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Tag protein_design [187 articles]

Recent papers classified by the tag protein_design.
  • Optimal Design of Thermally Stable Proteins
    Bioinformatics (22 August 2008), btn450.
    by Vanitha Suresh, Ryan M Bannen, George N Phillips, Stephen J Wright, Julie C Mitchell
    posted to protein_design structure_aided by phoenixzxl on 2008-08-27 02:04:46 as ** along with 2 people friendpine zwang
  • Design of protein function leaps by directed domain interface evolution
    Proceedings of the National Academy of Sciences (29 April 2008), 0801097105.
    by Jin Huang, Akiko Koide, Koki Makabe, Shohei Koide
    posted to directed_evolution protein_design by phoenixzxl on 2008-08-27 08:23:52 as ** along with 4 people cmzmasek choonpeng zwang marck
  • 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 protein_design review synthetic_biology 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 coiled_coil protein_design specificity 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
  • 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
  • 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
  • Toward Full-Sequence De Novo Protein Design with Flexible Templates for Human Beta-Defensin-2
    Biophys. J., Vol. 94, No. 2. (15 January 2008), pp. 584-599.
    by Ho K Fung, Christodoulos A Floudas, Martin S Taylor, Li Zhang, Dimitrios Morikis
    posted to protein_design by msuarezdiez on 2008-07-08 10:54:40 as **
  • Are database-derived potentials valid for scoring both forward and inverted protein folding?
    Protein Eng., Vol. 8, No. 9. (1 September 1995), pp. 849-858.
    by Marianne J Rooman, Shoshana J Wodak
    posted to protein_design by msuarezdiez on 2008-09-01 15:21:14 as **
  • Protein Folding in the Absence of the Solvent Ordering Contribution to the Hydrophobic Interaction
    Journal of Molecular Biology, Vol. 229, No. 2. (20 January 1993), pp. 502-511.
    by Derek N Woolfson, Alan Cooper, Margaret M Harding, Dudley H Williams, Philip A Evans
    posted to protein_design solvent by msuarezdiez on 2008-07-15 16:07:48 as ***
  • Role of residual structure in the unfolded state of a thermophilic protein.
    Proc Natl Acad Sci U S A, Vol. 100, No. 20. (30 September 2003), pp. 11345-11349.
    by S Robic, M Guzman-Casado, JM Sanchez-Ruiz, S Marqusee
    posted to protein_design unfolded_state by msuarezdiez on 2008-07-22 10:09:46 as ** along with 1 person choonpeng
  • Design of Multi-Specificity in Protein Interfaces
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e164.
    by Elisabeth L Humphris, Tanja Kortemme
    posted to protein_design multipurpose by msuarezdiez on 2008-09-08 15:29:03 as read along with 7 people and 3 groups jwm bicko Einat dpollard Scis0000002 phoenixzxl marck structural_bioinformatics Bioinformatics EisenLab
  • Energy Functions for Protein Design: Adjustment with Protein-Protein Complex Affinities, Models for the Unfolded State, and Negative Design of Solubility and Specificity
    Journal of Molecular Biology, Vol. 347, No. 1. (18 March 2005), pp. 203-227.
    by Navin Pokala, Tracy M Handel
    posted to protein_design by msuarezdiez on 2008-07-22 12:56:58 as **
  • Extending Iterative Protein Redesign and Optimization (IPRO) in Protein Library Design for Ligand Specificity
    Biophys. J., Vol. 92, No. 6. (15 March 2007), pp. 2120-2130.
    by Hossein Fazelinia, Patrick C Cirino, Costas D Maranas
    posted to optimization protein_design by msuarezdiez on 2008-07-23 09:39:07 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 ***
  • 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 **
  • Solvated docking: introducing water into the modelling of biomolecular complexes.
