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 *

166 related articles for article (PubMed ID: 26154740)

  • 21. Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.
    Burusco KK; Bruce NJ; Alibay I; Bryce RA
    Chemphyschem; 2015 Oct; 16(15):3233-41. PubMed ID: 26418190
    [TBL] [Abstract][Full Text] [Related]  

  • 22. Free-energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling.
    Graf MM; Maurer M; Oostenbrink C
    J Comput Chem; 2016 Nov; 37(29):2597-605. PubMed ID: 27634475
    [TBL] [Abstract][Full Text] [Related]  

  • 23. Effects of pH and temperature on the structural and thermodynamic character of alpha-syn12 peptide in aqueous solution.
    Cao Z; Liu L; Wang J
    J Biomol Struct Dyn; 2010 Dec; 28(3):343-53. PubMed ID: 20919750
    [TBL] [Abstract][Full Text] [Related]  

  • 24. Efficient Alchemical Intermediate States in Free Energy Calculations Using λ-Enveloping Distribution Sampling.
    König G; Ries B; Hünenberger PH; Riniker S
    J Chem Theory Comput; 2021 Sep; 17(9):5805-5815. PubMed ID: 34476947
    [TBL] [Abstract][Full Text] [Related]  

  • 25. MuSTAR MD: multi-scale sampling using temperature accelerated and replica exchange molecular dynamics.
    Yamamori Y; Kitao A
    J Chem Phys; 2013 Oct; 139(14):145105. PubMed ID: 24116651
    [TBL] [Abstract][Full Text] [Related]  

  • 26. Alchemical Free Energy Differences in Flexible Molecules from Thermodynamic Integration or Free Energy Perturbation Combined with Driven Adiabatic Dynamics.
    Cuendet MA; Tuckerman ME
    J Chem Theory Comput; 2012 Oct; 8(10):3504-12. PubMed ID: 26592999
    [TBL] [Abstract][Full Text] [Related]  

  • 27. Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles.
    Ostermeir K; Zacharias M
    J Comput Chem; 2014 Jan; 35(2):150-8. PubMed ID: 24318649
    [TBL] [Abstract][Full Text] [Related]  

  • 28. Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation.
    Ding X; Vilseck JZ; Hayes RL; Brooks CL
    J Chem Theory Comput; 2017 Jun; 13(6):2501-2510. PubMed ID: 28510433
    [TBL] [Abstract][Full Text] [Related]  

  • 29. Scalable free energy calculation of proteins via multiscale essential sampling.
    Moritsugu K; Terada T; Kidera A
    J Chem Phys; 2010 Dec; 133(22):224105. PubMed ID: 21171681
    [TBL] [Abstract][Full Text] [Related]  

  • 30. Replica exchange simulation method using temperature and solvent viscosity.
    Nguyen PH
    J Chem Phys; 2010 Apr; 132(14):144109. PubMed ID: 20405987
    [TBL] [Abstract][Full Text] [Related]  

  • 31. 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]  

  • 32. 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]  

  • 33. Enhanced ligand sampling for relative protein-ligand binding free energy calculations.
    Kaus JW; McCammon JA
    J Phys Chem B; 2015 May; 119(20):6190-7. PubMed ID: 25906170
    [TBL] [Abstract][Full Text] [Related]  

  • 34. Biasing Potential Replica Exchange Multisite λ-Dynamics for Efficient Free Energy Calculations.
    Armacost KA; Goh GB; Brooks CL
    J Chem Theory Comput; 2015 Mar; 11(3):1267-77. PubMed ID: 26579773
    [TBL] [Abstract][Full Text] [Related]  

  • 35. Recipes for free energy calculations in biomolecular systems.
    Moradi M; Babin V; Sagui C; Roland C
    Methods Mol Biol; 2013; 924():313-37. PubMed ID: 23034754
    [TBL] [Abstract][Full Text] [Related]  

  • 36. Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing.
    Chodera JD; Shirts MR
    J Chem Phys; 2011 Nov; 135(19):194110. PubMed ID: 22112069
    [TBL] [Abstract][Full Text] [Related]  

  • 37. Replica exchange enveloping distribution sampling (RE-EDS): A robust method to estimate multiple free-energy differences from a single simulation.
    Sidler D; Schwaninger A; Riniker S
    J Chem Phys; 2016 Oct; 145(15):154114. PubMed ID: 27782485
    [TBL] [Abstract][Full Text] [Related]  

  • 38. Efficient and direct generation of multidimensional free energy surfaces via adiabatic dynamics without coordinate transformations.
    Abrams JB; Tuckerman ME
    J Phys Chem B; 2008 Dec; 112(49):15742-57. PubMed ID: 19367870
    [TBL] [Abstract][Full Text] [Related]  

  • 39. Applying efficient implicit nongeometric constraints in alchemical free energy simulations.
    Knight JL; Brooks CL
    J Comput Chem; 2011 Dec; 32(16):3423-32. PubMed ID: 21919014
    [TBL] [Abstract][Full Text] [Related]  

  • 40. Using enveloping distribution sampling to compute the free enthalpy difference between right- and left-handed helices of a β-peptide in solution.
    Lin Z; Timmerscheidt TA; van Gunsteren WF
    J Chem Phys; 2012 Aug; 137(6):064108. PubMed ID: 22897256
    [TBL] [Abstract][Full Text] [Related]  

    [Previous]   [Next]    [New Search]
    of 9.