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 *

253 related articles for article (PubMed ID: 23202432)

  • 1. Correcting pervasive errors in RNA crystallography through enumerative structure prediction.
    Chou FC; Sripakdeevong P; Dibrov SM; Hermann T; Das R
    Nat Methods; 2013 Jan; 10(1):74-6. PubMed ID: 23202432
    [TBL] [Abstract][Full Text] [Related]  

  • 2. RNA Structure Refinement Using the ERRASER-Phenix Pipeline.
    Chou FC; Echols N; Terwilliger TC; Das R
    Methods Mol Biol; 2016; 1320():269-82. PubMed ID: 26227049
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems.
    Adams PD; Baker D; Brunger AT; Das R; DiMaio F; Read RJ; Richardson DC; Richardson JS; Terwilliger TC
    Annu Rev Biophys; 2013; 42():265-87. PubMed ID: 23451892
    [TBL] [Abstract][Full Text] [Related]  

  • 4. High-throughput quantum-mechanics/molecular-mechanics (ONIOM) macromolecular crystallographic refinement with PHENIX/DivCon: the impact of mixed Hamiltonian methods on ligand and protein structure.
    Borbulevych O; Martin RI; Westerhoff LM
    Acta Crystallogr D Struct Biol; 2018 Nov; 74(Pt 11):1063-1077. PubMed ID: 30387765
    [TBL] [Abstract][Full Text] [Related]  

  • 5. RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone.
    Wang X; Kapral G; Murray L; Richardson D; Richardson J; Snoeyink J
    J Math Biol; 2008 Jan; 56(1-2):253-78. PubMed ID: 17401565
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Computational Methods for RNA Structure Validation and Improvement.
    Jain S; Richardson DC; Richardson JS
    Methods Enzymol; 2015; 558():181-212. PubMed ID: 26068742
    [TBL] [Abstract][Full Text] [Related]  

  • 7. RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures.
    Miao Z; Adamiak RW; Blanchet MF; Boniecki M; Bujnicki JM; Chen SJ; Cheng C; Chojnowski G; Chou FC; Cordero P; Cruz JA; Ferré-D'Amaré AR; Das R; Ding F; Dokholyan NV; Dunin-Horkawicz S; Kladwang W; Krokhotin A; Lach G; Magnus M; Major F; Mann TH; Masquida B; Matelska D; Meyer M; Peselis A; Popenda M; Purzycka KJ; Serganov A; Stasiewicz J; Szachniuk M; Tandon A; Tian S; Wang J; Xiao Y; Xu X; Zhang J; Zhao P; Zok T; Westhof E
    RNA; 2015 Jun; 21(6):1066-84. PubMed ID: 25883046
    [TBL] [Abstract][Full Text] [Related]  

  • 8. phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta.
    Terwilliger TC; Dimaio F; Read RJ; Baker D; Bunkóczi G; Adams PD; Grosse-Kunstleve RW; Afonine PV; Echols N
    J Struct Funct Genomics; 2012 Jun; 13(2):81-90. PubMed ID: 22418934
    [TBL] [Abstract][Full Text] [Related]  

  • 9. An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling.
    Sripakdeevong P; Kladwang W; Das R
    Proc Natl Acad Sci U S A; 2011 Dec; 108(51):20573-8. PubMed ID: 22143768
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Improved low-resolution crystallographic refinement with Phenix and Rosetta.
    DiMaio F; Echols N; Headd JJ; Terwilliger TC; Adams PD; Baker D
    Nat Methods; 2013 Nov; 10(11):1102-4. PubMed ID: 24076763
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Autofix for backward-fit sidechains: using MolProbity and real-space refinement to put misfits in their place.
    Headd JJ; Immormino RM; Keedy DA; Emsley P; Richardson DC; Richardson JS
    J Struct Funct Genomics; 2009 Mar; 10(1):83-93. PubMed ID: 19002604
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Building of RNA and DNA double helices into electron density.
    Pavelcik F; Schneider B
    Acta Crystallogr D Biol Crystallogr; 2008 Jun; 64(Pt 6):620-6. PubMed ID: 18560149
    [TBL] [Abstract][Full Text] [Related]  

  • 13. PHENIX: building new software for automated crystallographic structure determination.
    Adams PD; Grosse-Kunstleve RW; Hung LW; Ioerger TR; McCoy AJ; Moriarty NW; Read RJ; Sacchettini JC; Sauter NK; Terwilliger TC
    Acta Crystallogr D Biol Crystallogr; 2002 Nov; 58(Pt 11):1948-54. PubMed ID: 12393927
    [TBL] [Abstract][Full Text] [Related]  

  • 14. RCrane: semi-automated RNA model building.
    Keating KS; Pyle AM
    Acta Crystallogr D Biol Crystallogr; 2012 Aug; 68(Pt 8):985-95. PubMed ID: 22868764
    [TBL] [Abstract][Full Text] [Related]  

  • 15. 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]  

  • 16. Improvements of the hierarchical approach for predicting RNA tertiary structure.
    Zhao Y; Gong Z; Xiao Y
    J Biomol Struct Dyn; 2011 Apr; 28(5):815-26. PubMed ID: 21294592
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution.
    Headd JJ; Echols N; Afonine PV; Grosse-Kunstleve RW; Chen VB; Moriarty NW; Richardson DC; Richardson JS; Adams PD
    Acta Crystallogr D Biol Crystallogr; 2012 Apr; 68(Pt 4):381-90. PubMed ID: 22505258
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Towards automated crystallographic structure refinement with phenix.refine.
    Afonine PV; Grosse-Kunstleve RW; Echols N; Headd JJ; Moriarty NW; Mustyakimov M; Terwilliger TC; Urzhumtsev A; Zwart PH; Adams PD
    Acta Crystallogr D Biol Crystallogr; 2012 Apr; 68(Pt 4):352-67. PubMed ID: 22505256
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Computational modeling of RNA 3D structure based on experimental data.
    Ponce-Salvatierra A; Astha ; Merdas K; Nithin C; Ghosh P; Mukherjee S; Bujnicki JM
    Biosci Rep; 2019 Feb; 39(2):. PubMed ID: 30670629
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix.
    Moriarty NW; Janowski PA; Swails JM; Nguyen H; Richardson JS; Case DA; Adams PD
    Acta Crystallogr D Struct Biol; 2020 Jan; 76(Pt 1):51-62. PubMed ID: 31909743
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 13.