BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

228 related articles for article (PubMed ID: 22198474)

  • 1. Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations.
    König G; Brooks BR
    J Comput Aided Mol Des; 2012 May; 26(5):543-50. PubMed ID: 22198474
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Thermodynamic integration to predict host-guest binding affinities.
    Lawrenz M; Wereszczynski J; Ortiz-Sánchez JM; Nichols SE; McCammon JA
    J Comput Aided Mol Des; 2012 May; 26(5):569-76. PubMed ID: 22350568
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.
    Lee J; Tofoleanu F; Pickard FC; König G; Huang J; Damjanović A; Baek M; Seok C; Brooks BR
    J Comput Aided Mol Des; 2017 Jan; 31(1):71-85. PubMed ID: 27677749
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge.
    Tofoleanu F; Lee J; Pickard Iv FC; König G; Huang J; Baek M; Seok C; Brooks BR
    J Comput Aided Mol Des; 2017 Jan; 31(1):107-118. PubMed ID: 27696242
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Comparison of thermodynamic integration and Bennett acceptance ratio for calculating relative protein-ligand binding free energies.
    de Ruiter A; Boresch S; Oostenbrink C
    J Comput Chem; 2013 May; 34(12):1024-34. PubMed ID: 23335287
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field.
    Beckstein O; Iorga BI
    J Comput Aided Mol Des; 2012 May; 26(5):635-45. PubMed ID: 22187140
    [TBL] [Abstract][Full Text] [Related]  

  • 7. On the fly estimation of host-guest binding free energies using the movable type method: participation in the SAMPL5 blind challenge.
    Bansal N; Zheng Z; Cerutti DS; Merz KM
    J Comput Aided Mol Des; 2017 Jan; 31(1):47-60. PubMed ID: 27699553
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge.
    Song LF; Bansal N; Zheng Z; Merz KM
    J Comput Aided Mol Des; 2018 Oct; 32(10):1013-1026. PubMed ID: 30143917
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Prediction of SAMPL3 host-guest binding affinities: evaluating the accuracy of generalized force-fields.
    Muddana HS; Gilson MK
    J Comput Aided Mol Des; 2012 May; 26(5):517-25. PubMed ID: 22274835
    [TBL] [Abstract][Full Text] [Related]  

  • 10. AMOEBA binding free energies for the SAMPL7 TrimerTrip host-guest challenge.
    Shi Y; Laury ML; Wang Z; Ponder JW
    J Comput Aided Mol Des; 2021 Jan; 35(1):79-93. PubMed ID: 33140208
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method.
    Bruckner S; Boresch S
    J Comput Chem; 2011 May; 32(7):1303-19. PubMed ID: 21425288
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM).
    Gallicchio E; Levy RM
    J Comput Aided Mol Des; 2012 May; 26(5):505-16. PubMed ID: 22354755
    [TBL] [Abstract][Full Text] [Related]  

  • 13. The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method.
    Yin J; Henriksen NM; Slochower DR; Gilson MK
    J Comput Aided Mol Des; 2017 Jan; 31(1):133-145. PubMed ID: 27638809
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Efficiency of alchemical free energy simulations. II. Improvements for thermodynamic integration.
    Bruckner S; Boresch S
    J Comput Chem; 2011 May; 32(7):1320-33. PubMed ID: 21425289
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Binding Thermodynamics of Host-Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative.
    Slochower DR; Henriksen NM; Wang LP; Chodera JD; Mobley DL; Gilson MK
    J Chem Theory Comput; 2019 Nov; 15(11):6225-6242. PubMed ID: 31603667
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic model.
    Wickstrom L; Gallicchio E; Chen L; Kurtzman T; Deng N
    Phys Chem Chem Phys; 2022 Mar; 24(10):6037-6052. PubMed ID: 35212338
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Energy-entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host-guest challenge.
    Ali HS; Chakravorty A; Kalayan J; de Visser SP; Henchman RH
    J Comput Aided Mol Des; 2021 Aug; 35(8):911-921. PubMed ID: 34264476
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T).
    Caldararu O; Olsson MA; Riplinger C; Neese F; Ryde U
    J Comput Aided Mol Des; 2017 Jan; 31(1):87-106. PubMed ID: 27600554
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Fast free energy estimates from λ-dynamics with bias-updated Gibbs sampling.
    Robo MT; Hayes RL; Ding X; Pulawski B; Vilseck JZ
    Nat Commun; 2023 Dec; 14(1):8515. PubMed ID: 38129400
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches.
    Miyamoto S; Kollman PA
    Proteins; 1993 Jul; 16(3):226-45. PubMed ID: 8346190
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 12.