 2 groups Einat structural_bioinformatics Bioinformatics
  • A physical basis for protein secondary structure
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, No. 25. (1999), pp. 14258-14263.
    by R Srinivasan, GD Rose
    posted to protein_design protein_structure by barry on 2006-04-10 19:43:36 as **** along with 1 person and 2 groups Einat structural_bioinformatics Bioinformatics
  • Three-dimensional structures and contexts associated with recurrent amino acid sequence patterns
    Protein Science: a Publication Of The Protein Society, Vol. 6, No. 7. (July 1997), pp. 1587-1590.
    by KF Han, C Bystroff, D Baker
    posted to protein_design protein_structure by barry on 2006-04-10 19:41:42 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Rotamer Libraries in the 21st Century
    Current Opinion in Structural Biology, Vol. 12, No. 4. (01 August 2002), pp. 431-440.
    by Jr Dunbrack
    posted to protein_design protein_dynamics protein_structure by barry on 2006-04-10 19:39:07 as ** along with 3 people and 5 groups apaydin joergkurtwegner LamBras structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics
  • The penultimate rotamer library
    Proteins, Vol. 40, No. 3. (15 August 2000), pp. 389-408.
    by SC Lovell, JM Word, JS Richardson, DC Richardson
    posted to protein_design protein_dynamics protein_structure by barry on 2006-04-10 19:37:07 as ***** along with 2 people and 5 groups joergkurtwegner LamBras structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics
  • Structure validation by Calpha geometry: phi,psi and Cbeta deviation
    Proteins, Vol. 50, No. 3. (15 February 2003), pp. 437-450.
    by Simon C Lovell, Ian W Davis, Arendall, Paul I de Bakker, Michael J Word, Michael G Prisant, Jane S Richardson, David C Richardson
    posted to protein_design protein_structure by barry on 2006-04-10 19:34:42 as ***** along with 2 people and 6 groups sangeetha joergkurtwegner structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics insilicodrug
  • Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms
    Journal of Molecular Biology, Vol. 285, No. 4. (29 January 1999), pp. 1711-1733.
    by Michael J Word, Simon C Lovell, Thomas H Labean, Hope C Taylor, Michael E Zalis, Brent K Presley, Jane S Richardson, David C Richardson
    posted to protein_design protein_structure by barry on 2006-04-10 19:27:22 as *** along with 2 people and 5 groups chad_davis joergkurtwegner structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics
  • notes 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 on 2006-04-07 20:25:19 as ***** along with 14 people and 5 groups bpcusack stevanspringer pansapiens imouthesmp dayjm Einat marcius i41m nirfriedman cmm RowanBarrett ramensky Vaquero Ema structural_bioinformatics Bioinformatics FAB-lab BioinfoCIPF SGU-CIPF
  • Some fundamental aspects of building protein structures from fragment libraries.
    Protein Sci, Vol. 13, No. 6. (June 2004), pp. 1636-1650.
    by JB Holmes, J Tsai
    posted to protein_design protein_fragments by barry on 2006-03-22 20:21:32 as ** along with 2 people and 2 groups eckart_bindewald wouterboomsma structural_bioinformatics Bioinformatics
  • Folding free energy function selects native-like protein sequences in the core but not on the surface
    PNAS, Vol. 99, No. 21. (15 October 2002), pp. 13554-13559.
    by Alfonso Jaramillo, Lorenz Wernisch, Stephanie Hery, Shoshana J Wodak
    posted to protein_design protein_structure by barry on 2006-03-22 20:18:42 as ** along with 2 groups structural_bioinformatics 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 on 2006-03-22 20:15:18 as *** along with 3 people and 5 groups thaliana dgront joergkurtwegner structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics
  • Packing of secondary structural elements in proteins. Analysis and prediction of inter-helix distances.
    J Mol Biol, Vol. 233, No. 3. (5 October 1993), pp. 464-479.
    by BV Reddy, TL Blundell
    posted to protein_design protein_structure by barry on 2006-03-22 20:11:09 as ** along with 3 people and 2 groups ana pansapiens medic0747 structural_bioinformatics Bioinformatics
  • Analysis of interactive packing of secondary structural elements in alpha/beta units in proteins.
    Protein Sci, Vol. 8, No. 3. (March 1999), pp. 573-586.
    by BV Reddy, HA Nagarajaram, TL Blundell
    posted to protein_design protein_structure by barry on 2006-03-22 20:10:20 as ** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • Helix packing angle preferences
    Nat Struct Mol Biol, Vol. 4, No. 11. (November 1997), pp. 915-917.
    by James U Bowie
    posted to protein_design protein_structure by barry on 2006-03-22 20:08:47 as ** along with 2 people and 2 groups ana pansapiens structural_bioinformatics Bioinformatics
  • Geometry and symmetry presculpt the free-energy landscape of proteins
    PNAS, Vol. 101, No. 21. (25 May 2004), pp. 7960-7964.
