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タグ: protein_design [172 articles]

Recent papers classified by the tag protein_design.
  • Protein Design by Directed Evolution
    Annual Review of Biophysics, Vol. 37, No. 1. (2008), pp. 153-173.
    by Christian Jackel, Peter Kast, Donald Hilvert
    posted to synthetic_biology review protein_design by phoenixzxl on 2008-06-25 08:26:36 as ** along with 1 person zwang
  • Automated design of specificity in molecular recognition.
    Nat Struct Biol, Vol. 10, No. 1. (January 2003), pp. 45-52.
    by JJ Havranek, PB Harbury
    posted to specificity protein_design coiled_coil by phoenixzxl on 2008-06-24 02:54:54 as *** along with 1 person bethbromley
  • A seven-helix coiled coil
    PNAS, Vol. 103, No. 42. (17 October 2006), pp. 15457-15462.
    by Jie Liu, Qi Zheng, Yiqun Deng, Chao-Sheng Cheng, Neville R Kallenbach, Min Lu
    posted to buried_polar_interactions cavity helixhelix_interfaces protein_design protein_structure by namtonthat on 2006-10-19 00:24:29 as read
  • De Novo Protein Design. I. In Search of Stability and Specificity
    Journal of Molecular Biology (November 1999), pp. 1161-1181.
    by P Koehl, M Levitt
    posted to protein_design by msuarezdiez on 2008-06-19 11:43:00 as **
  • Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences.
    Proteins, Vol. 62, No. 3. (15 March 2006), pp. 739-748.
    by X Hu, B Kuhlman
    posted to protein_design by msuarezdiez on 2008-06-25 15:14:47 as ** along with 2 people apaydin cat_worth
  • Energy estimation in protein design
    Current Opinion in Structural Biology, Vol. 12, No. 4. (1 August 2002), pp. 441-446.
    by Joaquim Mendes, Raphael Guerois, Luis Serrano
    posted to protein_design by msuarezdiez on 2008-06-19 10:39:22 as **
  • Computational protein design
    Current Opinion in Chemical Biology, Vol. 5, No. 6. (1 December 2001), pp. 690-695.
    by Christina M Kraemer-Pecore, Andrew M Wollacott, John R Desjarlais
    posted to protein_design by msuarezdiez on 2008-06-19 10:31:10 as ***
  • Advances in computational protein design
    Current Opinion in Structural Biology, Vol. 14, No. 4. (August 2004), pp. 487-494.
    by Sheldon Park, Xi Yang, Jeffery G Saven
    posted to protein_design by msuarezdiez on 2008-03-27 12:23:05 as ** along with 1 person and 1 group allPowerde The_Festival_of_Doubt
  • De novo protein design: fully automated sequence selection.
    Science, Vol. 278, No. 5335. (3 October 1997), pp. 82-87.
    by BI Dahiyat, SL Mayo
    posted to protein_design by medic0747 on 2007-02-10 12:22:17 as ** along with 2 people jwm kevinchannon
  • Review: Protein Design--Where We Were, Where We Are, Where We're Going
    Journal of Structural Biology, Vol. 134, No. 2-3. (May 2001), pp. 269-281.
    by Navin Pokala, Tracy M Handel
    posted to protein_design by medic0747 on 2007-02-10 12:18:00 as ** along with 1 person msuarezdiez
  • Problems and solutions in protein engineering--towards rational design.
    Trends Biotechnol, Vol. 12, No. 5. (May 1994), pp. 145-148.
    by TL Blundell
    posted to protein_design tlb by medic0747 on 2007-02-20 18:49:01 as **
  • A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences
    Nucleic Acids Research, Vol. 34, No. 22. (December 2006), pp. e149-e149.
    by J Smith, S Grizot, S Arnould, A Duclert, J Epinat, P Chames, J Prieto, P Redondo, F Blanco, J Bravo, G Montoya, F Paques, P Duchateau
    posted to bioengineering protein_design by marcius on 2007-01-03 13:03:20 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Branch-and-Terminate: a combinatorial optimization algorithm for protein design
    Structure, Vol. 7, No. 9. (September 1999), pp. 1089-1098.
    by DB Gordon, SL Mayo
    posted to protein_design protein_structure scp by karbak on 2005-12-03 18:03:49 as ***
  • Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm.