    Bioinformatics (9 August 2006)
    by Aalt D J D van Dijk, Alexandre M J J M Bonvin
    posted to water protein_docking protein_design by msuarezdiez on 2008-09-01 13:32:10 as ** along with 5 people and 1 group arlam BragilMassoud bicko jteyra Lombardo_7 group
  • 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 **
  • Design of a Hyperstable Protein by Rational Consideration of Unfolded State Interactions
    J. Am. Chem. Soc., Vol. 128, No. 10. (15 March 2006), pp. 3144-3145.
    by B Anil, R Craig-Schapiro, DP Raleigh
    posted to protein_design unfolded_state by msuarezdiez on 2008-07-22 10:25:41 as **
  • 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 2 people msuarezdiez joseph_x_zhou
  • 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
  • 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
  • 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 **
  • 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 blackbart carlk
  • 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 9 people nigham bicko blackbart bluvsh1 rsantana mijam jwm carlk newton1234
  • 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
  • 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 ***
  • 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 **
  • 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
  • Functional rapidly folding proteins from simplified amino acid sequences.
    Nat Struct Biol, Vol. 4, No. 10. (October 1997), pp. 805-809.
    by DS Riddle, JV Santiago, ST Bray-Hall, N Doshi, VP Grantcharova, Q Yi, D Baker
    posted to protein_design rosetta by jwm on 2007-11-26 10:24:40 as **
  • Designed to be stable: crystal structure of a consensus ankyrin repeat protein.
    Proc Natl Acad Sci U S A, Vol. 100, No. 4. (18 February 2003), pp. 1700-1705.
    by A Kohl, HK Binz, P Forrer, MT Stumpp, A Plückthun, MG Grütter
    posted to ankyrin crystallization protein_design by jwm on 2005-09-28 18:00:06 as ** along with 2 groups Radiation_Damage Stressosome
  • 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 **
  • 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
  • Computational design of a water-soluble analog of phospholamban.
    Protein Sci, Vol. 12, No. 2. (February 2003), pp. 337-348.
    by AM Slovic, CM Summa, JD Lear, WF DeGrado
    posted to membrane2soluble protein_design by jwm on 2007-12-06 10:50:44 as **
  • 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
  • Protein engineering of cytochrome b562 for quinone binding and light-induced electron transfer.
    Proc Natl Acad Sci U S A, Vol. 101, No. 51. (21 December 2004), pp. 17675-17680.
    by S Hay, BB Wallace, TA Smith, KP Ghiggino, T Wydrzynski
    posted to bioenergy protein_design protein_engineering by jwm on 2007-10-07 16:40:16 as **
  • Converting a maltose receptor into a nascent binuclear copper oxygenase by computational design.
    Biochemistry, Vol. 41, No. 9. (5 March 2002), pp. 3262-3269.
    by DE Benson, AE Haddy, HW Hellinga
    posted to protein_design by jwm on 2008-04-27 15:26:14 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 **
  • Different mechanisms of the binding of soluble electron donors to the photosynthetic reaction center of Rubrivivax gelatinosus and Blastochloris viridis.
    J Biol Chem, Vol. 276, No. 26. (29 June 2001), pp. 24108-24112.
    by A Osyczka, KV Nagashima, S Sogabe, K Miki, K Shimada, K Matsuura
    posted to cytochrome_c protein_design reaction_centre by jwm on 2007-10-07 16:33:50 as **
  • 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 hydrogenase maquette protein_design by jwm on 2008-05-28 13:27:50 as **
  • Computational design of water-soluble analogues of the potassium channel KcsA.
    Proc Natl Acad Sci U S A, Vol. 101, No. 7. (17 February 2004), pp. 1828-1833.
    by AM Slovic, H Kono, JD Lear, JG Saven, WF DeGrado
    posted to membrane2soluble protein_design by jwm on 2007-12-06 10:38:11 as **
  • 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
  • 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
  • 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
  • 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
  • Designing repeat proteins: well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins.
    J Mol Biol, Vol. 332, No. 2. (12 September 2003), pp. 489-503.
    by HK Binz, MT Stumpp, P Forrer, P Amstutz, A Plückthun
    posted to ankyrin crystallization protein_design by jwm on 2005-09-28 17:58:58 as ** along with 2 groups Radiation_Damage Stressosome
  • 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 pentameric coiled-coil: decoding the motif for tetramer versus pentamer formation in water-soluble phospholamban
    Journal of Peptide Research, Vol. 65, No. 3. (March 2005), pp. 312-321.
    by AM Slovic, JD Lear, WF Degrado
    posted to membrane2soluble protein_design by jwm on 2007-12-06 10:50:30 as **
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