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 *

332 related articles for article (PubMed ID: 27563170)

  • 21. Rapid Convergence of Energy and Free Energy Profiles with Quantum Mechanical Size in Quantum Mechanical-Molecular Mechanical Simulations of Proton Transfer in DNA.
    Das S; Nam K; Major DT
    J Chem Theory Comput; 2018 Mar; 14(3):1695-1705. PubMed ID: 29446946
    [TBL] [Abstract][Full Text] [Related]  

  • 22. BAR-based multi-dimensional nonequilibrium pulling for indirect construction of a QM/MM free energy landscape.
    Wang X; He Q; Sun Z
    Phys Chem Chem Phys; 2019 Mar; 21(12):6672-6688. PubMed ID: 30855611
    [TBL] [Abstract][Full Text] [Related]  

  • 23. Accurate QM/MM Free Energy Calculations of Enzyme Reactions:  Methylation by Catechol O-Methyltransferase.
    Rod TH; Ryde U
    J Chem Theory Comput; 2005 Nov; 1(6):1240-51. PubMed ID: 26631668
    [TBL] [Abstract][Full Text] [Related]  

  • 24. A quantum chemical approach to the free energy calculations in condensed systems: the QM/MM method combined with the theory of energy representation.
    Takahashi H; Matubayasi N; Nakahara M; Nitta T
    J Chem Phys; 2004 Sep; 121(9):3989-99. PubMed ID: 15332945
    [TBL] [Abstract][Full Text] [Related]  

  • 25. Practically Efficient QM/MM Alchemical Free Energy Simulations: The Orthogonal Space Random Walk Strategy.
    Min D; Zheng L; Harris W; Chen M; Lv C; Yang W
    J Chem Theory Comput; 2010 Aug; 6(8):2253-66. PubMed ID: 26613484
    [TBL] [Abstract][Full Text] [Related]  

  • 26. Binding free energies in the SAMPL6 octa-acid host-guest challenge calculated with MM and QM methods.
    Caldararu O; Olsson MA; Misini Ignjatović M; Wang M; Ryde U
    J Comput Aided Mol Des; 2018 Oct; 32(10):1027-1046. PubMed ID: 30203229
    [TBL] [Abstract][Full Text] [Related]  

  • 27. Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis.
    Titmuss SJ; Cummins PL; Rendell AP; Bliznyuk AA; Gready JE
    J Comput Chem; 2002 Nov; 23(14):1314-22. PubMed ID: 12214314
    [TBL] [Abstract][Full Text] [Related]  

  • 28. Development of Range-Corrected Deep Learning Potentials for Fast, Accurate Quantum Mechanical/Molecular Mechanical Simulations of Chemical Reactions in Solution.
    Zeng J; Giese TJ; Ekesan Ş; York DM
    J Chem Theory Comput; 2021 Nov; 17(11):6993-7009. PubMed ID: 34644071
    [TBL] [Abstract][Full Text] [Related]  

  • 29. A Monte Carlo Resampling Approach for the Calculation of Hybrid Classical and Quantum Free Energies.
    Cave-Ayland C; Skylaris CK; Essex JW
    J Chem Theory Comput; 2017 Feb; 13(2):415-424. PubMed ID: 28029794
    [TBL] [Abstract][Full Text] [Related]  

  • 30. Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions.
    Rosta E; Klähn M; Warshel A
    J Phys Chem B; 2006 Feb; 110(6):2934-41. PubMed ID: 16471904
    [TBL] [Abstract][Full Text] [Related]  

  • 31. Exchange-repulsion energy in QM/EFP.
    Viquez Rojas CI; Fine J; Slipchenko LV
    J Chem Phys; 2018 Sep; 149(9):094103. PubMed ID: 30195305
    [TBL] [Abstract][Full Text] [Related]  

  • 32. Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett's Acceptance Ratio Methods.
    Giese TJ; York DM
    J Chem Theory Comput; 2019 Oct; 15(10):5543-5562. PubMed ID: 31507179
    [TBL] [Abstract][Full Text] [Related]  

  • 33. A simple QM/MM approach for capturing polarization effects in protein-ligand binding free energy calculations.
    Beierlein FR; Michel J; Essex JW
    J Phys Chem B; 2011 May; 115(17):4911-26. PubMed ID: 21476567
    [TBL] [Abstract][Full Text] [Related]  

  • 34. Enhanced sampling and free energy calculations for protein simulations.
    Liao Q
    Prog Mol Biol Transl Sci; 2020; 170():177-213. PubMed ID: 32145945
    [TBL] [Abstract][Full Text] [Related]  

  • 35. Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching.
    Pan X; Li P; Ho J; Pu J; Mei Y; Shao Y
    Phys Chem Chem Phys; 2019 Oct; 21(37):20595-20605. PubMed ID: 31508625
    [TBL] [Abstract][Full Text] [Related]  

  • 36. Single-Ion Thermodynamics from First Principles: Calculation of the Absolute Hydration Free Energy and Single-Electrode Potential of Aqueous Li
    Prasetyo N; Hünenberger PH; Hofer TS
    J Chem Theory Comput; 2018 Dec; 14(12):6443-6459. PubMed ID: 30284829
    [TBL] [Abstract][Full Text] [Related]  

  • 37. BAR-based multi-dimensional nonequilibrium pulling for indirect construction of QM/MM free energy landscapes: from semi-empirical to ab initio.
    Sun Z
    Phys Chem Chem Phys; 2019 Oct; 21(39):21942-21959. PubMed ID: 31552953
    [TBL] [Abstract][Full Text] [Related]  

  • 38. Atomic-resolution dissection of the energetics and mechanism of isomerization of hydrated ATP-Mg(2+) through the SOMA string method.
    Branduardi D; Marinelli F; Faraldo-Gómez JD
    J Comput Chem; 2016 Mar; 37(6):575-86. PubMed ID: 26149527
    [TBL] [Abstract][Full Text] [Related]  

  • 39. Combined QM/MM, Machine Learning Path Integral Approach to Compute Free Energy Profiles and Kinetic Isotope Effects in RNA Cleavage Reactions.
    Giese TJ; Zeng J; Ekesan Ş; York DM
    J Chem Theory Comput; 2022 Jul; 18(7):4304-4317. PubMed ID: 35709391
    [TBL] [Abstract][Full Text] [Related]  

  • 40. Calculation of solvation free energy utilizing a constrained QM/MM approach combined with a theory of solutions.
    Takahashi H; Kambe H; Morita A
    J Chem Phys; 2019 Mar; 150(11):114109. PubMed ID: 30902001
    [TBL] [Abstract][Full Text] [Related]  

    [Previous]   [Next]    [New Search]
    of 17.