BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

214 related articles for article (PubMed ID: 22612113)

  • 1. Elastic network normal modes provide a basis for protein structure refinement.
    Gniewek P; Kolinski A; Jernigan RL; Kloczkowski A
    J Chem Phys; 2012 May; 136(19):195101. PubMed ID: 22612113
    [TBL] [Abstract][Full Text] [Related]  

  • 2. A unification of the elastic network model and the Gaussian network model for optimal description of protein conformational motions and fluctuations.
    Zheng W
    Biophys J; 2008 May; 94(10):3853-7. PubMed ID: 18234807
    [TBL] [Abstract][Full Text] [Related]  

  • 3. Analysis of conformational motions and residue fluctuations for Escherichia coli ribose-binding protein revealed with elastic network models.
    Li HY; Cao ZX; Zhao LL; Wang JH
    Int J Mol Sci; 2013 May; 14(5):10552-69. PubMed ID: 23698778
    [TBL] [Abstract][Full Text] [Related]  

  • 4. Protein elastic network models and the ranges of cooperativity.
    Yang L; Song G; Jernigan RL
    Proc Natl Acad Sci U S A; 2009 Jul; 106(30):12347-52. PubMed ID: 19617554
    [TBL] [Abstract][Full Text] [Related]  

  • 5. Generalized spring tensor models for protein fluctuation dynamics and conformation changes.
    Na H; Lin TL; Song G
    Adv Exp Med Biol; 2014; 805():107-35. PubMed ID: 24446359
    [TBL] [Abstract][Full Text] [Related]  

  • 6. Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models.
    Eyal E; Chennubhotla C; Yang LW; Bahar I
    Bioinformatics; 2007 Jul; 23(13):i175-84. PubMed ID: 17646294
    [TBL] [Abstract][Full Text] [Related]  

  • 7. Loop motions of triosephosphate isomerase observed with elastic networks.
    Kurkcuoglu O; Jernigan RL; Doruker P
    Biochemistry; 2006 Jan; 45(4):1173-82. PubMed ID: 16430213
    [TBL] [Abstract][Full Text] [Related]  

  • 8. Identifying essential pairwise interactions in elastic network model using the alpha shape theory.
    Xia F; Tong D; Yang L; Wang D; Hoi SC; Koehl P; Lu L
    J Comput Chem; 2014 Jun; 35(15):1111-21. PubMed ID: 24648309
    [TBL] [Abstract][Full Text] [Related]  

  • 9. Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models.
    Zimmermann MT; Leelananda SP; Gniewek P; Feng Y; Jernigan RL; Kloczkowski A
    J Struct Funct Genomics; 2011 Jul; 12(2):137-47. PubMed ID: 21674234
    [TBL] [Abstract][Full Text] [Related]  

  • 10. Elastic network models capture the motions apparent within ensembles of RNA structures.
    Zimmermann MT; Jernigan RL
    RNA; 2014 Jun; 20(6):792-804. PubMed ID: 24759093
    [TBL] [Abstract][Full Text] [Related]  

  • 11. An analysis of the influence of protein intrinsic dynamical properties on its thermal unfolding behavior.
    Su JG; Xu XJ; Li CH; Chen WZ; Wang CX
    J Biomol Struct Dyn; 2011 Aug; 29(1):105-21. PubMed ID: 21696228
    [TBL] [Abstract][Full Text] [Related]  

  • 12. Tensorial elastic network model for protein dynamics: integration of the anisotropic network model with bond-bending and twist elasticities.
    Srivastava A; Halevi RB; Veksler A; Granek R
    Proteins; 2012 Dec; 80(12):2692-700. PubMed ID: 22847894
    [TBL] [Abstract][Full Text] [Related]  

  • 13. Sampling of near-native protein conformations during protein structure refinement using a coarse-grained model, normal modes, and molecular dynamics simulations.
    Stumpff-Kane AW; Maksimiak K; Lee MS; Feig M
    Proteins; 2008 Mar; 70(4):1345-56. PubMed ID: 17876825
    [TBL] [Abstract][Full Text] [Related]  

  • 14. Bend-twist-stretch model for coarse elastic network simulation of biomolecular motion.
    Stember JN; Wriggers W
    J Chem Phys; 2009 Aug; 131(7):074112. PubMed ID: 19708737
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Distance matrix-based approach to protein structure prediction.
    Kloczkowski A; Jernigan RL; Wu Z; Song G; Yang L; Kolinski A; Pokarowski P
    J Struct Funct Genomics; 2009 Mar; 10(1):67-81. PubMed ID: 19224393
    [TBL] [Abstract][Full Text] [Related]  

  • 16. A connection rule for alpha-carbon coarse-grained elastic network models using chemical bond information.
    Jeong JI; Jang Y; Kim MK
    J Mol Graph Model; 2006 Jan; 24(4):296-306. PubMed ID: 16289973
    [TBL] [Abstract][Full Text] [Related]  

  • 17. Protein promiscuity: drug resistance and native functions--HIV-1 case.
    Fernández A; Tawfik DS; Berkhout B; Sanders R; Kloczkowski A; Sen T; Jernigan B
    J Biomol Struct Dyn; 2005 Jun; 22(6):615-24. PubMed ID: 15842167
    [TBL] [Abstract][Full Text] [Related]  

  • 18. Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields.
    Chen M; Lin X; Lu W; Schafer NP; Onuchic JN; Wolynes PG
    J Chem Theory Comput; 2018 Nov; 14(11):6102-6116. PubMed ID: 30240202
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a Spatial Hierarchy of Protein Motion.
    Budday D; Leyendecker S; van den Bedem H
    J Chem Inf Model; 2018 Oct; 58(10):2108-2122. PubMed ID: 30240209
    [TBL] [Abstract][Full Text] [Related]  

  • 20. Identification of motions in membrane proteins by elastic network models and their experimental validation.
    Isin B; Tirupula KC; Oltvai ZN; Klein-Seetharaman J; Bahar I
    Methods Mol Biol; 2012; 914():285-317. PubMed ID: 22976035
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 11.