    by Trinh X Hoang, Antonio Trovato, Flavio Seno, Jayanth R Banavar, Amos Maritan
    posted to protein_design protein_folding protein_structure by barry on 2006-03-08 23:10:47 as ***** along with 3 people and 2 groups ana mtw naitsabes structural_bioinformatics 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 on 2006-03-02 22:37:16 as ** along with 6 people and 2 groups pansapiens sriram_s cjeans mingzhi Pao-Yang marti structural_bioinformatics Bioinformatics
  • Allosteric Regulation of Hsp70 Chaperones by a Proline Switch
    Molecular Cell, Vol. 21, No. 3. (3 February 2006), pp. 359-367.
    by Markus Vogel, Bernd Bukau, Matthias P Mayer
    posted to allosteric hsp70 protein_design protein_dynamics protein_structure by barry on 2006-02-03 02:52:39 as *** along with 1 person and 3 groups pdelosri structural_bioinformatics Bioinformatics EPFL_SB_ITP_LBS
  • 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 on 2006-01-07 03:57:13 as ***** along with 2 groups structural_bioinformatics Bioinformatics
  • Characterizing Conserved Structural Contacts by Pair-wise Relative Contacts and Relative Packing Groups
    Journal of Molecular Biology, Vol. 354, No. 3. (2 December 2005), pp. 706-721.
    by Bradley J Holmes, Jerry Tsai
    posted to bioinf_methods contacts networks protein_design protein_structure structural_bioinformatics structure_comparison by barry on 2005-11-18 18:50:02 as ***** along with 2 people and 2 groups ana Einat structural_bioinformatics Bioinformatics
  • Statistical coevolution analysis and molecular dynamics: identification of amino acid pairs essential for catalysis.
    Proc Natl Acad Sci U S A, Vol. 102, No. 4. (25 January 2005), pp. 994-999.
    by RA Estabrook, J Luo, MM Purdy, V Sharma, P Weakliem, TC Bruice, NO Reich
    posted to correlated_motions correlated_mutations protein_design protein_dynamics protein_evolution by barry on 2005-10-26 00:16:13 as *** along with 4 people and 2 groups ana pansapiens dimka gbart structural_bioinformatics 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 contacts core_residues protein_design protein_dynamics protein_evolution protein_folding by barry on 2005-10-12 23:58:56 as **** along with 3 people and 4 groups ana Einat marcius structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • 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 on 2005-10-10 09:29:59 as ***** along with 2 groups structural_bioinformatics Bioinformatics
  • Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme.
    Proteins, Vol. 30, No. 2. (1 February 1998), pp. 144-154.
    by S Hayward, HJ Berendsen
    posted to bioinf_methods domain_motions protein_design protein_dynamics protein_structure by barry on 2005-10-09 08:22:02 as read along with 2 groups structural_bioinformatics 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 on 2005-10-09 01:28:18 as read along with 1 person and 2 groups Einat structural_bioinformatics Bioinformatics
  • notes Automatic Analysis of Protein Conformational Changes by Multiple Linkage Clustering
    Journal of Molecular Biology, Vol. 253, No. 4. (3 November 1995), pp. 633-647.
    by Nathalie S Boutonnet, Marianne J Rooman, Shoshana J Wodak
    posted to bioinf_methods protein_design protein_dynamics protein_structure by barry on 2005-09-28 01:16:22 as ***** along with 2 groups structural_bioinformatics Bioinformatics
  • Small-world view of the amino acids that play a key role in protein folding.
    Phys Rev E Stat Nonlin Soft Matter Phys, Vol. 65, No. 6 Pt 1. (June 2002)
    by M Vendruscolo, NV Dokholyan, E Paci, M Karplus
    posted to protein_design protein_folding small_world by barry on 2005-09-27 23:23:45 as ***** along with 3 people and 8 groups ana shantanu choonpeng structural_bioinformatics MathBio Biostatistics Bioinformatics microRNA Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology
  • Natural-like function in artificial WW domains
    Nature, Vol. 437, No. 7058., pp. 579-583.
    by William P Russ, Drew M Lowery, Prashant Mishra, Michael B Yaffe, Rama Ranganathan
    posted to correlated_mutations protein_design protein_sequence protein_structure by barry on 2005-09-22 22:31:34 as *** along with 6 people and 5 groups ana balajis marcius caporaso bethbromley ca3295 structural_bioinformatics Bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF
  • notes Structural biologyForm and function instructions
    Nature, Vol. 437, No. 7058. (21 September 2005), pp. 486-487.
    by Jeffery W Kelly
    posted to correlated_mutations protein_design by barry on 2005-09-22 22:29:11 as read along with 2 people and 2 groups ana dayjm structural_bioinformatics 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 bioinf_methods correlated_mutations protein_design protein_evolution protein_sequence protein_structure by barry on 2005-09-22 22:16:31 as ***** along with 14 people and 5 groups ana lna bpb Einat balajis marcius gbart analogAI nirfriedman caporaso massivemayhem mingzhi bethbromley ca3295 structural_bioinformatics Bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF
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