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 *

151 related articles for article (PubMed ID: 37622458)

  • 1. RNA tertiary structure prediction in CASP15 by the GeneSilico group: Folding simulations based on statistical potentials and spatial restraints.
    Baulin EF; Mukherjee S; Moafinejad SN; Wirecki TK; Badepally NG; Jaryani F; Stefaniak F; Amiri Farsani M; Ray A; Rocha de Moura T; Bujnicki JM
    Proteins; 2023 Dec; 91(12):1800-1810. PubMed ID: 37622458
    [TBL] [Abstract][Full Text] [Related]  

  • 2. 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]  

  • 3. SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories.
    Moafinejad SN; de Aquino BRH; Boniecki MJ; Pandaranadar Jeyeram IPN; Nikolaev G; Magnus M; Farsani MA; Badepally NG; Wirecki TK; Stefaniak F; Bujnicki JM
    Nucleic Acids Res; 2024 Jul; 52(W1):W368-W373. PubMed ID: 38738621
    [TBL] [Abstract][Full Text] [Related]  

  • 4. 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]  

  • 5. 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]  

  • 6. QRNAS: software tool for refinement of nucleic acid structures.
    Stasiewicz J; Mukherjee S; Nithin C; Bujnicki JM
    BMC Struct Biol; 2019 Mar; 19(1):5. PubMed ID: 30898165
    [TBL] [Abstract][Full Text] [Related]  

  • 7. RNA tertiary structure prediction using RNAComposer in CASP15.
    Sarzynska J; Popenda M; Antczak M; Szachniuk M
    Proteins; 2023 Dec; 91(12):1790-1799. PubMed ID: 37615316
    [TBL] [Abstract][Full Text] [Related]  

  • 8. TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences.
    Harmanci AO; Sharma G; Mathews DH
    BMC Bioinformatics; 2011 Apr; 12():108. PubMed ID: 21507242
    [TBL] [Abstract][Full Text] [Related]  

  • 9. 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]  

  • 10. RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling.
    Li J; Chen SJ
    Nucleic Acids Res; 2023 Apr; 51(7):3341-3356. PubMed ID: 36864729
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure.
    Reinharz V; Major F; Waldispühl J
    Bioinformatics; 2012 Jun; 28(12):i207-14. PubMed ID: 22689763
    [TBL] [Abstract][Full Text] [Related]  

  • 12. ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes.
    Waleń T; Chojnowski G; Gierski P; Bujnicki JM
    Nucleic Acids Res; 2014 Oct; 42(19):e151. PubMed ID: 25159614
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Enhancement of accuracy and efficiency for RNA secondary structure prediction by sequence segmentation and MapReduce.
    Zhang B; Yehdego DT; Johnson KL; Leung MY; Taufer M
    BMC Struct Biol; 2013; 13 Suppl 1(Suppl 1):S3. PubMed ID: 24564983
    [TBL] [Abstract][Full Text] [Related]  

  • 14. New in silico approach to assessing RNA secondary structures with non-canonical base pairs.
    Rybarczyk A; Szostak N; Antczak M; Zok T; Popenda M; Adamiak R; Blazewicz J; Szachniuk M
    BMC Bioinformatics; 2015 Sep; 16(1):276. PubMed ID: 26329823
    [TBL] [Abstract][Full Text] [Related]  

  • 15. 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]  

  • 16. Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms.
    Ding F; Sharma S; Chalasani P; Demidov VV; Broude NE; Dokholyan NV
    RNA; 2008 Jun; 14(6):1164-73. PubMed ID: 18456842
    [TBL] [Abstract][Full Text] [Related]  

  • 17. RNA structure and dynamics: a base pairing perspective.
    Halder S; Bhattacharyya D
    Prog Biophys Mol Biol; 2013 Nov; 113(2):264-83. PubMed ID: 23891726
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Physics-based de novo prediction of RNA 3D structures.
    Cao S; Chen SJ
    J Phys Chem B; 2011 Apr; 115(14):4216-26. PubMed ID: 21413701
    [TBL] [Abstract][Full Text] [Related]  

  • 19. RNA 3D structure prediction guided by independent folding of homologous sequences.
    Magnus M; Kappel K; Das R; Bujnicki JM
    BMC Bioinformatics; 2019 Oct; 20(1):512. PubMed ID: 31640563
    [TBL] [Abstract][Full Text] [Related]  

  • 20. RNAmap2D - calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures.
    Pietal MJ; Szostak N; Rother KM; Bujnicki JM
    BMC Bioinformatics; 2012 Dec; 13():333. PubMed ID: 23259794
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 8.