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 *

230 related articles for article (PubMed ID: 25573551)

  • 1. Extracting the diffusion tensor from molecular dynamics simulation with Milestoning.
    Mugnai ML; Elber R
    J Chem Phys; 2015 Jan; 142(1):014105. PubMed ID: 25573551
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Position-Dependent Diffusion from Biased Simulations and Markov State Model Analysis.
    Sicard F; Koskin V; Annibale A; Rosta E
    J Chem Theory Comput; 2021 Apr; 17(4):2022-2033. PubMed ID: 33728916
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Extending molecular dynamics time scales with milestoning: example of complex kinetics in a solvated peptide.
    West AM; Elber R; Shalloway D
    J Chem Phys; 2007 Apr; 126(14):145104. PubMed ID: 17444753
    [TBL] [Abstract][Full Text] [Related]  

  • 4. The multi-dimensional generalized Langevin equation for conformational motion of proteins.
    Lee HS; Ahn SH; Darve EF
    J Chem Phys; 2019 May; 150(17):174113. PubMed ID: 31067888
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides.
    Itoh SG; Okumura H
    J Comput Chem; 2013 Nov; 34(29):2493-7. PubMed ID: 23925979
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Water-mediated conformations of the alanine dipeptide as revealed by distributed umbrella sampling simulations, quantum mechanics based calculations, and experimental data.
    Cruz V; Ramos J; Martínez-Salazar J
    J Phys Chem B; 2011 Apr; 115(16):4880-6. PubMed ID: 21469661
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Kinetics and reaction coordinate for the isomerization of alanine dipeptide by a forward flux sampling protocol.
    Velez-Vega C; Borrero EE; Escobedo FA
    J Chem Phys; 2009 Jun; 130(22):225101. PubMed ID: 19530790
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Self-guided Langevin dynamics via generalized Langevin equation.
    Wu X; Brooks BR; Vanden-Eijnden E
    J Comput Chem; 2016 Mar; 37(6):595-601. PubMed ID: 26183423
    [TBL] [Abstract][Full Text] [Related]  

  • 9. A systematic study of minima in alanine dipeptide.
    Mironov V; Alexeev Y; Mulligan VK; Fedorov DG
    J Comput Chem; 2019 Jan; 40(2):297-309. PubMed ID: 30368851
    [TBL] [Abstract][Full Text] [Related]  

  • 10. ScMiles2: A Script to Conduct and Analyze Milestoning Trajectories for Long Time Dynamics.
    Cardenas AE; Hunter A; Wang H; Elber R
    J Chem Theory Comput; 2022 Nov; 18(11):6952-6965. PubMed ID: 36191005
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Optimization of partial multicanonical molecular dynamics simulations applied to an alanine dipeptide in explicit water solvent.
    Okumura H
    Phys Chem Chem Phys; 2011 Jan; 13(1):114-26. PubMed ID: 21038036
    [TBL] [Abstract][Full Text] [Related]  

  • 12. How accurate are the nonlinear chemical Fokker-Planck and chemical Langevin equations?
    Grima R; Thomas P; Straube AV
    J Chem Phys; 2011 Aug; 135(8):084103. PubMed ID: 21895155
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Exact milestoning.
    Bello-Rivas JM; Elber R
    J Chem Phys; 2015 Mar; 142(9):094102. PubMed ID: 25747056
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning.
    Yang X; Liu C; Ren P
    J Chem Theory Comput; 2024 May; 20(10):4065-4075. PubMed ID: 38742922
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Two Relations to Estimate Membrane Permeability Using Milestoning.
    Votapka LW; Lee CT; Amaro RE
    J Phys Chem B; 2016 Aug; 120(33):8606-16. PubMed ID: 27154639
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Multiple time step diffusive Langevin dynamics for proteins.
    Eastman P; Doniach S
    Proteins; 1998 Feb; 30(3):215-27. PubMed ID: 9517537
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Computing committors via Mahalanobis diffusion maps with enhanced sampling data.
    Evans L; Cameron MK; Tiwary P
    J Chem Phys; 2022 Dec; 157(21):214107. PubMed ID: 36511548
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Global Langevin model of multidimensional biomolecular dynamics.
    Schaudinnus N; Lickert B; Biswas M; Stock G
    J Chem Phys; 2016 Nov; 145(18):184114. PubMed ID: 27846702
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Markovian and Non-Markovian Modeling of Membrane Dynamics with Milestoning.
    Cardenas AE; Elber R
    J Phys Chem B; 2016 Aug; 120(33):8208-16. PubMed ID: 27016332
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Equipartition terms in transition path ensemble: Insights from molecular dynamics simulations of alanine dipeptide.
    Li W
    J Chem Phys; 2018 Feb; 148(8):084105. PubMed ID: 29495774
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 12.