BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

155 related articles for article (PubMed ID: 26894545)

  • 1. A new default restraint library for the protein backbone in Phenix: a conformation-dependent geometry goes mainstream.
    Moriarty NW; Tronrud DE; Adams PD; Karplus PA
    Acta Crystallogr D Struct Biol; 2016 Jan; 72(Pt 1):176-9. PubMed ID: 26894545
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Improved ligand geometries in crystallographic refinement using AFITT in PHENIX.
    Janowski PA; Moriarty NW; Kelley BP; Case DA; York DM; Adams PD; Warren GL
    Acta Crystallogr D Struct Biol; 2016 Sep; 72(Pt 9):1062-72. PubMed ID: 27599738
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement.
    Moriarty NW; Tronrud DE; Adams PD; Karplus PA
    FEBS J; 2014 Sep; 281(18):4061-71. PubMed ID: 24890778
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package.
    Borbulevych OY; Plumley JA; Martin RI; Merz KM; Westerhoff LM
    Acta Crystallogr D Biol Crystallogr; 2014 May; 70(Pt 5):1233-47. PubMed ID: 24816093
    [TBL] [Abstract][Full Text] [Related]  

  • 5. 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]  

  • 6. Conformation-dependent restraints for polynucleotides: the sugar moiety.
    Kowiel M; Brzezinski D; Gilski M; Jaskolski M
    Nucleic Acids Res; 2020 Jan; 48(2):962-973. PubMed ID: 31799624
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Real-space refinement in PHENIX for cryo-EM and crystallography.
    Afonine PV; Poon BK; Read RJ; Sobolev OV; Terwilliger TC; Urzhumtsev A; Adams PD
    Acta Crystallogr D Struct Biol; 2018 Jun; 74(Pt 6):531-544. PubMed ID: 29872004
    [TBL] [Abstract][Full Text] [Related]  

  • 8. 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]  

  • 9. An editor for the generation and customization of geometry restraints.
    Moriarty NW; Draizen EJ; Adams PD
    Acta Crystallogr D Struct Biol; 2017 Feb; 73(Pt 2):123-130. PubMed ID: 28177308
    [TBL] [Abstract][Full Text] [Related]  

  • 10. The critical role of QM/MM X-ray refinement and accurate tautomer/protomer determination in structure-based drug design.
    Borbulevych OY; Martin RI; Westerhoff LM
    J Comput Aided Mol Des; 2021 Apr; 35(4):433-451. PubMed ID: 33108589
    [TBL] [Abstract][Full Text] [Related]  

  • 11. Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins.
    Tronrud DE; Berkholz DS; Karplus PA
    Acta Crystallogr D Biol Crystallogr; 2010 Jul; 66(Pt 7):834-42. PubMed ID: 20606264
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Arginine off-kilter: guanidinium is not as planar as restraints denote.
    Moriarty NW; Liebschner D; Tronrud DE; Adams PD
    Acta Crystallogr D Struct Biol; 2020 Dec; 76(Pt 12):1159-1166. PubMed ID: 33263321
    [TBL] [Abstract][Full Text] [Related]  

  • 13. 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]  

  • 14. A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution.
    Tronrud DE; Karplus PA
    Acta Crystallogr D Biol Crystallogr; 2011 Aug; 67(Pt 8):699-706. PubMed ID: 21795811
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Keep it together: restraints in crystallographic refinement of macromolecule-ligand complexes.
    Steiner RA; Tucker JA
    Acta Crystallogr D Struct Biol; 2017 Feb; 73(Pt 2):93-102. PubMed ID: 28177305
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Restraint validation of biomolecular structures determined by NMR in the Protein Data Bank.
    Baskaran K; Ploskon E; Tejero R; Yokochi M; Harrus D; Liang Y; Peisach E; Persikova I; Ramelot TA; Sekharan M; Tolchard J; Westbrook JD; Bardiaux B; Schwieters CD; Patwardhan A; Velankar S; Burley SK; Kurisu G; Hoch JC; Montelione GT; Vuister GW; Young JY
    Structure; 2024 Jun; 32(6):824-837.e1. PubMed ID: 38490206
    [TBL] [Abstract][Full Text] [Related]  

  • 17. 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]  

  • 18. A complete Fourier-synthesis-based backbone-conformation-dependent library for proteins.
    Tronrud DE; Karplus PA
    Acta Crystallogr D Struct Biol; 2021 Feb; 77(Pt 2):249-266. PubMed ID: 33559613
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Conformation dependence of backbone geometry in proteins.
    Berkholz DS; Shapovalov MV; Dunbrack RL; Karplus PA
    Structure; 2009 Oct; 17(10):1316-25. PubMed ID: 19836332
    [TBL] [Abstract][Full Text] [Related]  

  • 20. In situ ligand restraints from quantum-mechanical methods.
    Liebschner D; Moriarty NW; Poon BK; Adams PD
    Acta Crystallogr D Struct Biol; 2023 Feb; 79(Pt 2):100-110. PubMed ID: 36762856
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 8.