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xdeupi's theory [15 articles]

Recent papers added to xdeupi's library classified by the tag theory. You can also see everyone's theory.
  • Proline-induced distortions of transmembrane helices.
    J Mol Biol, Vol. 323, No. 5. (8 November 2002), pp. 951-960.
    by FS Cordes, JN Bright, MS Sansom
    posted to activation helix membrane_proteins pro-kink structure theory transmembrane by xdeupi on 2008-05-27 11:58:27 as ** along with 1 person thaliana
  • Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions.
    Q Rev Biophys, Vol. 37, No. 2. (May 2004), pp. 121-146.
    by U Lehnert, Y Xia, TE Royce, CS Goh, Y Liu, A Senes, H Yu, ZL Zhang, DM Engelman, M Gerstein
    posted to membrane_proteins review serthr_paper structure theory transmembrane by xdeupi on 2008-05-01 19:11:17 as ***** along with 1 person thaliana
  • notes 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 flexibility modeling theory by xdeupi on 2008-04-07 14:23:45 as ** along with 4 people and 2 groups csrocha barry jwm Ema structural_bioinformatics Bioinformatics
  • notes Protein-Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations
    Journal of Molecular Biology, Vol. 331, No. 1. (1 August 2003), pp. 281-299.
    by Jeffrey J Gray, Stewart Moughon, Chu Wang, Ora Schueler-Furman, Brian Kuhlman, Carol A Rohl, David Baker
    posted to dimer docking modeling theory by xdeupi on 2008-04-07 14:18:56 as ** along with 4 people ima bluvsh1 selrac timg
  • The relation between the divergence of sequence and structure in proteins.
    EMBO J, Vol. 5, No. 4. (April 1986), pp. 823-826.
    by C Chothia, AM Lesk
    posted to sequence structure theory by xdeupi on 2008-04-02 15:48:23 as ** along with 7 people and 6 groups ana pansapiens jwm Einat marcius ffranca insectopalo structural_bioinformatics Radiation_Damage Stressosome Bioinformatics BioinfoCIPF SGU-CIPF
  • FRET Study of Membrane Proteins: Simulation-Based Fitting for Analysis of Membrane Protein Embedment and Association
    Biophys. J., Vol. 91, No. 2. (15 July 2006), pp. 454-466.
    by Petr V Nazarov, Rob B Koehorst, Werner L Vos, Vladimir V Apanasovich, Marcus A Hemminga
    posted to dimer fluorescence fret theory by xdeupi on 2008-04-02 13:50:03 as ***** along with 1 person dimka
  • Primary photoprocess in vision: minimal motion to reach the photo- and bathorhodopsin intermediates.
    J Phys Chem B, Vol. 109, No. 18. (12 May 2005), pp. 9104-9110.
    by F Blomgren, S Larsson
    posted to activation retinal rhodopsin theory by xdeupi on 2007-07-30 16:59:24 as ** along with 1 group LabCompMed
  • Refinement of a homology model of the mu-opioid receptor using distance constraints from intrinsic and engineered zinc-binding sites.
    Biochemistry, Vol. 43, No. 27. (13 July 2004), pp. 8700-8710.
    by CB Fowler, ID Pogozheva, H LeVine, HI Mosberg
    posted to active-state modeling opioid structure theory by xdeupi on 2007-07-11 16:51:53 as ** along with 1 person and 1 group merj LabCompMed
  • Development and testing of a general amber force field.
    J Comput Chem, Vol. 25, No. 9. (15 July 2004), pp. 1157-1174.
    by J Wang, RM Wolf, JW Caldwell, PA Kollman, DA Case
    posted to amber dynamics md theory by xdeupi on 2007-06-26 13:51:26 as ** along with 8 people and 1 group nigham lillekatt gane5h kazemi megs easybakemuffin AndreaColetta pavanghatty LabCompMed
  • Performance of the general amber force field in modeling aqueous POPC membrane bilayers.
    J Comput Chem, Vol. 28, No. 12. (12 April 2007), pp. 2051-2058.
    by Balázs Jójárt, Tamás A A Martinek
    posted to amber dynamics md membrane modeling theory by xdeupi on 2007-06-26 13:32:45 as ** along with 2 people and 1 group easybakemuffin viktor21614 LabCompMed
  • Effect of different treatments of long-range interactions and sampling conditions in molecular dynamic simulations of rhodopsin embedded in a dipalmitoyl phosphatidylcholine bilayer.
    J Comput Chem (31 January 2007)
    by Arnau Cordomí, Olle Edholm, Juan J J Perez
    posted to dynamics md membrane rhodopsin theory by xdeupi on 2007-06-25 10:30:55 as ** along with 2 people and 1 group patricia arnaucordomi LabCompMed
  • Refinement of Protein Structures by Iterative Comparative Modeling and CryoEM Density Fitting
    Journal of Molecular Biology, Vol. 357, No. 5. (14 April 2006), pp. 1655-1668.
    by Maya Topf, Matthew L Baker, Marc A Marti-Renom, Wah Chiu, Andrej Sali
    posted to crystallography em modeling structure theory by xdeupi on 2007-06-12 11:28:16 as ** along with 1 group LabCompMed
  • Structures and spectral signatures of protonated water networks in bacteriorhodopsin.
    Proc Natl Acad Sci U S A, Vol. 104, No. 17. (24 April 2007), pp. 6980-6985.
    by G Mathias, D Marx
    posted to activation gpcr protonation retinal_binding_proteins rhodopsin theory water by xdeupi on 2007-06-11 10:25:44 as *** along with 1 person and 1 group saravan LabCompMed
  • An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies
    Protein Eng., Vol. 9, No. 11. (1996), pp. 1063-1065.
    by Lawrence A Kelley, Stephen P Gardner, Michael J Sutcliffe
    posted to dynamics helix md modeling structure theory by xdeupi on 2007-05-31 10:31:28 as ** along with 1 group LabCompMed
  • Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package.
    J Phys Chem A (24 May 2007)
    by Gustavo D Seabra, Ross C Walker, Marcus Elstner, David A Case, Adrian E Roitberg
    posted to amber dynamics theory by xdeupi on 2007-05-28 08:54:09 as ** along with 1 group LabCompMed
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