    Proteins, Vol. 33, No. 2. (1 November 1998), pp. 227-239.
    by AR Leach, AP Lemon
    posted to protein_design protein_structure scp by karbak on 2005-12-03 17:34:27 as **
  • A graph-theory algorithm for rapid protein side-chain prediction.
    Protein Sci, Vol. 12, No. 9. (September 2003), pp. 2001-2014.
    by AA Canutescu, AA Shelenkov, RL Dunbrack
    posted to protein_design protein_structure scp by karbak on 2005-12-03 17:31:15 as ** along with 8 people carlk jwm nigham bicko blackbart bluvsh1 rsantana mijam
  • Modelling protein side-chain conformations using constraint logic programming.
    Comput Chem, Vol. 26, No. 1. (December 2001), pp. 85-95.
    by MT Swain, GJ Kemp
    posted to protein_design protein_structure scp by karbak on 2005-12-03 17:25:25 as *** along with 1 person carlk
  • Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library.
    Protein Sci, Vol. 13, No. 3. (March 2004), pp. 735-751.
    by RW Peterson, PL Dutton, AJ Wand
    posted to protein_design protein_structure scp by karbak on 2005-12-03 17:17:27 as *** along with 2 people carlk blackbart
  • STRUCTURAL BIOLOGY: Learning to Speak the Language of Proteins
    Science, Vol. 302, No. 5649. (21 November 2003), pp. 1347-1348.
    by David T Jones
    posted to bioinformatics computational protein_design protein_structure by karbak on 2005-05-05 06:41:10 as *** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • An approach to crystallizing proteins by synthetic symmetrization.
    Proc Natl Acad Sci U S A, Vol. 103, No. 44. (31 October 2006), pp. 16230-16235.
    by DR Banatao, D Cascio, CS Crowley, MR Fleissner, HL Tienson, TO Yeates
    posted to protein_crystallization protein_design protein_engineering by jwm on 2007-11-26 13:33:00 as **
  • Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with pre-defined geometry.
    J Mol Biol, Vol. 222, No. 3. (5 December 1991), pp. 763-785.
    by HW Hellinga, FM Richards
    posted to protein_design xtal_software by jwm on 2007-10-11 20:26:10 as **
  • De novo design of a single-chain diphenylporphyrin metalloprotein.
    J Am Chem Soc, Vol. 129, No. 35. (5 September 2007), pp. 10732-10740.
    by GM Bender, A Lehmann, H Zou, H Cheng, HC Fry, D Engel, MJ Therien, JK Blasie, H Roder, JG Saven, WF DeGrado
    posted to de_novo_protein met metalloprotein protein_design by jwm on 2007-12-04 08:39:31 as **
  • The construction of metal centers in proteins by rational design.
    Fold Des, Vol. 3, No. 1. (1998)
    by HW Hellinga
    posted to protein_design by jwm on 2007-10-11 19:54:34 as **
  • Sequence-specific recruitment of transcriptional co-repressor Cabin1 by myocyte enhancer factor-2.
    Nature, Vol. 422, No. 6933. (17 April 2003), pp. 730-734.
    by A Han, F Pan, JC Stroud, HD Youn, JO Liu, L Chen
    posted to crystallization protein_design by jwm on 2005-12-05 09:58:14 as ** along with 2 groups Radiation_Damage Stressosome
  • De novo prediction of three-dimensional structures for major protein families.
