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Journal Abstract Search

489 related items for PubMed ID: 18041759

  • 1. Modeling of metal interaction geometries for protein-ligand docking.
    Seebeck B, Reulecke I, Kämper A, Rarey M.
    Proteins; 2008 May 15; 71(3):1237-54. PubMed ID: 18041759
    [Abstract] [Full Text] [Related]

  • 2. 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]

  • 3. First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations.
    Dudev T, Lin YL, Dudev M, Lim C.
    J Am Chem Soc; 2003 Mar 12; 125(10):3168-80. PubMed ID: 12617685
    [Abstract] [Full Text] [Related]

  • 4. Femtomolar Zn(II) affinity in a peptide-based ligand designed to model thiolate-rich metalloprotein active sites.
    Petros AK, Reddi AR, Kennedy ML, Hyslop AG, Gibney BR.
    Inorg Chem; 2006 Dec 11; 45(25):9941-58. PubMed ID: 17140191
    [Abstract] [Full Text] [Related]

  • 5. Flexibility of metal binding sites in proteins on a database scale.
    Babor M, Greenblatt HM, Edelman M, Sobolev V.
    Proteins; 2005 May 01; 59(2):221-30. PubMed ID: 15726624
    [Abstract] [Full Text] [Related]

  • 6. Computational protocol for predicting the binding affinities of zinc containing metalloprotein-ligand complexes.
    Jain T, Jayaram B.
    Proteins; 2007 Jun 01; 67(4):1167-78. PubMed ID: 17380508
    [Abstract] [Full Text] [Related]

  • 7. Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid residues involved in the coordination.
    Dokmanić I, Sikić M, Tomić S.
    Acta Crystallogr D Biol Crystallogr; 2008 Mar 01; 64(Pt 3):257-63. PubMed ID: 18323620
    [Abstract] [Full Text] [Related]

  • 8. Crystal structure based design of functional metal/protein hybrids.
    Ueno T, Yokoi N, Abe S, Watanabe Y.
    J Inorg Biochem; 2007 Nov 01; 101(11-12):1667-75. PubMed ID: 17675160
    [Abstract] [Full Text] [Related]

  • 9. Binding response: a descriptor for selecting ligand binding site on protein surfaces.
    Zhong S, MacKerell AD.
    J Chem Inf Model; 2007 Nov 01; 47(6):2303-15. PubMed ID: 17900106
    [Abstract] [Full Text] [Related]

  • 10. Accounting for ligand-bound metal ions in docking small molecules on adenylyl cyclase toxins.
    Chen D, Menche G, Power TD, Sower L, Peterson JW, Schein CH.
    Proteins; 2007 May 15; 67(3):593-605. PubMed ID: 17311351
    [Abstract] [Full Text] [Related]

  • 11. Postprocessing of docked protein-ligand complexes using implicit solvation models.
    Lindström A, Edvinsson L, Johansson A, Andersson CD, Andersson IE, Raubacher F, Linusson A.
    J Chem Inf Model; 2011 Feb 28; 51(2):267-82. PubMed ID: 21309544
    [Abstract] [Full Text] [Related]

  • 12. DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction.
    Velec HF, Gohlke H, Klebe G.
    J Med Chem; 2005 Oct 06; 48(20):6296-303. PubMed ID: 16190756
    [Abstract] [Full Text] [Related]

  • 13. Novel statistical-thermodynamic methods to predict protein-ligand binding positions using probability distribution functions.
    Ruvinsky AM, Kozintsev AV.
    Proteins; 2006 Jan 01; 62(1):202-8. PubMed ID: 16287127
    [Abstract] [Full Text] [Related]

  • 14. Estimating protein-ligand binding free energy: atomic solvation parameters for partition coefficient and solvation free energy calculation.
    Pei J, Wang Q, Zhou J, Lai L.
    Proteins; 2004 Dec 01; 57(4):651-64. PubMed ID: 15390269
    [Abstract] [Full Text] [Related]

  • 15. Extension of QM/MM docking and its applications to metalloproteins.
    Cho AE, Rinaldo D.
    J Comput Chem; 2009 Dec 01; 30(16):2609-16. PubMed ID: 19373896
    [Abstract] [Full Text] [Related]

  • 16. MolDock: a new technique for high-accuracy molecular docking.
    Thomsen R, Christensen MH.
    J Med Chem; 2006 Jun 01; 49(11):3315-21. PubMed ID: 16722650
    [Abstract] [Full Text] [Related]

  • 17. Virtual screening against metalloenzymes for inhibitors and substrates.
    Irwin JJ, Raushel FM, Shoichet BK.
    Biochemistry; 2005 Sep 20; 44(37):12316-28. PubMed ID: 16156645
    [Abstract] [Full Text] [Related]

  • 18. Docking studies of matrix metalloproteinase inhibitors: zinc parameter optimization to improve the binding free energy prediction.
    Hu X, Shelver WH.
    J Mol Graph Model; 2003 Nov 20; 22(2):115-26. PubMed ID: 12932782
    [Abstract] [Full Text] [Related]

  • 19. The architecture of metal coordination groups in proteins.
    Harding MM.
    Acta Crystallogr D Biol Crystallogr; 2004 May 20; 60(Pt 5):849-59. PubMed ID: 15103130
    [Abstract] [Full Text] [Related]

  • 20. Individual metal ligands play distinct functional roles in the zinc sensor Staphylococcus aureus CzrA.
    Pennella MA, Arunkumar AI, Giedroc DP.
    J Mol Biol; 2006 Mar 10; 356(5):1124-36. PubMed ID: 16406068
    [Abstract] [Full Text] [Related]

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