BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

291 related articles for article (PubMed ID: 19722597)

  • 1. Efficient free energy calculations for compounds with multiple stable conformations separated by high energy barriers.
    Hritz J; Oostenbrink C
    J Phys Chem B; 2009 Sep; 113(38):12711-20. PubMed ID: 19722597
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Free-energy differences between states with different conformational ensembles.
    Garate JA; Oostenbrink C
    J Comput Chem; 2013 Jun; 34(16):1398-408. PubMed ID: 23526629
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Hamiltonian replica exchange molecular dynamics using soft-core interactions.
    Hritz J; Oostenbrink C
    J Chem Phys; 2008 Apr; 128(14):144121. PubMed ID: 18412437
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Optimization of replica exchange molecular dynamics by fast mimicking.
    Hritz J; Oostenbrink C
    J Chem Phys; 2007 Nov; 127(20):204104. PubMed ID: 18052416
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Free energy calculations from one-step perturbations.
    Oostenbrink C
    Methods Mol Biol; 2012; 819():487-99. PubMed ID: 22183553
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Absolute free energies of binding of peptide analogs to the HIV-1 protease from molecular dynamics simulations.
    Bartels C; Widmer A; Ehrhardt C
    J Comput Chem; 2005 Sep; 26(12):1294-305. PubMed ID: 15981257
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Conformation, dynamics, solvation and relative stabilities of selected beta-hexopyranoses in water: a molecular dynamics study with the GROMOS 45A4 force field.
    Kräutler V; Müller M; Hünenberger PH
    Carbohydr Res; 2007 Oct; 342(14):2097-124. PubMed ID: 17573054
    [TBL] [Abstract][Full Text] [Related]  

  • 8. A selective integrated tempering method.
    Yang L; Qin Gao Y
    J Chem Phys; 2009 Dec; 131(21):214109. PubMed ID: 19968339
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods.
    Lu N; Kofke DA; Woolf TB
    J Comput Chem; 2004 Jan; 25(1):28-39. PubMed ID: 14634991
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: assessing entropic and environmental effects.
    Faraldo-Gómez JD; Roux B
    J Comput Chem; 2007 Jul; 28(10):1634-47. PubMed ID: 17342721
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Refinement of X-ray data on dual cosubstrate specificity of CK2 kinase by free energy calculations based on molecular dynamics simulation.
    Setny P; Geller M
    Proteins; 2005 Feb; 58(3):511-7. PubMed ID: 15624214
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Simulated annealing coupled replica exchange molecular dynamics--an efficient conformational sampling method.
    Kannan S; Zacharias M
    J Struct Biol; 2009 Jun; 166(3):288-94. PubMed ID: 19272454
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Reversible scaling of dihedral angle barriers during molecular dynamics to improve structure prediction of cyclic peptides.
    Riemann RN; Zacharias M
    J Pept Res; 2004 Apr; 63(4):354-64. PubMed ID: 15102053
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Efficient and precise solvation free energies via alchemical adiabatic molecular dynamics.
    Abrams JB; Rosso L; Tuckerman ME
    J Chem Phys; 2006 Aug; 125(7):074115. PubMed ID: 16942330
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Calculation of absolute protein-ligand binding free energy using distributed replica sampling.
    Rodinger T; Howell PL; Pomès R
    J Chem Phys; 2008 Oct; 129(15):155102. PubMed ID: 19045232
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Conformational free energies of methyl-alpha-L-iduronic and methyl-beta-D-glucuronic acids in water.
    Babin V; Sagui C
    J Chem Phys; 2010 Mar; 132(10):104108. PubMed ID: 20232948
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Efficient free energy calculations on small molecule host-guest systems - a combined linear interaction energy/one-step perturbation approach.
    Oostenbrink C
    J Comput Chem; 2009 Jan; 30(2):212-21. PubMed ID: 18785242
    [TBL] [Abstract][Full Text] [Related]  

  • 18. A simple method of estimating sampling consistency based on free energy map distance.
    Son WJ; Jang S; Shin S
    J Mol Graph Model; 2008 Oct; 27(3):321-5. PubMed ID: 18619879
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Absolute free-energy calculations of liquids using a harmonic reference state.
    Tyka MD; Sessions RB; Clarke AR
    J Phys Chem B; 2007 Aug; 111(32):9571-80. PubMed ID: 17655215
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations.
    van der Vaart A; Karplus M
    J Chem Phys; 2007 Apr; 126(16):164106. PubMed ID: 17477588
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 15.