These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.


BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

153 related articles for article (PubMed ID: 20495851)

  • 1. Dependency of ligand free energy landscapes on charge parameters and solvent models.
    Okamoto Y; Tanaka T; Kokubo H
    J Comput Aided Mol Des; 2010 Aug; 24(8):699-712. PubMed ID: 20495851
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation.
    Roe DR; Okur A; Wickstrom L; Hornak V; Simmerling C
    J Phys Chem B; 2007 Feb; 111(7):1846-57. PubMed ID: 17256983
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.
    Mobley DL; Dumont E; Chodera JD; Dill KA
    J Phys Chem B; 2007 Mar; 111(9):2242-54. PubMed ID: 17291029
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Why Computed Protein Folding Landscapes Are Sensitive to the Water Model.
    Anandakrishnan R; Izadi S; Onufriev AV
    J Chem Theory Comput; 2019 Jan; 15(1):625-636. PubMed ID: 30514080
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Free energy landscape of protein folding in water: explicit vs. implicit solvent.
    Zhou R
    Proteins; 2003 Nov; 53(2):148-61. PubMed ID: 14517967
    [TBL] [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; 32(4):399-413. PubMed ID: 9726412
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Conformational energy penalties of protein-bound ligands.
    Boström J; Norrby PO; Liljefors T
    J Comput Aided Mol Des; 1998 Jul; 12(4):383-96. PubMed ID: 9777496
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Improving the description of salt bridge strength and geometry in a Generalized Born model.
    Shang Y; Nguyen H; Wickstrom L; Okur A; Simmerling C
    J Mol Graph Model; 2011 Feb; 29(5):676-84. PubMed ID: 21168352
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.
    Katkova EV; Onufriev AV; Aguilar B; Sulimov VB
    J Mol Graph Model; 2017 Mar; 72():70-80. PubMed ID: 28064081
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions.
    Olson MA; Feig M; Brooks CL
    J Comput Chem; 2008 Apr; 29(5):820-31. PubMed ID: 17876760
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Robust scoring functions for protein-ligand interactions with quantum chemical charge models.
    Wang JC; Lin JH; Chen CM; Perryman AL; Olson AJ
    J Chem Inf Model; 2011 Oct; 51(10):2528-37. PubMed ID: 21932857
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.
    Deng N; Zhang BW; Levy RM
    J Chem Theory Comput; 2015 Jun; 11(6):2868-78. PubMed ID: 26236174
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Communication: Quantum polarized fluctuating charge model: a practical method to include ligand polarizability in biomolecular simulations.
    Kimura SR; Rajamani R; Langley DR
    J Chem Phys; 2011 Dec; 135(23):231101. PubMed ID: 22191857
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model.
    Shivakumar D; Deng Y; Roux B
    J Chem Theory Comput; 2009 Apr; 5(4):919-30. PubMed ID: 26609601
    [TBL] [Abstract][Full Text] [Related]  

  • 15. ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model.
    Vorobjev YN; Hermans J
    Biophys Chem; 1999 Apr; 78(1-2):195-205. PubMed ID: 10343388
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Replica-Exchange Methods for Biomolecular Simulations.
    Sugita Y; Kamiya M; Oshima H; Re S
    Methods Mol Biol; 2019; 2022():155-177. PubMed ID: 31396903
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Rapid alchemical free energy calculation employing a generalized born implicit solvent model.
    Ostermeir K; Zacharias M
    J Phys Chem B; 2015 Jan; 119(3):968-75. PubMed ID: 25160060
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations.
    Anandakrishnan R; Drozdetski A; Walker RC; Onufriev AV
    Biophys J; 2015 Mar; 108(5):1153-64. PubMed ID: 25762327
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water.
    Xia B; Tsui V; Case DA; Dyson HJ; Wright PE
    J Biomol NMR; 2002 Apr; 22(4):317-31. PubMed ID: 12018480
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation.
    Yu Y; Wang J; Shao Q; Shi J; Zhu W
    J Chem Phys; 2015 Mar; 142(12):125105. PubMed ID: 25833612
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 8.