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 *

146 related articles for article (PubMed ID: 26547154)

  • 1. Reducing the cost of evaluating the committor by a fitting procedure.
    Li W; Ma A
    J Chem Phys; 2015 Nov; 143(17):174103. PubMed ID: 26547154
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide.
    Ren W; Vanden-Eijnden E; Maragakis P; E W
    J Chem Phys; 2005 Oct; 123(13):134109. PubMed ID: 16223277
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Automatic method for identifying reaction coordinates in complex systems.
    Ma A; Dinner AR
    J Phys Chem B; 2005 Apr; 109(14):6769-79. PubMed ID: 16851762
    [TBL] [Abstract][Full Text] [Related]  

  • 4. 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]  

  • 5. 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]  

  • 6. Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI).
    Kikutsuji T; Mori Y; Okazaki KI; Mori T; Kim K; Matubayasi N
    J Chem Phys; 2022 Apr; 156(15):154108. PubMed ID: 35459300
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide.
    Mori Y; Okazaki KI; Mori T; Kim K; Matubayasi N
    J Chem Phys; 2020 Aug; 153(5):054115. PubMed ID: 32770909
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Finding transition pathways using the string method with swarms of trajectories.
    Pan AC; Sezer D; Roux B
    J Phys Chem B; 2008 Mar; 112(11):3432-40. PubMed ID: 18290641
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Multiple pathways in conformational transitions of the alanine dipeptide: an application of dynamic importance sampling.
    Jang H; Woolf TB
    J Comput Chem; 2006 Aug; 27(11):1136-41. PubMed ID: 16721720
    [TBL] [Abstract][Full Text] [Related]  

  • 10. 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]  

  • 11. Committor-Consistent Variational String Method.
    He Z; Chipot C; Roux B
    J Phys Chem Lett; 2022 Oct; 13(40):9263-9271. PubMed ID: 36173307
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Harmonic Fourier beads method for studying rare events on rugged energy surfaces.
    Khavrutskii IV; Arora K; Brooks CL
    J Chem Phys; 2006 Nov; 125(17):174108. PubMed ID: 17100430
    [TBL] [Abstract][Full Text] [Related]  

  • 13. An exploration of machine learning models for the determination of reaction coordinates associated with conformational transitions.
    Naleem N; Abreu CRA; Warmuz K; Tong M; Kirmizialtin S; Tuckerman ME
    J Chem Phys; 2023 Jul; 159(3):. PubMed ID: 37458344
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Analysis of the adaptive multilevel splitting method on the isomerization of alanine dipeptide.
    Lopes LJS; Lelièvre T
    J Comput Chem; 2019 Apr; 40(11):1198-1208. PubMed ID: 30697777
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Robosample: A rigid-body molecular simulation program based on robot mechanics.
    Spiridon L; Şulea TA; Minh DDL; Petrescu AJ
    Biochim Biophys Acta Gen Subj; 2020 Aug; 1864(8):129616. PubMed ID: 32298789
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Reaction coordinates of biomolecular isomerization.
    Bolhuis PG; Dellago C; Chandler D
    Proc Natl Acad Sci U S A; 2000 May; 97(11):5877-82. PubMed ID: 10801977
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors.
    Covino R; Woodside MT; Hummer G; Szabo A; Cossio P
    J Chem Phys; 2019 Oct; 151(15):154115. PubMed ID: 31640370
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Global energy minimization of alanine dipeptide via barrier function methods.
    Ng KM; Solayappan M; Poh KL
    Comput Biol Chem; 2011 Feb; 35(1):19-23. PubMed ID: 21317044
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Metadynamics in essential coordinates: free energy simulation of conformational changes.
    Spiwok V; Lipovová P; Králová B
    J Phys Chem B; 2007 Mar; 111(12):3073-6. PubMed ID: 17388445
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Reaction mechanism and reaction coordinates from the viewpoint of energy flow.
    Li W; Ma A
    J Chem Phys; 2016 Mar; 144(11):114103. PubMed ID: 27004858
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 8.