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Journal Abstract Search

108 related items for PubMed ID: 19939735

  • 1. Toward the fast blind docking of a peptide to a target protein by using a four-body statistical pseudo-potential.
    Aita T, Nishigaki K, Husimi Y.
    Comput Biol Chem; 2010 Feb; 34(1):53-62. PubMed ID: 19939735
    [Abstract] [Full Text] [Related]

  • 2. FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function.
    Taylor RD, Jewsbury PJ, Essex JW.
    J Comput Chem; 2003 Oct; 24(13):1637-56. PubMed ID: 12926007
    [Abstract] [Full Text] [Related]

  • 3. Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential.
    Liu Z, Dominy BN, Shakhnovich EI.
    J Am Chem Soc; 2004 Jul 14; 126(27):8515-28. PubMed ID: 15238009
    [Abstract] [Full Text] [Related]

  • 4. DynaDock: A new molecular dynamics-based algorithm for protein-peptide docking including receptor flexibility.
    Antes I.
    Proteins; 2010 Apr 14; 78(5):1084-104. PubMed ID: 20017216
    [Abstract] [Full Text] [Related]

  • 5. SuperStar: improved knowledge-based interaction fields for protein binding sites.
    Verdonk ML, Cole JC, Watson P, Gillet V, Willett P.
    J Mol Biol; 2001 Mar 30; 307(3):841-59. PubMed ID: 11273705
    [Abstract] [Full Text] [Related]

  • 6. The structural basis of peptide-protein binding strategies.
    London N, Movshovitz-Attias D, Schueler-Furman O.
    Structure; 2010 Feb 10; 18(2):188-99. PubMed ID: 20159464
    [Abstract] [Full Text] [Related]

  • 7. EADock: docking of small molecules into protein active sites with a multiobjective evolutionary optimization.
    Grosdidier A, Zoete V, Michielin O.
    Proteins; 2007 Jun 01; 67(4):1010-25. PubMed ID: 17380512
    [Abstract] [Full Text] [Related]

  • 8. Nonequilibrium, multiple-timescale simulations of ligand-receptor interactions in structured protein systems.
    Zhang Y, Peters MH, Li Y.
    Proteins; 2003 Aug 15; 52(3):339-48. PubMed ID: 12866048
    [Abstract] [Full Text] [Related]

  • 9. FlexE: efficient molecular docking considering protein structure variations.
    Claussen H, Buning C, Rarey M, Lengauer T.
    J Mol Biol; 2001 Apr 27; 308(2):377-95. PubMed ID: 11327774
    [Abstract] [Full Text] [Related]

  • 10. Flexible docking of peptide ligands to proteins.
    Desmet J, De Maeyer M, Spriet J, Lasters I.
    Methods Mol Biol; 2000 Apr 27; 143():359-76. PubMed ID: 11084914
    [No Abstract] [Full Text] [Related]

  • 11. Searching for protein-protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues.
    Terashi G, Takeda-Shitaka M, Takaya D, Komatsu K, Umeyama H.
    Proteins; 2005 Aug 01; 60(2):289-95. PubMed ID: 15981245
    [Abstract] [Full Text] [Related]

  • 12. Phage display screening against a set of targets to establish peptide-based sugar mimetics and molecular docking to predict binding site.
    Yu L, Yu PS, Yee Yen Mui E, McKelvie JC, Pham TP, Yap YW, Wong WQ, Wu J, Deng W, Orner BP.
    Bioorg Med Chem; 2009 Jul 01; 17(13):4825-32. PubMed ID: 19447041
    [Abstract] [Full Text] [Related]

  • 13. Examination of shape complementarity in docking of unbound proteins.
    Norel R, Petrey D, Wolfson HJ, Nussinov R.
    Proteins; 1999 Aug 15; 36(3):307-17. PubMed ID: 10409824
    [Abstract] [Full Text] [Related]

  • 14. Separation of time scale and coupling in the motion governed by the coarse-grained and fine degrees of freedom in a polypeptide backbone.
    Murarka RK, Liwo A, Scheraga HA.
    J Chem Phys; 2007 Oct 21; 127(15):155103. PubMed ID: 17949219
    [Abstract] [Full Text] [Related]

  • 15. LigEvolutioner, a new strategy for modification and optimization of lead compounds in receptor/ligand complexes.
    Zhou P, Tian F, Shang Z.
    Chem Biol Drug Des; 2008 Dec 21; 72(6):525-32. PubMed ID: 19090919
    [Abstract] [Full Text] [Related]

  • 16. Empirical rules facilitate the search for binding sites on protein surfaces.
    te Heesen H, Schlitter AM, Schlitter J.
    J Mol Graph Model; 2007 Jan 21; 25(5):671-9. PubMed ID: 16781176
    [Abstract] [Full Text] [Related]

  • 17. Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking.
    Huang SY, Zou X.
    Proteins; 2007 Feb 01; 66(2):399-421. PubMed ID: 17096427
    [Abstract] [Full Text] [Related]

  • 18. CORCEMA refinement of the bound ligand conformation within the protein binding pocket in reversibly forming weak complexes using STD-NMR intensities.
    Jayalakshmi V, Rama Krishna N.
    J Magn Reson; 2004 May 01; 168(1):36-45. PubMed ID: 15082247
    [Abstract] [Full Text] [Related]

  • 19. High resolution fast quantitative docking using Fourier domain correlation techniques.
    Blom NS, Sygusch J.
    Proteins; 1997 Apr 01; 27(4):493-506. PubMed ID: 9141130
    [Abstract] [Full Text] [Related]

  • 20. Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition.
    Ma XH, Li CH, Shen LZ, Gong XQ, Chen WZ, Wang CX.
    Proteins; 2005 Aug 01; 60(2):319-23. PubMed ID: 15981260
    [Abstract] [Full Text] [Related]

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