    J Mol Biol, Vol. 322, No. 1. (6 September 2002), pp. 65-78.
    by R Bonneau, CE Strauss, CA Rohl, D Chivian, P Bradley, L Malmström, T Robertson, D Baker
    posted to protein_design protein_structure_prediction rosetta by jwm on 2007-11-08 11:41:25 as ** along with 1 person mijam
  • Design of a novel globular protein fold with atomic-level accuracy.
    Science, Vol. 302, No. 5649. (21 November 2003), pp. 1364-1368.
    by B Kuhlman, G Dantas, GC Ireton, G Varani, BL Stoddard, D Baker
    posted to protein_denovo_design protein_design protein_engineering rosetta by jwm on 2007-11-07 12:00:44 as ** along with 5 people ca3295 chad_davis hmk heymiki kevinchannon
  • The backrub motion: how protein backbone shrugs when a sidechain dances.
    Structure, Vol. 14, No. 2. (February 2006), pp. 265-274.
    by IW Davis, WB Arendall, DC Richardson, JS Richardson
    posted to protein_design rosetta validation by jwm on 2007-11-12 17:21:19 as ** along with 2 people and 2 groups ana nigham structural_bioinformatics Bioinformatics
  • Structures of ruthenium-modified Pseudomonas aeruginosa azurin and [Ru(2,2'-bipyridine)2(imidazole)2]SO4 x 10H2O.
    Acta Crystallogr D Biol Crystallogr, Vol. 55, No. Pt 2. (February 1999), pp. 379-385.
    by S Faham, MW Day, WB Connick, BR Crane, AJ Di Bilio, WP Schaefer, DC Rees, HB Gray
    posted to artificial_photosynthesis protein_design by jwm on 2007-10-19 20:08:24 as **
  • Light-induced reduction of bovine adrenodoxin via the covalently bound ruthenium(II) bipyridyl complex: intramolecular electron transfer and crystal structure.
    Biochemistry, Vol. 45, No. 3. (24 January 2006), pp. 709-718.
    by A Halavaty, JJ Müller, J Contzen, C Jung, F Hannemann, R Bernhardt, M Galander, F Lendzian, U Heinemann
    posted to artificial_photosynthesis protein_design ruthenium by jwm on 2007-11-07 20:24:02 as **
  • Spectroscopy and reactivity of a photogenerated tryptophan radical in a structurally defined protein environment.
    J Am Chem Soc, Vol. 125, No. 47. (26 November 2003), pp. 14220-14221.
    by JE Miller, C Grădinaru, BR Crane, AJ Di Bilio, WA Wehbi, S Un, JR Winkler, HB Gray
    posted to artificial_photosynthesis protein_design by jwm on 2007-11-07 20:06:42 as **
  • Inaugural article: retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins.
    Proc Natl Acad Sci U S A, Vol. 97, No. 12. (6 June 2000), pp. 6298-6305.
    by A Lombardi, CM Summa, S Geremia, L Randaccio, V Pavone, WF DeGrado
    posted to de_novo_protein mn protein_design by jwm on 2005-08-09 12:04:02 as ** along with 2 groups Radiation_Damage Stressosome
  • Designing supramolecular protein assemblies.
    Curr Opin Struct Biol, Vol. 12, No. 4. (August 2002), pp. 464-470.
    by TO Yeates, JE Padilla
    posted to crystallization nanoparticle protein_design protein_engineering by jwm on 2005-09-20 15:45:11 as ** along with 2 groups Radiation_Damage Stressosome
  • 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 rosetta by jwm on 2008-04-07 13:38:39 as ** along with 10 people and 2 groups ucbcjbm barry aalibes aprasad dgront zwang sobolevnrm davidlott msuarezdiez scienbox structural_bioinformatics baker-group
  • Kemp elimination catalysts by computational enzyme design
    Nature (19 March 2008)
    by Daniela Röthlisberger, Olga Khersonsky, Andrew M Wollacott, Lin Jiang, Jason Dechancie, Jamie Betker, Jasmine L Gallaher, Eric A Althoff, Alexandre Zanghellini, Orly Dym, Shira Albeck, Kendall N Houk, Dan S Tawfik, David Baker
    posted to protein_design rosetta by jwm on 2008-04-07 13:37:16 as ** along with 5 people and 1 group sobolevnrm austin neils cactus msuarezdiez baker-group
  • Engineering of beta-propeller protein scaffolds by multiple gene duplication and fusion of an idealized WD repeat.
