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 *

532 related articles for article (PubMed ID: 20136072)

  • 1. Current status of the AMOEBA polarizable force field.
    Ponder JW; Wu C; Ren P; Pande VS; Chodera JD; Schnieders MJ; Haque I; Mobley DL; Lambrecht DS; DiStasio RA; Head-Gordon M; Clark GN; Johnson ME; Head-Gordon T
    J Phys Chem B; 2010 Mar; 114(8):2549-64. PubMed ID: 20136072
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there?
    Dauber-Osguthorpe P; Hagler AT
    J Comput Aided Mol Des; 2019 Feb; 33(2):133-203. PubMed ID: 30506158
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Accurate Host-Guest Binding Free Energies Using the AMOEBA Polarizable Force Field.
    Chung MKJ; Miller RJ; Novak B; Wang Z; Ponder JW
    J Chem Inf Model; 2023 May; 63(9):2769-2782. PubMed ID: 37075788
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Evaluation of solvation free energies for small molecules with the AMOEBA polarizable force field.
    Mohamed NA; Bradshaw RT; Essex JW
    J Comput Chem; 2016 Dec; 37(32):2749-2758. PubMed ID: 27757978
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Toward polarizable AMOEBA thermodynamics at fixed charge efficiency using a dual force field approach: application to organic crystals.
    Nessler IJ; Litman JM; Schnieders MJ
    Phys Chem Chem Phys; 2016 Nov; 18(44):30313-30322. PubMed ID: 27524378
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field.
    Corrigan RA; Qi G; Thiel AC; Lynn JR; Walker BD; Casavant TL; Lagardere L; Piquemal JP; Ponder JW; Ren P; Schnieders MJ
    J Chem Theory Comput; 2021 Apr; 17(4):2323-2341. PubMed ID: 33769814
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model.
    Aleksandrov A; Lin FY; Roux B; MacKerell AD
    J Comput Chem; 2018 Aug; 39(22):1707-1719. PubMed ID: 29737546
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Absolute binding free energies for the SAMPL6 cucurbit[8]uril host-guest challenge via the AMOEBA polarizable force field.
    Laury ML; Wang Z; Gordon AS; Ponder JW
    J Comput Aided Mol Des; 2018 Oct; 32(10):1087-1095. PubMed ID: 30324303
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum.
    Schnieders MJ; Baker NA; Ren P; Ponder JW
    J Chem Phys; 2007 Mar; 126(12):124114. PubMed ID: 17411115
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the AMOEBA force field.
    Jing Z; Qi R; Liu C; Ren P
    J Chem Phys; 2017 Oct; 147(16):161733. PubMed ID: 29096462
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Estimating and modeling charge transfer from the SAPT induction energy.
    Deng S; Wang Q; Ren P
    J Comput Chem; 2017 Oct; 38(26):2222-2231. PubMed ID: 28766729
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Representation of Ion-Protein Interactions Using the Drude Polarizable Force-Field.
    Li H; Ngo V; Da Silva MC; Salahub DR; Callahan K; Roux B; Noskov SY
    J Phys Chem B; 2015 Jul; 119(29):9401-16. PubMed ID: 25578354
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Improvements to the AMOEBA Force Field by Introducing Anisotropic Atomic Polarizability of the Water Molecule.
    Das AK; Demerdash ON; Head-Gordon T
    J Chem Theory Comput; 2018 Dec; 14(12):6722-6733. PubMed ID: 30428257
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Improving Condensed-Phase Water Dynamics with Explicit Nuclear Quantum Effects: The Polarizable Q-AMOEBA Force Field.
    Mauger N; Plé T; Lagardère L; Huppert S; Piquemal JP
    J Phys Chem B; 2022 Nov; 126(43):8813-8826. PubMed ID: 36270033
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Trypsin-ligand binding free energy calculation with AMOEBA.
    Shi Y; Jiao D; Schnieders MJ; Ren P
    Annu Int Conf IEEE Eng Med Biol Soc; 2009; 2009():2328-31. PubMed ID: 19965178
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Polarizable AMOEBA Model for Simulating Mg
    Delgado JM; Nagy PR; Varma S
    J Chem Inf Model; 2024 Jan; 64(2):378-392. PubMed ID: 38051630
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Evaluating Parametrization Protocols for Hydration Free Energy Calculations with the AMOEBA Polarizable Force Field.
    Bradshaw RT; Essex JW
    J Chem Theory Comput; 2016 Aug; 12(8):3871-83. PubMed ID: 27341007
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.
    Peng X; Zhang Y; Chu H; Li G
    J Comput Chem; 2016 Mar; 37(6):614-22. PubMed ID: 26493154
    [TBL] [Abstract][Full Text] [Related]  

  • 19. A semiempirical free energy force field with charge-based desolvation.
    Huey R; Morris GM; Olson AJ; Goodsell DS
    J Comput Chem; 2007 Apr; 28(6):1145-52. PubMed ID: 17274016
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Prediction of hydration free energies for the SAMPL4 data set with the AMOEBA polarizable force field.
    Manzoni F; Söderhjelm P
    J Comput Aided Mol Des; 2014 Mar; 28(3):235-44. PubMed ID: 24577872
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 27.