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 *

295 related articles for article (PubMed ID: 22868759)

  • 1. Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX.
    Bell JA; Ho KL; Farid R
    Acta Crystallogr D Biol Crystallogr; 2012 Aug; 68(Pt 8):935-52. PubMed ID: 22868759
    [TBL] [Abstract][Full Text] [Related]  

  • 2. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation.
    Word JM; Lovell SC; Richardson JS; Richardson DC
    J Mol Biol; 1999 Jan; 285(4):1735-47. PubMed ID: 9917408
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms.
    Word JM; Lovell SC; LaBean TH; Taylor HC; Zalis ME; Presley BK; Richardson JS; Richardson DC
    J Mol Biol; 1999 Jan; 285(4):1711-33. PubMed ID: 9917407
    [TBL] [Abstract][Full Text] [Related]  

  • 4. A new force field (ECEPP-05) for peptides, proteins, and organic molecules.
    Arnautova YA; Jagielska A; Scheraga HA
    J Phys Chem B; 2006 Mar; 110(10):5025-44. PubMed ID: 16526746
    [TBL] [Abstract][Full Text] [Related]  

  • 5. A Gibbs free energy correlation for automated docking of carbohydrates.
    Hill AD; Reilly PJ
    J Comput Chem; 2008 May; 29(7):1131-41. PubMed ID: 18074341
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Automated minimization of steric clashes in protein structures.
    Ramachandran S; Kota P; Ding F; Dokholyan NV
    Proteins; 2011 Jan; 79(1):261-70. PubMed ID: 21058396
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Short nonbonded contact distances in organic molecules and their use as atom-clash criteria in conformer validation and searching.
    Taylor R
    J Chem Inf Model; 2011 Apr; 51(4):897-908. PubMed ID: 21417266
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Low Resolution Refinement of Atomic Models Against Crystallographic Data.
    Nicholls RA; Kovalevskiy O; Murshudov GN
    Methods Mol Biol; 2017; 1607():565-593. PubMed ID: 28573589
    [TBL] [Abstract][Full Text] [Related]  

  • 9. A set of van der Waals and coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking.
    Li AJ; Nussinov R
    Proteins; 1998 Jul; 32(1):111-27. PubMed ID: 9672047
    [TBL] [Abstract][Full Text] [Related]  

  • 10. 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]  

  • 11. 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]  

  • 12. Reintroducing electrostatics into protein X-ray structure refinement: bulk solvent treated as a dielectric continuum.
    Moulinier L; Case DA; Simonson T
    Acta Crystallogr D Biol Crystallogr; 2003 Dec; 59(Pt 12):2094-103. PubMed ID: 14646067
    [TBL] [Abstract][Full Text] [Related]  

  • 13. A geometry force field which converts low-resolution X-ray models to structures with properties found at ultra high resolution.
    McMartin C
    Protein Sci; 2012 Jan; 21(1):75-83. PubMed ID: 22057834
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Structure Refinement at Atomic Resolution.
    Jaskolski M
    Methods Mol Biol; 2017; 1607():549-563. PubMed ID: 28573588
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Propensities of polar and aromatic amino acids in noncanonical interactions: nonbonded contacts analysis of protein-ligand complexes in crystal structures.
    Imai YN; Inoue Y; Yamamoto Y
    J Med Chem; 2007 Mar; 50(6):1189-96. PubMed ID: 17315854
    [TBL] [Abstract][Full Text] [Related]  

  • 16. Getting the chemistry right: protonation, tautomers and the importance of H atoms in biological chemistry.
    Bax B; Chung CW; Edge C
    Acta Crystallogr D Struct Biol; 2017 Feb; 73(Pt 2):131-140. PubMed ID: 28177309
    [TBL] [Abstract][Full Text] [Related]  

  • 17. High-resolution structure prediction and the crystallographic phase problem.
    Qian B; Raman S; Das R; Bradley P; McCoy AJ; Read RJ; Baker D
    Nature; 2007 Nov; 450(7167):259-64. PubMed ID: 17934447
    [TBL] [Abstract][Full Text] [Related]  

  • 18. A hierarchical approach to all-atom protein loop prediction.
    Jacobson MP; Pincus DL; Rapp CS; Day TJ; Honig B; Shaw DE; Friesner RA
    Proteins; 2004 May; 55(2):351-67. PubMed ID: 15048827
    [TBL] [Abstract][Full Text] [Related]  

  • 19. "Conditional Restraints": Restraining the Free Atoms in ARP/wARP.
    Mooij WT; Cohen SX; Joosten K; Murshudov GN; Perrakis A
    Structure; 2009 Feb; 17(2):183-9. PubMed ID: 19217389
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Revealing noncovalent interactions.
    Johnson ER; Keinan S; Mori-Sánchez P; Contreras-García J; Cohen AJ; Yang W
    J Am Chem Soc; 2010 May; 132(18):6498-506. PubMed ID: 20394428
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 15.