    Biomol Eng, Vol. 23, No. 4. (September 2006), pp. 185-194.
    by M Nikkhah, Z Jawad-Alami, M Demydchuk, D Ribbons, M Paoli
    posted to beta_propeller protein_design by jwm on 2006-09-07 16:58:49 as ** along with 2 groups Radiation_Damage Stressosome
  • Synthetic hydrogenases: incorporation of an iron carbonyl thiolate into a designed peptide.
    Journal of the American Chemical Society, Vol. 129, No. 48. (5 December 2007), pp. 14844-14845.
    by AK Jones, BR Lichtenstein, A Dutta, G Gordon, PL Dutton
    posted to protein_design maquette hydrogenase by jwm on 2008-05-28 13:27:50 as **
  • Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution
    Journal of Molecular Biology, Vol. 279, No. 5. (26 June 1998), pp. 1211-1227.
    by Robert B Russell
    posted to protein_design by jwm on 2008-04-08 10:31:31 as ** along with 2 people shadowman Evangelia
  • Metal search: a computer program that helps design tetrahedral metal-binding sites.
    Proteins, Vol. 23, No. 2. (October 1995), pp. 256-263.
    by ND Clarke, SM Yuan
    posted to protein_design by jwm on 2008-04-08 10:30:25 as **
  • Inherent protein structural flexibility at the RNA-binding interface of L30e.
    J Mol Biol, Vol. 326, No. 4. (28 February 2003), pp. 999-1004.
    by JA Chao, GS Prasad, SA White, CD Stout, JR Williamson
    posted to crystallization protein_design by jwm on 2005-09-21 19:02:22 as ** along with 2 groups Radiation_Damage Stressosome
  • Photoactive peptides for light-initiated tyrosyl radical generation and transport into ribonucleotide reductase.
    J Am Chem Soc, Vol. 129, No. 27. (11 July 2007), pp. 8500-8509.
    by SY Reece, MR Seyedsayamdost, J Stubbe, DG Nocera
    posted to artificial_photosynthesis protein_design by jwm on 2007-10-19 14:22:22 as **
  • Use of a fusion protein to obtain crystals suitable for X-ray analysis: crystallization of a GST-fused protein containing the DNA-binding domain of DNA replication-related element-binding factor, DREF.
    Protein Sci, Vol. 6, No. 8. (August 1997), pp. 1783-1786.
    by M Kuge, Y Fujii, T Shimizu, F Hirose, A Matsukage, T Hakoshima
    posted to crystallization protein_design by jwm on 2005-09-21 19:00:08 as ** along with 2 groups Radiation_Damage Stressosome
  • A thioredoxin fusion protein of VanH, a D-lactate dehydrogenase from Enterococcus faecium: cloning, expression, purification, kinetic analysis, and crystallization.
    Protein Sci, Vol. 7, No. 5. (May 1998), pp. 1147-1155.
    by VS Stoll, AV Manohar, W Gillon, EL Macfarlane, RC Hynes, EF Pai
    posted to crystallization protein_design by jwm on 2005-09-21 18:58:43 as ** along with 2 groups Radiation_Damage Stressosome
  • X-ray structures of the maltose-maltodextrin-binding protein of the thermoacidophilic bacterium Alicyclobacillus acidocaldarius provide insight into acid stability of proteins.
