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Journal Abstract Search

282 related items for PubMed ID: 21120864

  • 1. Accounting for conformational entropy in predicting binding free energies of protein-protein interactions.
    Kamisetty H, Ramanathan A, Bailey-Kellogg C, Langmead CJ.
    Proteins; 2011 Feb; 79(2):444-62. PubMed ID: 21120864
    [Abstract] [Full Text] [Related]

  • 2. 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]

  • 3. 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]

  • 4. Comparison between computational alanine scanning and per-residue binding free energy decomposition for protein-protein association using MM-GBSA: application to the TCR-p-MHC complex.
    Zoete V, Michielin O.
    Proteins; 2007 Jun 01; 67(4):1026-47. PubMed ID: 17377991
    [Abstract] [Full Text] [Related]

  • 5. Amino acid conformational preferences and solvation of polar backbone atoms in peptides and proteins.
    Avbelj F.
    J Mol Biol; 2000 Jul 28; 300(5):1335-59. PubMed ID: 10903873
    [Abstract] [Full Text] [Related]

  • 6. Cancer-related mutations in BRCA1-BRCT cause long-range structural changes in protein-protein binding sites: a molecular dynamics study.
    Gough CA, Gojobori T, Imanishi T.
    Proteins; 2007 Jan 01; 66(1):69-86. PubMed ID: 17063491
    [Abstract] [Full Text] [Related]

  • 7. Computational protein design with side-chain conformational entropy.
    Sciretti D, Bruscolini P, Pelizzola A, Pretti M, Jaramillo A.
    Proteins; 2009 Jan 01; 74(1):176-91. PubMed ID: 18618711
    [Abstract] [Full Text] [Related]

  • 8. Temperature dependence of the backbone dynamics of ribonuclease A in the ground state and bound to the inhibitor 5'-phosphothymidine (3'-5')pyrophosphate adenosine 3'-phosphate.
    Kovrigin EL, Cole R, Loria JP.
    Biochemistry; 2003 May 13; 42(18):5279-91. PubMed ID: 12731869
    [Abstract] [Full Text] [Related]

  • 9. 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]

  • 10. Determination of atomic desolvation energies from the structures of crystallized proteins.
    Zhang C, Vasmatzis G, Cornette JL, DeLisi C.
    J Mol Biol; 1997 Apr 04; 267(3):707-26. PubMed ID: 9126848
    [Abstract] [Full Text] [Related]

  • 11. Increased protein backbone conformational entropy upon hydrophobic ligand binding.
    Zídek L, Novotny MV, Stone MJ.
    Nat Struct Biol; 1999 Dec 04; 6(12):1118-21. PubMed ID: 10581552
    [Abstract] [Full Text] [Related]

  • 12. 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]

  • 13. Characterization of the backbone and side chain dynamics of the CaM-CaMKIp complex reveals microscopic contributions to protein conformational entropy.
    Frederick KK, Kranz JK, Wand AJ.
    Biochemistry; 2006 Aug 15; 45(32):9841-8. PubMed ID: 16893184
    [Abstract] [Full Text] [Related]

  • 14. Role of main-chain electrostatics, hydrophobic effect and side-chain conformational entropy in determining the secondary structure of proteins.
    Avbelj F, Fele L.
    J Mol Biol; 1998 Jun 12; 279(3):665-84. PubMed ID: 9641985
    [Abstract] [Full Text] [Related]

  • 15. 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]

  • 16. Solvation properties of N-substituted cis and trans amides are not identical: significant enthalpy and entropy changes are revealed by the use of variable temperature 1H NMR in aqueous and chloroform solutions and ab initio calculations.
    Troganis AN, Sicilia E, Barbarossou K, Gerothanassis IP, Russo N.
    J Phys Chem A; 2005 Dec 29; 109(51):11878-84. PubMed ID: 16366639
    [Abstract] [Full Text] [Related]

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  • 19. The impact of protein flexibility on protein-protein docking.
    Ehrlich LP, Nilges M, Wade RC.
    Proteins; 2005 Jan 01; 58(1):126-33. PubMed ID: 15515181
    [Abstract] [Full Text] [Related]

  • 20. Thermodynamics of the interactions of lac repressor with variants of the symmetric lac operator: effects of converting a consensus site to a non-specific site.
    Frank DE, Saecker RM, Bond JP, Capp MW, Tsodikov OV, Melcher SE, Levandoski MM, Record MT.
    J Mol Biol; 1997 Apr 18; 267(5):1186-206. PubMed ID: 9150406
    [Abstract] [Full Text] [Related]

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