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 *

143 related articles for article (PubMed ID: 39312140)

  • 21. An allosteric ribozyme generator and an inverse folding ribozyme generator: Two computer programs for automated computational design of oligonucleotide-sensing allosteric hammerhead ribozymes with YES Boolean logic function based on experimentally validated algorithms.
    Kaloudas D; Penchovsky R
    Comput Biol Med; 2022 Jun; 145():105469. PubMed ID: 35398809
    [TBL] [Abstract][Full Text] [Related]  

  • 22. Geometric deep learning methods and applications in 3D structure-based drug design.
    Bai Q; Xu T; Huang J; Pérez-Sánchez H
    Drug Discov Today; 2024 Jul; 29(7):104024. PubMed ID: 38759948
    [TBL] [Abstract][Full Text] [Related]  

  • 23. MetalionRNA: computational predictor of metal-binding sites in RNA structures.
    Philips A; Milanowska K; Lach G; Boniecki M; Rother K; Bujnicki JM
    Bioinformatics; 2012 Jan; 28(2):198-205. PubMed ID: 22110243
    [TBL] [Abstract][Full Text] [Related]  

  • 24. Predicting 3D RNA structure from the nucleotide sequence using Euclidean neural networks.
    Sha CM; Wang J; Dokholyan NV
    Biophys J; 2024 Sep; 123(17):2671-2681. PubMed ID: 37838833
    [TBL] [Abstract][Full Text] [Related]  

  • 25. 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]  

  • 26. ARTEMIS: a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment.
    Bohdan DR; Bujnicki JM; Baulin EF
    Nucleic Acids Res; 2024 Oct; 52(18):10850-10861. PubMed ID: 39258540
    [TBL] [Abstract][Full Text] [Related]  

  • 27. VfoldLA: A web server for loop assembly-based prediction of putative 3D RNA structures.
    Xu X; Zhao C; Chen SJ
    J Struct Biol; 2019 Sep; 207(3):235-240. PubMed ID: 31173857
    [TBL] [Abstract][Full Text] [Related]  

  • 28. Modulating RNA structure and catalysis: lessons from small cleaving ribozymes.
    Reymond C; Beaudoin JD; Perreault JP
    Cell Mol Life Sci; 2009 Dec; 66(24):3937-50. PubMed ID: 19718544
    [TBL] [Abstract][Full Text] [Related]  

  • 29. RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures.
    Antczak M; Zok T; Osowiecki M; Popenda M; Adamiak RW; Szachniuk M
    BMC Bioinformatics; 2018 Aug; 19(1):304. PubMed ID: 30134831
    [TBL] [Abstract][Full Text] [Related]  

  • 30. Exploring RNA structure by integrative molecular modelling.
    Masquida B; Beckert B; Jossinet F
    N Biotechnol; 2010 Jul; 27(3):170-83. PubMed ID: 20206310
    [TBL] [Abstract][Full Text] [Related]  

  • 31. Computational design and experimental verification of pseudoknotted ribozymes.
    Najeh S; Zandi K; Kharma N; Perreault J
    RNA; 2023 Jun; 29(6):764-776. PubMed ID: 36868786
    [TBL] [Abstract][Full Text] [Related]  

  • 32. Rosetta:MSF:NN: Boosting performance of multi-state computational protein design with a neural network.
    Nazet J; Lang E; Merkl R
    PLoS One; 2021; 16(8):e0256691. PubMed ID: 34437621
    [TBL] [Abstract][Full Text] [Related]  

  • 33. sincFold: end-to-end learning of short- and long-range interactions in RNA secondary structure.
    Bugnon LA; Di Persia L; Gerard M; Raad J; Prochetto S; Fenoy E; Chorostecki U; Ariel F; Stegmayer G; Milone DH
    Brief Bioinform; 2024 May; 25(4):. PubMed ID: 38855913
    [TBL] [Abstract][Full Text] [Related]  

  • 34. Datasets for Benchmarking RNA Design Algorithms.
    Badura J; Zok T; Rybarczyk A
    Methods Mol Biol; 2025; 2847():229-240. PubMed ID: 39312148
    [TBL] [Abstract][Full Text] [Related]  

  • 35. Design of RNAs: comparing programs for inverse RNA folding.
    Churkin A; Retwitzer MD; Reinharz V; Ponty Y; Waldispühl J; Barash D
    Brief Bioinform; 2018 Mar; 19(2):350-358. PubMed ID: 28049135
    [TBL] [Abstract][Full Text] [Related]  

  • 36. Reconstruction of natural RNA sequences from RNA shape, thermodynamic stability, mutational robustness, and linguistic complexity by evolutionary computation.
    Dromi N; Avihoo A; Barash D
    J Biomol Struct Dyn; 2008 Aug; 26(1):147-62. PubMed ID: 18533734
    [TBL] [Abstract][Full Text] [Related]  

  • 37. RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers.
    Miao Z; Adamiak RW; Antczak M; Boniecki MJ; Bujnicki J; Chen SJ; Cheng CY; Cheng Y; Chou FC; Das R; Dokholyan NV; Ding F; Geniesse C; Jiang Y; Joshi A; Krokhotin A; Magnus M; Mailhot O; Major F; Mann TH; Piątkowski P; Pluta R; Popenda M; Sarzynska J; Sun L; Szachniuk M; Tian S; Wang J; Wang J; Watkins AM; Wiedemann J; Xiao Y; Xu X; Yesselman JD; Zhang D; Zhang Y; Zhang Z; Zhao C; Zhao P; Zhou Y; Zok T; Żyła A; Ren A; Batey RT; Golden BL; Huang L; Lilley DM; Liu Y; Patel DJ; Westhof E
    RNA; 2020 Aug; 26(8):982-995. PubMed ID: 32371455
    [TBL] [Abstract][Full Text] [Related]  

  • 38. Predicting RNA structure by multiple template homology modeling.
    Flores SC; Wan Y; Russell R; Altman RB
    Pac Symp Biocomput; 2010; ():216-27. PubMed ID: 19908374
    [TBL] [Abstract][Full Text] [Related]  

  • 39. Sequence Design Using RNAstructure.
    Zhu M; Mathews DH
    Methods Mol Biol; 2025; 2847():17-31. PubMed ID: 39312134
    [TBL] [Abstract][Full Text] [Related]  

  • 40. Design, construction, and analysis of a novel class of self-folding RNA.
    Ikawa Y; Fukada K; Watanabe S; Shiraishi H; Inoue T
    Structure; 2002 Apr; 10(4):527-34. PubMed ID: 11937057
    [TBL] [Abstract][Full Text] [Related]  

    [Previous]   [Next]    [New Search]
    of 8.