    J Mol Biol, Vol. 335, No. 1. (2 January 2004), pp. 261-274.
    by K Schäfer, U Magnusson, F Scheffel, A Schiefner, MO Sandgren, K Diederichs, W Welte, A Hülsmann, E Schneider, SL Mowbray
    posted to crystallization protein_design by jwm on 2005-09-23 15:25:46 as ** along with 1 person and 2 groups evodeva Radiation_Damage Stressosome
  • Nanohedra: using symmetry to design self assembling protein cages, layers, crystals, and filaments.
    Proc Natl Acad Sci U S A, Vol. 98, No. 5. (27 February 2001), pp. 2217-2221.
    by JE Padilla, C Colovos, TO Yeates
    posted to crystallization nanoparticle protein_design protein_engineering by jwm on 2005-09-21 14:08:22 as ** along with 1 person and 2 groups bethbromley Radiation_Damage Stressosome
  • Mis-translation of a Computationally Designed Protein Yields an Exceptionally Stable Homodimer: Implications for Protein Engineering and Evolution
    Journal of Molecular Biology, Vol. 362, No. 5. (6 October 2006), pp. 1004-1024.
    by Gautam Dantas, Alexander L Watters, Bradley M Lunde, Ziad M Eletr, Nancy G Isern, Toby Roseman, Jan Lipfert, Sebastian Doniach, Martin Tompa, Brian Kuhlman, Barry L Stoddard, Gabriele Varani, David Baker
    posted to protein_design rosetta by jwm on 2007-11-09 09:16:48 as ** along with 1 person lundbra
  • A designed heterotrimeric coiled coil.
    Biochemistry, Vol. 34, No. 37. (19 September 1995), pp. 11645-11651.
    by S Nautiyal, DN Woolfson, DS King, T Alber
    posted to crystallization protein_design by jwm on 2005-09-21 18:36:33 as ** along with 2 groups Radiation_Damage Stressosome
  • Protein engineering 20 years on.
    Nat Rev Mol Cell Biol, Vol. 3, No. 12. (December 2002), pp. 964-970.
    by JA Brannigan, AJ Wilkinson
    posted to protein_design by jwm on 2007-02-05 11:10:23 as ** along with 2 groups Radiation_Damage Stressosome
  • High-resolution structural validation of the computational redesign of human U1A protein.
    Structure, Vol. 14, No. 5. (May 2006), pp. 847-856.
    by N Dobson, G Dantas, D Baker, G Varani
    posted to protein_design protein_redesign rosetta by jwm on 2007-11-09 09:15:49 as **
  • The crystal structure of the designed trimeric coiled coil coil-VaLd: implications for engineering crystals and supramolecular assemblies.
    Protein Sci, Vol. 6, No. 1. (January 1997), pp. 80-88.
    by NL Ogihara, MS Weiss, WF Degrado, D Eisenberg
    posted to crystallization protein_design by jwm on 2005-09-21 18:35:34 as ** along with 1 person and 2 groups paulinepad Radiation_Damage Stressosome
  • High-resolution Structural and Thermodynamic Analysis of Extreme Stabilization of Human Procarboxypeptidase by Computational Protein Design.
    J Mol Biol (2 December 2006)
    by Gautam Dantas, Colin Corrent, Steve L L Reichow, James J J Havranek, Ziad M M Eletr, Nancy G G Isern, Brian Kuhlman, Gabriele Varani, Ethan A A Merritt, David Baker
    posted to protein_design protein_redesign rosetta by jwm on 2007-11-09 09:15:23 as ** along with 1 person kentsis
  • A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins.
    J Mol Biol, Vol. 332, No. 2. (12 September 2003), pp. 449-460.
    by G Dantas, B Kuhlman, D Callender, M Wong, D Baker
    posted to protein_design protein_structure_prediction rosetta by jwm on 2007-11-09 09:13:45 as ** along with 2 people leelarcombe bethbromley
    • 注: このページを引用する時は次のURLでどうぞ: http://www.citeulike.org/tag/protein_design

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