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2518 related items for PubMed ID: 19643976
1. Incorporating receptor flexibility in the molecular design of protein interfaces. Li L, Liang S, Pilcher MM, Meroueh SO. Protein Eng Des Sel; 2009 Sep; 22(9):575-86. PubMed ID: 19643976 [Abstract] [Full Text] [Related]
2. Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations. Liang S, Li L, Hsu WL, Pilcher MN, Uversky V, Zhou Y, Dunker AK, Meroueh SO. Biochemistry; 2009 Jan 20; 48(2):399-414. PubMed ID: 19113835 [Abstract] [Full Text] [Related]
3. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. Jackson RM, Gabb HA, Sternberg MJ. J Mol Biol; 1998 Feb 13; 276(1):265-85. PubMed ID: 9514726 [Abstract] [Full Text] [Related]
4. Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase. Archontis G, Simonson T, Karplus M. J Mol Biol; 2001 Feb 16; 306(2):307-27. PubMed ID: 11237602 [Abstract] [Full Text] [Related]
5. Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials. Hassan SA, Mehler EL, Zhang D, Weinstein H. Proteins; 2003 Apr 01; 51(1):109-25. PubMed ID: 12596268 [Abstract] [Full Text] [Related]
6. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model. Vorobjev YN, Almagro JC, Hermans J. Proteins; 1998 Sep 01; 32(4):399-413. PubMed ID: 9726412 [Abstract] [Full Text] [Related]
7. A computational investigation of allostery in the catabolite activator protein. Li L, Uversky VN, Dunker AK, Meroueh SO. J Am Chem Soc; 2007 Dec 19; 129(50):15668-76. PubMed ID: 18041838 [Abstract] [Full Text] [Related]
8. Molecular dynamics-solvated interaction energy studies of protein-protein interactions: the MP1-p14 scaffolding complex. Cui Q, Sulea T, Schrag JD, Munger C, Hung MN, Naïm M, Cygler M, Purisima EO. J Mol Biol; 2008 Jun 13; 379(4):787-802. PubMed ID: 18479705 [Abstract] [Full Text] [Related]
9. 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 13; 24(13):1637-56. PubMed ID: 12926007 [Abstract] [Full Text] [Related]
10. Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease. Sham YY, Chu ZT, Tao H, Warshel A. Proteins; 2000 Jun 01; 39(4):393-407. PubMed ID: 10813821 [Abstract] [Full Text] [Related]
11. Molecular insight into pseudolysin inhibition using the MM-PBSA and LIE methods. Adekoya OA, Willassen NP, Sylte I. J Struct Biol; 2006 Feb 01; 153(2):129-44. PubMed ID: 16376106 [Abstract] [Full Text] [Related]
12. Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides. Pitera JW, Kollman PA. Proteins; 2000 Nov 15; 41(3):385-97. PubMed ID: 11025549 [Abstract] [Full Text] [Related]
13. 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]
14. Structure, thermodynamics and cooperativity of the glucocorticoid receptor DNA-binding domain in complex with different response elements. Molecular dynamics simulation and free energy perturbation studies. Eriksson MA, Nilsson L. J Mol Biol; 1995 Oct 27; 253(3):453-72. PubMed ID: 7473727 [Abstract] [Full Text] [Related]
15. On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy. Levy RM, Zhang LY, Gallicchio E, Felts AK. J Am Chem Soc; 2003 Aug 06; 125(31):9523-30. PubMed ID: 12889983 [Abstract] [Full Text] [Related]
16. 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]
17. Free-energy component analysis of 40 protein-DNA complexes: a consensus view on the thermodynamics of binding at the molecular level. Jayaram B, McConnell K, Dixit SB, Das A, Beveridge DL. J Comput Chem; 2002 Jan 15; 23(1):1-14. PubMed ID: 11913374 [Abstract] [Full Text] [Related]
18. 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]
19. Conformational sampling by NMR solution structures calculated with the program DIANA evaluated by comparison with long-time molecular dynamics calculations in explicit water. Berndt KD, Güntert P, Wüthrich K. Proteins; 1996 Mar 14; 24(3):304-13. PubMed ID: 8778777 [Abstract] [Full Text] [Related]
20. Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides. Beck DA, Armen RS, Daggett V. Biochemistry; 2005 Jan 18; 44(2):609-16. PubMed ID: 15641786 [Abstract] [Full Text] [Related] Page: [Next] [New Search]