BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

225 related articles for article (PubMed ID: 27125734)

  • 1. Coarse-grained modeling of RNA 3D structure.
    Dawson WK; Maciejczyk M; Jankowska EJ; Bujnicki JM
    Methods; 2016 Jul; 103():138-56. PubMed ID: 27125734
    [TBL] [Abstract][Full Text] [Related]  

  • 2. SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.
    Boniecki MJ; Lach G; Dawson WK; Tomala K; Lukasz P; Soltysinski T; Rother KM; Bujnicki JM
    Nucleic Acids Res; 2016 Apr; 44(7):e63. PubMed ID: 26687716
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Modeling and predicting RNA three-dimensional structures.
    Waldispühl J; Reinharz V
    Methods Mol Biol; 2015; 1269():101-21. PubMed ID: 25577374
    [TBL] [Abstract][Full Text] [Related]  

  • 4. RNA 3D Structure Modeling by Combination of Template-Based Method ModeRNA, Template-Free Folding with SimRNA, and Refinement with QRNAS.
    Piatkowski P; Kasprzak JM; Kumar D; Magnus M; Chojnowski G; Bujnicki JM
    Methods Mol Biol; 2016; 1490():217-35. PubMed ID: 27665602
    [TBL] [Abstract][Full Text] [Related]  

  • 5. HiRE-RNA: a high resolution coarse-grained energy model for RNA.
    Pasquali S; Derreumaux P
    J Phys Chem B; 2010 Sep; 114(37):11957-66. PubMed ID: 20795690
    [TBL] [Abstract][Full Text] [Related]  

  • 6. SimRNAweb: a web server for RNA 3D structure modeling with optional restraints.
    Magnus M; Boniecki MJ; Dawson W; Bujnicki JM
    Nucleic Acids Res; 2016 Jul; 44(W1):W315-9. PubMed ID: 27095203
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Coarse-grained simulations of RNA and DNA duplexes.
    Cragnolini T; Derreumaux P; Pasquali S
    J Phys Chem B; 2013 Jul; 117(27):8047-60. PubMed ID: 23730911
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Ab initio RNA folding.
    Cragnolini T; Derreumaux P; Pasquali S
    J Phys Condens Matter; 2015 Jun; 27(23):233102. PubMed ID: 25993396
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models.
    Krokhotin A; Dokholyan NV
    Methods Enzymol; 2015; 553():65-89. PubMed ID: 25726461
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Modeling and Predicting RNA Three-Dimensional Structures.
    Reinharz V; Sarrazin-Gendron R; Waldispühl J
    Methods Mol Biol; 2021; 2284():17-42. PubMed ID: 33835435
    [TBL] [Abstract][Full Text] [Related]  

  • 11. One-bead coarse-grained model for RNA dynamics.
    Villada-Balbuena M; Carbajal-Tinoco MD
    J Chem Phys; 2017 Jan; 146(4):045101. PubMed ID: 28147510
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability.
    Zhao C; Zhang D; Jiang Y; Chen SJ
    Biophys J; 2020 Oct; 119(7):1439-1455. PubMed ID: 32949490
    [TBL] [Abstract][Full Text] [Related]  

  • 13. A coarse-grained model with implicit salt for RNAs: predicting 3D structure, stability and salt effect.
    Shi YZ; Wang FH; Wu YY; Tan ZJ
    J Chem Phys; 2014 Sep; 141(10):105102. PubMed ID: 25217954
    [TBL] [Abstract][Full Text] [Related]  

  • 14. RNA 3D structure prediction by using a coarse-grained model and experimental data.
    Xia Z; Bell DR; Shi Y; Ren P
    J Phys Chem B; 2013 Mar; 117(11):3135-44. PubMed ID: 23438338
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Modeling of Three-Dimensional RNA Structures Using SimRNA.
    Wirecki TK; Nithin C; Mukherjee S; Bujnicki JM; Boniecki MJ
    Methods Mol Biol; 2020; 2165():103-125. PubMed ID: 32621221
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Computational modeling of RNA 3D structures and interactions.
    Dawson WK; Bujnicki JM
    Curr Opin Struct Biol; 2016 Apr; 37():22-8. PubMed ID: 26689764
    [TBL] [Abstract][Full Text] [Related]  

  • 17. RNA 3D Structure Prediction Using Coarse-Grained Models.
    Li J; Chen SJ
    Front Mol Biosci; 2021; 8():720937. PubMed ID: 34277713
    [TBL] [Abstract][Full Text] [Related]  

  • 18. ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems.
    Tosti Guerra F; Poppleton E; Šulc P; Rovigatti L
    J Chem Phys; 2024 May; 160(20):. PubMed ID: 38814009
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding.
    Mu ZC; Tan YL; Liu J; Zhang BG; Shi YZ
    Molecules; 2023 Jun; 28(12):. PubMed ID: 37375388
    [TBL] [Abstract][Full Text] [Related]  

  • 20. IsRNA: An Iterative Simulated Reference State Approach to Modeling Correlated Interactions in RNA Folding.
    Zhang D; Chen SJ
    J Chem Theory Comput; 2018 Apr; 14(4):2230-2239. PubMed ID: 29499114
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 12.