BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

187 related articles for article (PubMed ID: 23379664)

  • 21. Alchemical prediction of hydration free energies for SAMPL.
    Mobley DL; Liu S; Cerutti DS; Swope WC; Rice JE
    J Comput Aided Mol Des; 2012 May; 26(5):551-62. PubMed ID: 22198475
    [TBL] [Abstract][Full Text] [Related]  

  • 22. Solvation Free Energy Calculations: The Combination between the Implicitly Polarized Fixed-charge Model and the Reference Potential Strategy.
    Jia X
    J Comput Chem; 2019 Dec; 40(32):2801-2809. PubMed ID: 31433076
    [TBL] [Abstract][Full Text] [Related]  

  • 23. Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model.
    Li P; Song LF; Merz KM
    J Chem Theory Comput; 2015 Apr; 11(4):1645-57. PubMed ID: 26574374
    [TBL] [Abstract][Full Text] [Related]  

  • 24. Calculation of the free energy of polarization: quantifying the effect of explicitly treating electronic polarization on the transferability of force-field parameters.
    Geerke DP; van Gunsteren WF
    J Phys Chem B; 2007 Jun; 111(23):6425-36. PubMed ID: 17508737
    [TBL] [Abstract][Full Text] [Related]  

  • 25. Accounting for polarization cost when using fixed charge force fields. II. Method and application for computing effect of polarization cost on free energy of hydration.
    Swope WC; Horn HW; Rice JE
    J Phys Chem B; 2010 Jul; 114(26):8631-45. PubMed ID: 20540502
    [TBL] [Abstract][Full Text] [Related]  

  • 26. Links between the charge model and bonded parameter force constants in biomolecular force fields.
    Cerutti DS; Debiec KT; Case DA; Chong LT
    J Chem Phys; 2017 Oct; 147(16):161730. PubMed ID: 29096508
    [TBL] [Abstract][Full Text] [Related]  

  • 27. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.
    Maier JA; Martinez C; Kasavajhala K; Wickstrom L; Hauser KE; Simmerling C
    J Chem Theory Comput; 2015 Aug; 11(8):3696-713. PubMed ID: 26574453
    [TBL] [Abstract][Full Text] [Related]  

  • 28. Some practical approaches to treating electrostatic polarization of proteins.
    Ji C; Mei Y
    Acc Chem Res; 2014 Sep; 47(9):2795-803. PubMed ID: 24883956
    [TBL] [Abstract][Full Text] [Related]  

  • 29. A Simple Method for Including Polarization Effects in Solvation Free Energy Calculations When Using Fixed-Charge Force Fields: Alchemically Polarized Charges.
    Kelly BD; Smith WR
    ACS Omega; 2020 Jul; 5(28):17170-17181. PubMed ID: 32715202
    [TBL] [Abstract][Full Text] [Related]  

  • 30. Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations.
    Miller MS; Lay WK; Li S; Hacker WC; An J; Ren J; Elcock AH
    J Chem Theory Comput; 2017 Apr; 13(4):1812-1826. PubMed ID: 28296391
    [TBL] [Abstract][Full Text] [Related]  

  • 31. Calculation of the free energy of solvation for neutral analogs of amino acid side chains.
    Villa A; Mark AE
    J Comput Chem; 2002 Apr; 23(5):548-53. PubMed ID: 11948581
    [TBL] [Abstract][Full Text] [Related]  

  • 32. Predicting hydration Gibbs energies of alkyl-aromatics using molecular simulation: a comparison of current force fields and the development of a new parameter set for accurate solvation data.
    Garrido NM; Jorge M; Queimada AJ; Gomes JR; Economou IG; Macedo EA
    Phys Chem Chem Phys; 2011 Oct; 13(38):17384-94. PubMed ID: 21881653
    [TBL] [Abstract][Full Text] [Related]  

  • 33. Free energy profiles of amino acid side chain analogs near water-vapor interface obtained via MD simulations.
    Shaytan AK; Ivanov VA; Shaitan KV; Khokhlov AR
    J Comput Chem; 2010 Jan; 31(1):204-16. PubMed ID: 19421988
    [TBL] [Abstract][Full Text] [Related]  

  • 34. Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent.
    Li P; Roberts BP; Chakravorty DK; Merz KM
    J Chem Theory Comput; 2013 Jun; 9(6):2733-2748. PubMed ID: 23914143
    [TBL] [Abstract][Full Text] [Related]  

  • 35. Ab initio study of hydrogen-bond formation between aliphatic and phenolic hydroxy groups and selected amino acid side chains.
    Nagy PI; Erhardt PW
    J Phys Chem A; 2008 May; 112(18):4342-54. PubMed ID: 18373368
    [TBL] [Abstract][Full Text] [Related]  

  • 36. Communication: modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions.
    Bardhan JP; Knepley MG
    J Chem Phys; 2014 Oct; 141(13):131103. PubMed ID: 25296776
    [TBL] [Abstract][Full Text] [Related]  

  • 37. Charge asymmetries in hydration of polar solutes.
    Mobley DL; Baker JR; Barber AE; Fennell CJ; Dill KA
    J Phys Chem B; 2008 Feb; 112(8):2405-14. PubMed ID: 18251538
    [TBL] [Abstract][Full Text] [Related]  

  • 38. Simple physics-based analytical formulas for the potentials of mean force for the interaction of amino acid side chains in water. 2. Tests with simple spherical systems.
    Makowski M; Liwo A; Maksimiak K; Makowska J; Scheraga HA
    J Phys Chem B; 2007 Mar; 111(11):2917-24. PubMed ID: 17388417
    [TBL] [Abstract][Full Text] [Related]  

  • 39. Calculation of the water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force field.
    MacCallum JL; Tieleman DP
    J Comput Chem; 2003 Nov; 24(15):1930-5. PubMed ID: 14515375
    [TBL] [Abstract][Full Text] [Related]  

  • 40. Interactions between ionizable amino acid side chains at a lipid bilayer-water interface.
    Yuzlenko O; Lazaridis T
    J Phys Chem B; 2011 Nov; 115(46):13674-84. PubMed ID: 21985663
    [TBL] [Abstract][Full Text] [Related]  

    [Previous]   [Next]    [New Search]
    of 10.