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barry's Baker [15 articles]

Recent papers posted to barry's library by the author Baker. You can also see everyone's Baker.
  • Molecular Dynamics Simulation of the Escherichia coli NikR Protein: Equilibrium Conformational Fluctuations Reveal Interdomain Allosteric Communication Pathways
    Journal of Molecular Biology, Vol. In Press, Corrected Proof
    by Michael J Bradley, Peter T Chivers, Nathan A Baker
    posted to md_simulation allosteric by barry on 2008-04-27 22:02:29 as * along with 2 people and 2 groups skoddet sobolevnrm structural_bioinformatics baker-group
  • 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 10 people and 2 groups ucbcjbm aalibes jwm aprasad dgront zwang sobolevnrm davidlott msuarezdiez scienbox structural_bioinformatics baker-group
  • Protein-Protein Docking with Backbone Flexibility
    Journal of Molecular Biology, Vol. 373, No. 2. (19 October 2007), pp. 503-519.
    by Chu Wang, Philip Bradley, David Baker
    posted to docking protein_protein by barry on 2007-09-27 17:40:34 as *** along with 3 people and 2 groups jwm xdeupi Ema structural_bioinformatics Bioinformatics
  • notes 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 hbond protein_structure review by barry on 2007-06-21 22:53:50 as read along with 2 groups structural_bioinformatics Bioinformatics
  • Dynamical properties of fasciculin-2
    Proteins: Structure, Function, and Genetics, Vol. 36, No. 4. (1999), pp. 447-453.
    by Nathan A Baker, Volkhard Helms, Andrew J Mccammon
    posted to md_simulation protein_dynamics protein_structure by barry on 2006-07-22 18:38:37 as * along with 2 groups 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
  • 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
  • notes Computational alanine scanning of protein-protein interfaces.
    Sci STKE, Vol. 2004, No. 219. (10 February 2004)
    by T Kortemme, DE Kim, D Baker
    posted to bioinf_methods protein_protein protein_structure by barry on 2005-12-07 23:56:00 as ***** along with 4 people and 6 groups skoddet sangeetha blackbart joergkurtwegner structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics insilicodrug
  • Improved side-chain modeling for protein-protein docking.
    Protein Sci, Vol. 14, No. 5. (May 2005), pp. 1328-1339.
    by C Wang, O Schueler-Furman, D Baker
    posted to protein_dynamics protein_protein by barry on 2005-10-17 18:53:58 as ** along with 9 people and 3 groups aqeel jwm bicko yongzhao blackbart bluvsh1 hmk selrac Evangelia structural_bioinformatics Bioinformatics TSRI_MGL
  • Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility.
    Proteins, Vol. 60, No. 2. (1 August 2005), pp. 187-194.
    by O Schueler-Furman, C Wang, D Baker
    posted to bioinf_methods protein_dynamics protein_protein by barry on 2005-10-17 18:52:59 as ** along with 3 people and 2 groups jwm bicko bluvsh1 structural_bioinformatics Bioinformatics
  • Affine invarient comparison of molecular shapes with properties
    (2004)
    by X Zang, C Bajaj, NA Baker
    posted to bioinf_methods electrostatics by barry on 2005-10-10 09:40:34 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Toward High-Resolution de Novo Structure Prediction for Small Proteins
    Science, Vol. 309, No. 5742. (16 September 2005), pp. 1868-1871.
    by Philip Bradley, Kira M Misura, David Baker
    posted to comparative_model core_structure protein_design by barry on 2005-09-16 19:05:11 as read along with 8 people and 4 groups BragilMassoud ana thaliana jwm vavi marcius gbart thamelry structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation.
    Proc Natl Acad Sci U S A, Vol. 101, No. 43. (26 October 2004), pp. 15346-15351.
    by B Qian, AR Ortiz, D Baker
    posted to comparative_model pca protein_design protein_dynamics protein_evolution protein_structure structure_comparison by barry on 2005-05-25 18:50:26 as ***** along with 4 people and 4 groups ana lna marcius dgront structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • Recapitulation of protein family divergence using flexible backbone protein design.
    J Mol Biol, Vol. 346, No. 2. (18 February 2005), pp. 631-644.
    by CT Saunders, D Baker
    posted to bioinf_methods protein_design protein_dynamics protein_evolution protein_sequence protein_structure structural_bioinformatics by barry on 2005-05-12 18:40:36 as ** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • notes A simple physical model for binding energy hot spots in protein-protein complexes
    Proceedings Of The National Academy Of Sciences Of The United States Of America, Vol. 99, No. 22. (29 October 2002), pp. 14116-14121.
    by Tanja Kortemme, David Baker
    posted to bioinf_methods gotit protein_protein structural_bioinformatics by barry on 2005-04-14 20:11:47 as ***** along with 2 groups structural_bioinformatics Bioinformatics
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