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103 related items for PubMed ID: 21916516
21. Analysis of ligand-bound water molecules in high-resolution crystal structures of protein-ligand complexes. Lu Y, Wang R, Yang CY, Wang S. J Chem Inf Model; 2007; 47(2):668-75. PubMed ID: 17266298 [Abstract] [Full Text] [Related]
22. A GRID-derived water network stabilizes molecular dynamics computer simulations of a protease. Wallnoefer HG, Liedl KR, Fox T. J Chem Inf Model; 2011 Nov 28; 51(11):2860-7. PubMed ID: 21970362 [Abstract] [Full Text] [Related]
23. Computational sampling of a cryptic drug binding site in a protein receptor: explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase. Frembgen-Kesner T, Elcock AH. J Mol Biol; 2006 May 26; 359(1):202-14. PubMed ID: 16616932 [Abstract] [Full Text] [Related]
24. Probing flexibility and "induced-fit" phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations. Sotriffer CA, Krämer O, Klebe G. Proteins; 2004 Jul 01; 56(1):52-66. PubMed ID: 15162486 [Abstract] [Full Text] [Related]
25. Structural dynamics of the box C/D RNA kink-turn and its complex with proteins: the role of the A-minor 0 interaction, long-residency water bridges, and structural ion-binding sites revealed by molecular simulations. Spacková N, Réblová K, Sponer J. J Phys Chem B; 2010 Aug 19; 114(32):10581-93. PubMed ID: 20701388 [Abstract] [Full Text] [Related]
26. Binding mode prediction for a flexible ligand in a flexible pocket using multi-conformation simulated annealing pseudo crystallographic refinement. Ota N, Agard DA. J Mol Biol; 2001 Nov 30; 314(3):607-17. PubMed ID: 11846570 [Abstract] [Full Text] [Related]
27. Molecular simulations of multimodal ligand-protein binding: elucidation of binding sites and correlation with experiments. Freed AS, Garde S, Cramer SM. J Phys Chem B; 2011 Nov 17; 115(45):13320-7. PubMed ID: 21942536 [Abstract] [Full Text] [Related]
28. Modeling protein-small molecule interactions: structure and thermodynamics of noble gases binding in a cavity in mutant phage T4 lysozyme L99A. Mann G, Hermans J. J Mol Biol; 2000 Sep 29; 302(4):979-89. PubMed ID: 10993736 [Abstract] [Full Text] [Related]
29. Structure and dynamics of the hydration shells of the Zn(2+) ion from ab initio molecular dynamics and combined ab initio and classical molecular dynamics simulations. Cauët E, Bogatko S, Weare JH, Fulton JL, Schenter GK, Bylaska EJ. J Chem Phys; 2010 May 21; 132(19):194502. PubMed ID: 20499974 [Abstract] [Full Text] [Related]
30. Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks. Rudling A, Orro A, Carlsson J. J Chem Inf Model; 2018 Feb 26; 58(2):350-361. PubMed ID: 29308882 [Abstract] [Full Text] [Related]
31. The role of aspartate-235 in the binding of cations to an artificial cavity at the radical site of cytochrome c peroxidase. Fitzgerald MM, Trester ML, Jensen GM, McRee DE, Goodin DB. Protein Sci; 1995 Sep 26; 4(9):1844-50. PubMed ID: 8528082 [Abstract] [Full Text] [Related]
32. Prediction of solvation sites at the interface of Src SH2 domain complexes using molecular dynamics simulations. Geroult S, Hooda M, Virdee S, Waksman G. Chem Biol Drug Des; 2007 Aug 26; 70(2):87-99. PubMed ID: 17683370 [Abstract] [Full Text] [Related]
33. Molecular dynamics study of Desulfovibrio africanus cytochrome c3 in oxidized and reduced forms. Bret C, Roth M, Nørager S, Hatchikian EC, Field MJ. Biophys J; 2002 Dec 26; 83(6):3049-65. PubMed ID: 12496077 [Abstract] [Full Text] [Related]
34. Electrostatic control of the tryptophan radical in cytochrome c peroxidase. Barrows TP, Bhaskar B, Poulos TL. Biochemistry; 2004 Jul 13; 43(27):8826-34. PubMed ID: 15236591 [Abstract] [Full Text] [Related]
35. Carbohydrate-binding proteins: Dissecting ligand structures through solvent environment occupancy. Gauto DF, Di Lella S, Guardia CM, Estrin DA, Martí MA. J Phys Chem B; 2009 Jun 25; 113(25):8717-24. PubMed ID: 19485380 [Abstract] [Full Text] [Related]
36. Computational study on the interaction of N1 substituted pyrazole derivatives with B-raf kinase: an unusual water wire hydrogen-bond network and novel interactions at the entrance of the active site. Alzate-Morales JH, Vergara-Jaque A, Caballero J. J Chem Inf Model; 2010 Jun 28; 50(6):1101-12. PubMed ID: 20524689 [Abstract] [Full Text] [Related]
37. 20ns molecular dynamics simulation of the antennapedia homeodomain-DNA complex: water interaction and DNA structure analysis. Roy S, Thakur AR. J Biomol Struct Dyn; 2010 Feb 28; 27(4):443-56. PubMed ID: 19916566 [Abstract] [Full Text] [Related]
38. Hydration properties of ligands and drugs in protein binding sites: tightly-bound, bridging water molecules and their effects and consequences on molecular design strategies. García-Sosa AT. J Chem Inf Model; 2013 Jun 24; 53(6):1388-405. PubMed ID: 23662606 [Abstract] [Full Text] [Related]
39. AcquaAlta: a directional approach to the solvation of ligand-protein complexes. Rossato G, Ernst B, Vedani A, Smiesko M. J Chem Inf Model; 2011 Aug 22; 51(8):1867-81. PubMed ID: 21714532 [Abstract] [Full Text] [Related]
40. Substrate binding and catalytic mechanism in phospholipase C from Bacillus cereus: a molecular mechanics and molecular dynamics study. da Graça Thrige D, Buur JR, Jørgensen FS. Biopolymers; 1997 Sep 22; 42(3):319-36. PubMed ID: 9279125 [Abstract] [Full Text] [Related] Page: [Previous] [Next] [New Search]